From 72a92a86c30876883e8af2af9803a3ecf38bdea7 Mon Sep 17 00:00:00 2001 From: pschloss Date: Wed, 28 Jan 2009 14:04:05 +0000 Subject: [PATCH] I've changed the listfile, sabundfile, etc. option handles to not need the "file" part - pat --- errorchecking.cpp | 36 ++++++++++++++++++------------------ globaldata.cpp | 36 ++++++++++++++++++------------------ helpcommand.cpp | 8 ++++---- validparameter.cpp | 2 +- 4 files changed, 41 insertions(+), 41 deletions(-) diff --git a/errorchecking.cpp b/errorchecking.cpp index 121a012..6ec145b 100644 --- a/errorchecking.cpp +++ b/errorchecking.cpp @@ -72,16 +72,16 @@ bool ErrorCheck::checkInput(string input) { //is it a valid parameter if (validParameter->isValidParameter(parameter) != true) { return false; } - if (parameter == "phylipfile" ) { phylipfile = value; } - if (parameter == "columnfile" ) { columnfile = value; } - if (parameter == "listfile" ) { listfile = value; } - if (parameter == "rabundfile" ) { rabundfile = value; } - if (parameter == "sabundfile" ) { sabundfile = value; } - if (parameter == "namefile" ) { namefile = value; } - if (parameter == "orderfile" ) { orderfile = value; } - if (parameter == "fastafile" ) { fastafile = value; } + if (parameter == "phylip" ) { phylipfile = value; } + if (parameter == "column" ) { columnfile = value; } + if (parameter == "list" ) { listfile = value; } + if (parameter == "rabund" ) { rabundfile = value; } + if (parameter == "sabund" ) { sabundfile = value; } + if (parameter == "name" ) { namefile = value; } + if (parameter == "order" ) { orderfile = value; } + if (parameter == "fasta" ) { fastafile = value; } if (parameter == "treefile" ) { treefile = value; } - if (parameter == "groupfile" ) { groupfile = value; } + if (parameter == "group" ) { groupfile = value; } if (parameter == "cutoff" ) { cutoff = value; } if (parameter == "precision" ) { precision = value; } if (parameter == "iters" ) { iters = value; } @@ -141,15 +141,15 @@ bool ErrorCheck::checkInput(string input) { //is it a valid parameter if (validParameter->isValidParameter(parameter) != true) { return false; } - if (parameter == "phylipfile" ) { phylipfile = value; } - if (parameter == "columnfile" ) { columnfile = value; } - if (parameter == "listfile" ) { listfile = value; } - if (parameter == "rabundfile" ) { rabundfile = value; } - if (parameter == "sabundfile" ) { sabundfile = value; } - if (parameter == "namefile" ) { namefile = value; } - if (parameter == "orderfile" ) { orderfile = value; } - if (parameter == "groupfile" ) { groupfile = value; } - if (parameter == "fastafile" ) { fastafile = value; } + if (parameter == "phylip" ) { phylipfile = value; } + if (parameter == "column" ) { columnfile = value; } + if (parameter == "list" ) { listfile = value; } + if (parameter == "rabund" ) { rabundfile = value; } + if (parameter == "sabund" ) { sabundfile = value; } + if (parameter == "name" ) { namefile = value; } + if (parameter == "order" ) { orderfile = value; } + if (parameter == "group" ) { groupfile = value; } + if (parameter == "fasta" ) { fastafile = value; } if (parameter == "treefile" ) { treefile = value; } if (parameter == "cutoff" ) { cutoff = value; } if (parameter == "precision" ) { precision = value; } diff --git a/globaldata.cpp b/globaldata.cpp index 87f1cca..713ae9a 100644 --- a/globaldata.cpp +++ b/globaldata.cpp @@ -97,16 +97,16 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ splitAtComma(value, optionText); splitAtEquals(key, value); - if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } - if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } - if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } - if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } - if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } - if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } + if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } + if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } + if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } + if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } + if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } + if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } if (key == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; } - if (key == "namefile" ) { namefile = value; } - if (key == "orderfile" ) { orderfile = value; } - if (key == "groupfile" ) { groupfile = value; } + if (key == "name" ) { namefile = value; } + if (key == "order" ) { orderfile = value; } + if (key == "group" ) { groupfile = value; } if (key == "cutoff" ) { cutoff = value; } if (key == "precision" ) { precision = value; } if (key == "iters" ) { iters = value; } @@ -162,16 +162,16 @@ void GlobalData::parseGlobalData(string commandString, string optionText){ //saves the last parameter value = optionText; splitAtEquals(key, value); - if (key == "phylipfile" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } - if (key == "columnfile" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } - if (key == "listfile" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } - if (key == "rabundfile" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } - if (key == "sabundfile" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } - if (key == "fastafile" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } + if (key == "phylip" ) { phylipfile = value; inputFileName = value; fileroot = value; format = "phylip"; } + if (key == "column" ) { columnfile = value; inputFileName = value; fileroot = value; format = "column"; } + if (key == "list" ) { listfile = value; inputFileName = value; fileroot = value; format = "list"; } + if (key == "rabund" ) { rabundfile = value; inputFileName = value; fileroot = value; format = "rabund"; } + if (key == "sabund" ) { sabundfile = value; inputFileName = value; fileroot = value; format = "sabund"; } + if (key == "fasta" ) { fastafile = value; inputFileName = value; fileroot = value; format = "fasta"; } if (key == "treefile" ) { treefile = value; inputFileName = value; fileroot = value; format = "tree"; } - if (key == "namefile" ) { namefile = value; } - if (key == "orderfile" ) { orderfile = value; } - if (key == "groupfile" ) { groupfile = value; } + if (key == "name" ) { namefile = value; } + if (key == "order" ) { orderfile = value; } + if (key == "group" ) { groupfile = value; } if (key == "cutoff" ) { cutoff = value; } if (key == "precision" ) { precision = value; } if (key == "iters" ) { iters = value; } diff --git a/helpcommand.cpp b/helpcommand.cpp index 565d742..0d9bdcd 100644 --- a/helpcommand.cpp +++ b/helpcommand.cpp @@ -24,12 +24,12 @@ int HelpCommand::execute(){ globaldata = GlobalData::getInstance(); if (globaldata->helpRequest == "read.dist") { - cout << "The read.dist command parameter options are phylipfile or columnfile, namefile, cutoff and precision" << "\n"; + cout << "The read.dist command parameter options are phylip or column, name, cutoff and precision" << "\n"; cout << "The read.dist command should be in the following format: " << "\n"; - cout << "read.dist(phylipfile=yourDistFile, namefile=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; - cout << "The phylipfile or columnfile parameter is required, but only one may be used. If you use a columnfile the namefile is required. " << "\n"; + cout << "read.dist(phylip=yourDistFile, name=yourNameFile, cutoff=yourCutoff, precision=yourPrecision) " << "\n"; + cout << "The phylip or column parameter is required, but only one may be used. If you use a column file the name filename is required. " << "\n"; cout << "If you do not provide a cutoff value 10.00 is assumed. If you do not provide a precision value then 100 is assumed." << "\n"; - cout << "Note: No spaces between parameter labels (i.e. distfile), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n"; + cout << "Note: No spaces between parameter labels (i.e. dist), '=' and parameters (i.e.yourDistfile)." << "\n" << "\n"; }else if (globaldata->helpRequest == "read.otu") { cout << "The read.otu command parameter options are listfile, rabundfile, sabundfile or orderfile." << "\n"; cout << "The read.otu command should be in the following format: " << "\n"; diff --git a/validparameter.cpp b/validparameter.cpp index 13976a4..10dad74 100644 --- a/validparameter.cpp +++ b/validparameter.cpp @@ -14,7 +14,7 @@ ValidParameters::ValidParameters() { try { - parameters["phylipfile"] = "phylipfile"; + parameters["phylip"] = "phylip"; parameters["columnfile"] = "columnfile"; parameters["listfile"] = "listfile"; parameters["rabundfile"] = "rabundfile"; -- 2.39.2