--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/lib/Constants.R	Tue May 13 22:00:40 2014 -0400
@@ -0,0 +1,119 @@
+#####################################################################################
+#Copyright (C) <2012>
+#
+#Permission is hereby granted, free of charge, to any person obtaining a copy of
+#this software and associated documentation files (the "Software"), to deal in the
+#Software without restriction, including without limitation the rights to use, copy,
+#modify, merge, publish, distribute, sublicense, and/or sell copies of the Software,
+#and to permit persons to whom the Software is furnished to do so, subject to
+#the following conditions:
+#
+#The above copyright notice and this permission notice shall be included in all copies
+#or substantial portions of the Software.
+#
+#THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED,
+#INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A
+#PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
+#HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+#OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE
+#SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
+#
+# This file is a component of the MaAsLin (Multivariate Associations Using Linear Models), 
+# authored by the Huttenhower lab at the Harvard School of Public Health
+# (contact Timothy Tickle, ttickle@hsph.harvard.edu).
+#####################################################################################
+
+inlinedocs <- function(
+##author<< Curtis Huttenhower <chuttenh@hsph.harvard.edu> and Timothy Tickle <ttickle@hsph.harvard.edu>
+##description<< Global project constants.
+) { return( pArgs ) }
+
+#General
+c_COMMA = ","
+c_DASH = "-"
+
+#For reading IO
+c_MATRIX_NAME = "Matrix:"
+c_FILE_NAME = "File:"
+c_DELIMITER = "Delimiter:"
+c_ID_ROW = "Name_Row_Number:"
+c_ID_COLUMN = "Name_Column_Number:"
+c_ROWS = "Read_Rows:"
+c_PCLROWS = "Read_PCL_Rows:"
+c_TSVROWS = "Read_TSV_Rows:"
+c_COLUMNS = "Read_Columns:"
+c_PCLCOLUMNS = "Read_PCL_Columns:"
+c_TSVCOLUMNS = "Read_TSV_Columns:"
+c_CHARACTER_DATA_TYPE = "DT_Character:"
+c_FACTOR_DATA_TYPE = "DT_Factor:"
+c_INTEGER_DATA_TYPE = "DT_Integer:"
+c_LOGICAL_DATA_TYPE = "DT_Logical:"
+c_NUMERIC_DATA_TYPE = "DT_Numeric:"
+c_ORDEREDFACTOR_DATA_TYPE = "DT_Ordered_Factor:"
+
+### The name of the data matrix read in using a read.config file
+c_strMatrixData	 <- "Abundance"
+### The name of the metadata matrix read in using a read.config file
+c_strMatrixMetadata <- "Metadata"
+# Settings for MFA visualization/ordination
+c_iMFA <- 30
+c_dHeight <- 9
+c_dDefaultScale = 0.5
+# The column that is used to determine if information meets a certain significance threshold (dSignificanceLevel) to include in the Summary text file)
+c_strKeywordEvaluatedForInclusion <- "Q.value"
+#The name of the custom process function
+c_strCustomProcessFunction = "processFunction"
+
+#Delimiters
+#Feature name delimiter
+c_cFeatureDelim = "|"
+c_cFeatureDelimRex = "\\|"
+
+#The word used for unclassified
+c_strUnclassified = "unclassified"
+
+#Maaslincore settings
+#If a metadata does not have more than count of unique values, it is changed to factor data mode.
+c_iNonFactorLevelThreshold = 3
+
+#Extensions
+c_sDetailFileSuffix = ".txt"
+c_sSummaryFileSuffix = ".txt"
+c_sLogFileSuffix = "_log"
+
+#Delimiter for output tables
+c_cTableDelimiter="\t"
+
+#Testing Related
+c_strTestingDirectory = "testing"
+c_strCorrectAnswers = "answers"
+c_strTemporaryFiles = "tmp"
+c_strTestingInput = "input"
+
+#Reading matrix defaults
+c_strDefaultMatrixDelimiter = "\t"
+c_strDefaultMatrixRowID = "1"
+c_strDefaultMatrixColID = "1"
+c_strDefaultReadRows = "-"
+c_strDefaultReadCols = "-"
+
+#Separator used when collapsing factor names
+c_sFactorNameSep = ""
+
+#Separator used by the mfa
+c_sMFANameSep1 = "_"
+c_sMFANameSep2 = "."
+
+#Analysis Module list positioning
+c_iSelection = 1
+c_iTransform = 2
+c_iAnalysis = 3
+c_iResults = 4
+c_iUnTransform = 5
+c_iIsUnivariate = 6
+
+#Count based models
+c_vCountBasedModels = c("neg_binomial","quasi")
+
+# Na action in anaylsis, placed here to standardize
+c_strNA_Action = "na.omit"