A B C D F G H I J M O P Q R S T U V W

R

R_OPTIONSFILE_F - Static variable in class IMPACT.Utilities

R software Options file Format

R_OPTIONSFILE_TYPE - Static variable in class IMPACT.Utilities

R software Options file Type

readAAIndex1Properties(String) - Method in class IMPACT.Utilities

Read AAIndex1 file and obtain property name.
AAIndex1 file is verified for proper file, during process.

readBppMLStatFile(String) - Method in class IMPACT.Utilities

Read BppML stat files (*params.txt).
Get values for Number of categories and Gamma shape parameter.

readCSVFile() - Method in class IMPACT.ResultsView

Read active CSV file.

readMSAFile() - Method in class IMPACT.AlignmentEditor

Read sequences from specified file and format.
File and Format instantiated through the constructor method.

readMSAfile() - Method in class IMPACT.FileFormatConverter

Read MSA file for instantiated source file and format.

readOptionsFile(String) - Method in class IMPACT.Utilities

Read file into hashtables.
Skips commented lines with #, // and block comments /*...*'/'
Block comments have precedence over the others.

readPhyMLStatFile(String) - Method in class IMPACT.Utilities

Read PhyML stat files (*phyml_stat.txt).
Get values for Number of categories and Gamma shape parameter.

readPrefsFromFile(boolean) - Method in class IMPACT.Utilities

If file for preferences exists, use its values to present to user instead of ones by default behaviour found by Utilities.

readROptionsFile(String) - Method in class IMPACT.Utilities

Read R options from file.

removeCanceledTMPFls(Utilities, String, boolean) - Method in class IMPACT.AlignmentEditor

Remove temporary files created for PhyML execution resulting from cancelation.

removeRTmpFiles() - Method in class IMPACT.Utilities

Delete R temporary files used for execution.

renameFile(String, String, boolean) - Method in class IMPACT.Utilities

Copies content from source file to destination file.
This way creating a rename operation.
This was created to overcome limitations of File.renameTo() method.
Replaces any destination file that may exist.

renamePhymlFiles(Utilities, String, boolean) - Method in class IMPACT.AlignmentEditor

Rename PhyML files created on directory Phylogeny to name specified by user.

replaceBPFileParameterW(String) - Method in class IMPACT.Utilities

Replace parameter properties.fileNUM existent in BP table for new key with new NUM.
Used when writing options to file.

replaceExt(String, String) - Method in class IMPACT.Utilities

Replace extension with one based on given format.

replaceExtBy(String, String) - Method in class IMPACT.Utilities

Replace extension with new given extension.

RESIDUE_LOCTXT_RESOURCE_PATH - Static variable in class IMPACT.Utilities

residues location example file path from IMPACT.resources

ResultsSummary - Class in IMPACT

Implementation of several methods to present a summary of results.
These are based in R output file, MSA file, and 3D location (created by user).

ResultsSummary(String, String, String, String, String, Utilities) - Constructor for class IMPACT.ResultsSummary

Initialize results summary.

ResultsView - Class in IMPACT

Implementation of several methods to allow reading Comma Separating Values (CSV) files.

ResultsView() - Constructor for class IMPACT.ResultsView

Constructor for instantiation of files later.

ResultsView(String, String) - Constructor for class IMPACT.ResultsView

Constructor for file1 and file2 instantiation.

REXE_KEY - Static variable in class IMPACT.Utilities

Key for access R executable absolute location

RSCRIPTS_KEY - Static variable in class IMPACT.Utilities

Key for access R scripts executables absolute location

RSoftwareTask - Class in IMPACT

Implementation of background task to run R scripts.