- CFILE_FORMATS - Static variable in class IMPACT_S.FileFormat
-
Collection of format names, only for ConTest.
- checkFailResponse(String) - Method in class IMPACT_S.RCSBTools
-
Check if the provided url already containing the pdbcode, points to an existing pdb file resource.
- checkPDBCodeTempLib(String) - Method in class IMPACT_S.ProtToSwissModel
-
Checks if given pdb code (pdbid + chainid) exists on Swiss Model Template Library.
- chiSquaredCritical(double, int) - Method in class IMPACT_S.Statistics
-
Returns critical chi-square value for given significance and degrees
of freedom.
- chiSquaredProbability(double, int) - Method in class IMPACT_S.Statistics
-
Returns chi-squared probability for given value and degrees
of freedom.
- CLUSTAL_F - Static variable in class IMPACT_S.FileFormat
-
CLUSTAL format name
- CLUSTAL_TYPE - Static variable in class IMPACT_S.FileFormat
-
CLUSTAL format type
- codemlCtrlflLocKey - Static variable in class IMPACT_S.CodemlOptions
-
Location key for user codeml control file.
- codemlDirLocKey - Static variable in class IMPACT_S.CodemlOptions
-
Location key for base codeml directory: based on the codeml executable location.
- CodemlExeKey - Static variable in class IMPACT_S.Utilities
-
Codeml program location
- CodemlOptions - Class in IMPACT_S
-
Support class for the GUICodemlOptions for choosing (other) Codeml options.
- CodemlOptions() - Constructor for class IMPACT_S.CodemlOptions
-
Initialize Codeml Options.
- CodemlTask - Class in IMPACT_S
-
Implementation of a background task for Codeml execution.
- CodemlTask(String, String, int) - Constructor for class IMPACT_S.CodemlTask
-
Initialize Codeml Task.
- CodemlTP - Class in IMPACT_S
-
Class to handle PAML (Codeml) results and input data.
- CodemlTP(Utilities) - Constructor for class IMPACT_S.CodemlTP
-
- collectResultsInfo(String) - Method in class IMPACT_S.CodemlTP
-
Collect codeml results file information.
- CommonModels - Static variable in class IMPACT_S.DatamonkeyTP
-
Common Models (All selected models common sites) code = 9.
- ControlFileKey - Static variable in class IMPACT_S.CodemlTP
-
Codeml control file key.
- convert(File, String, File, String) - Method in class IMPACT_S.FileFormatConverter
-
Convert from file with format, to file with format.
- convert_totmp(String[]) - Method in class IMPACT_S.FileFormatConverter
-
Creation of a temporary file, for phyml submission.
Temporary file must be of format Phylip (Interleaved or Sequential).
If source file, is of any other format convert to either Interleaved or
Sequential according to user choice in phyml options.
- countCharAt(String, char) - Method in class IMPACT_S.Utilities
-
Count occurrences of char in string.
- createJmolScript(int, int, int, String, boolean, boolean, boolean) - Method in class IMPACT_S.ResultsN3DTP
-
Create Jmol script based on scheme of colors chosen.
- CSVTableModel - Class in IMPACT_S
-
Implementation of specific Table Model for Comma Separated Values files.