- PAMLDataKey - Static variable in class IMPACT_S.Utilities
-
GUI Codeml data location
- PAMLResDirName - Static variable in class IMPACT_S.Utilities
-
GUI Codeml tab results directory name.
- PCLASSIC_F - Static variable in class IMPACT_S.FileFormat
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Phylip Classic format
- pdbFilePathLocKey - Static variable in class IMPACT_S.ResultsN3DTP
-
Location key for the PDB file selected by user
- PDBSeqColClrRenderer - Class in IMPACT_S
-
Implementation of specific Table Cell Renderer for presenting selected colors in PDB sequence table.
- PDBSeqColClrRenderer(Color, Color, Color, Color, int, int) - Constructor for class IMPACT_S.PDBSeqColClrRenderer
-
Constructor for defining Color Renderer, with given colors.
- PDBSeqTableModel - Class in IMPACT_S
-
Implementation of specific Table Model for PDB Sequence Coloring.
- PEXTENDED_F - Static variable in class IMPACT_S.FileFormat
-
Phylip Extended format
- PHYLIP_FTYPES - Static variable in class IMPACT_S.FileFormat
-
PHYLIP Format types for either Interleaved or Sequential: Classic/Extended
- PHYLIP_TYPE - Static variable in class IMPACT_S.FileFormat
-
PHYLIP format type
- PHYLIPG_F - Static variable in class IMPACT_S.FileFormat
-
PHYLIP GENERIC format name
- PHYLIPI_F - Static variable in class IMPACT_S.FileFormat
-
PHYLIP INTERLEAVED format name
- PHYLIPS_F - Static variable in class IMPACT_S.FileFormat
-
PHYLIP SEQUENTIAL format name
- PhyMLExeKey - Static variable in class IMPACT_S.Utilities
-
PhyML program location
- PhyMLTask - Class in IMPACT_S
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Implementation of a background task for PhyML execution.
- PhyMLTask(String, String, String[], int) - Constructor for class IMPACT_S.PhyMLTask
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Initialize PhyML Task.
- prepareToFile(String[], String) - Method in class IMPACT_S.TreeSAAPTP
-
From a list of ranges with properties associated, produce
a similar list but with indexes translated to names.
- preprocessTreeSAAPFile(String, String) - Method in class IMPACT_S.TreeSAAPTP
-
This procedure was created to standardize or correct, the csv format found in TreeSAAP files.
- printBranchStatisticsToFile(String) - Method in class IMPACT_S.TreeSAAPTP
-
Make two tables having separate information of branches information selected by user.
- println(String) - Method in class IMPACT_S.Utilities
-
- printMSNSSMap2File(String) - Method in class IMPACT_S.TreeSAAPTP
-
Print most significant sorted information from NSynSubs to file.
- printPBSMap2File(String) - Method in class IMPACT_S.TreeSAAPTP
-
Print properties by site information to file.
- printStatisticsToFile(String) - Method in class IMPACT_S.TreeSAAPTP
-
Print statistical information to file.
- PROGRAM_VERSION_RESOURCE_PATH - Static variable in class IMPACT_S.Utilities
-
image icon path from IMPACT.resources
- programName - Static variable in class IMPACT_S.Utilities
-
Program name used across all modules
- ProgramsKey - Static variable in class IMPACT_S.Utilities
-
GUI Programs directory location
- propsByRangeLocKey - Static variable in class IMPACT_S.ResultsN3DTP
-
Location key for properties by range file from TreeSAAP tab
- propsBySiteLocKey - Static variable in class IMPACT_S.ResultsN3DTP
-
Location key for properties by site file from TreeSAAP tab
- ProtToSwissModel - Class in IMPACT_S
-
Class to handle Swiss-Model submission and modeled pdb retrieval.
- ProtToSwissModel(Utilities) - Constructor for class IMPACT_S.ProtToSwissModel
-
Generic constructor for access to class values.
This is an empty constructor, use another constructor for doing submission of sequences in any of the project modes.
- ProtToSwissModel(String, String, String, String, String, String, Utilities) - Constructor for class IMPACT_S.ProtToSwissModel
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Use for Automated Mode.
Uses a refresh timer of 30 seconds (default) when waiting for results to be ready.
- ProtToSwissModel(String, String, String, String, String, String, String, Utilities) - Constructor for class IMPACT_S.ProtToSwissModel
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Use for Alignment Mode.
Uses a refresh timer of 30 seconds (default) when waiting for results to be ready.