- AAAminoJKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for Amino scheme from Jmol (predefined colors)
- AADMSitesKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for Datamonkey Sites file
- AAPAMLBEBM282Key - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for AAPAMLBEB BEB file (For Both Model 2 and Model 8: Common and Uncommon Sites)
- AAPAMLBEBM283Key - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for AAPAMLBEB BEB file (For Both Model 2 and Model 8: All Common Sites; Model 2 Uncommon Sites ; Model 8 Uncommon Sites)
- AAPAMLBEBM28Key - Static variable in class IMPACT_S.GUIColorSchemes
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(Amino-Acid) Color Scheme Key for AACodeml BEB file (For Model 2 or Model 8)
- AASeaviewKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for Seaview scheme (predefined colors)
- AAShapelyJKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for Shapely scheme from Jmol (predefined colors)
- AASideChainsKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for Side Chains scheme (predefined colors)
- AATSCMLMRKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for Merged ResulAATS file (for Both TreeSAAP PBR and BEB files)
- AATSType123Key - Static variable in class IMPACT_S.GUIColorSchemes
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(Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (All Type I,II,III schemes at once)
- AATSTypeIIIKey - Static variable in class IMPACT_S.GUIColorSchemes
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(Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (Six properties or more)
- AATSTypeIIIUKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (N properties or more)
- AATSTypeIIKey - Static variable in class IMPACT_S.GUIColorSchemes
-
(Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (Two-Five properties)
- AATSTypeIKey - Static variable in class IMPACT_S.GUIColorSchemes
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(Amino-Acid) Color Scheme Key for TreeSAAP PBR/PBS file (One property at most)
- ABOUTTXT_RESOURCE_PATH - Static variable in class IMPACT_S.Utilities
-
about text file path from IMPACT.resources
- addText(String) - Method in class IMPACT_S.GUIProgExecOutput
-
Add text to current output text.
- AlignmentEditor - Class in IMPACT_S
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Implementation of methods and data structures for GUIAlignmentEditor.
- AlignmentEditor(File, String) - Constructor for class IMPACT_S.AlignmentEditor
-
Constructor method for Alignment Editor.
- AlignmentOperations - Class in IMPACT_S
-
Class to handle any kinds of alignment operations.
- AlignmentOperations(Utilities) - Constructor for class IMPACT_S.AlignmentOperations
-
Alignment operations constructor.
- areLocationsEmpty() - Method in class IMPACT_S.CodemlOptions
-
Tell if there are empty locations set.
- ATVExeKey - Static variable in class IMPACT_S.Utilities
-
ATV program location