- SAVE - Static variable in class IMPACT_S.GUIFileChooser
-
constructor parameter 'mode' value, indicates Save selection.
- saveCurrentTable(String, Utilities) - Method in class IMPACT_S.ResultsView
-
Write current visible table to file.
- schemeChanged() - Method in class IMPACT_S.GUIColorSchemes
-
Tell whether user has changed colors on scheme.
- SequenceTranslator - Class in IMPACT_S
-
Translate sequences from DNA or RNA into Protein,
allowing choice of a specific translation table and start site.
- SequenceTranslator(FileFormatConverter, boolean) - Constructor for class IMPACT_S.SequenceTranslator
-
Initialize sequence translator.
- setActiveFile(int) - Method in class IMPACT_S.ResultsView
-
Set the file1 for use in all methods in this class.
- setCDLocation(String, String) - Method in class IMPACT_S.CodemlTP
-
Set value for specified key.
- setCloseOp(boolean) - Method in class IMPACT_S.GUIProgExecOutput
-
Disable any chance of closing this window.
- setCOLocation(String, String) - Method in class IMPACT_S.CodemlOptions
-
Set codeml location of files.
- setCtrlFlLocations(CodemlTP, String) - Method in class IMPACT_S.CodemlOptions
-
Set locations for user specified codeml control file mode.
- setCurrText(String) - Method in class IMPACT_S.GUIProgExecOutput
-
Set new current text.
Used for text area updates.
- setDLocation(String, String) - Method in class IMPACT_S.DatamonkeyTP
-
Set Datamonkey location.
- setEnableOutput(String, String) - Method in class IMPACT_S.FileFormatReader
-
Enable saving sequences to file.
This is useful when data read previously from file
should not be lost and thus still used for saving.
- setFiles(String, String, String, String) - Method in class IMPACT_S.AlignmentOperations
-
Set files for alignment filtering.
- setFstFile(String) - Method in class IMPACT_S.ResultsView
-
Instantiate File1.
- setInputFile(String) - Method in class IMPACT_S.FileFormat
-
Set input file for reading data.
- setJmolColorScheme(Color[], String[], int, boolean, boolean) - Method in class IMPACT_S.ResultsN3DTP
-
Set scheme of colors selected by user.
- setLocation(String, String) - Method in class IMPACT_S.Utilities
-
Set location to key.
- setLocations(CodemlTP, String) - Method in class IMPACT_S.CodemlOptions
-
Set locations for files.
- setModelledRange(String[]) - Method in class IMPACT_S.ResultsN3DTP
-
Set modeled range obtained from modeling.
- setMSANames(String[]) - Method in class IMPACT_S.GUIProtToSwissModel
-
Set the list of sequences names to show in GUI list.
- setNameFile(String) - Method in class IMPACT_S.GUIFileChooser
-
Set new file name, for further operations.
- setNewTableHeader(String[]) - Method in class IMPACT_S.GUIAlignmentEditor
-
Choose new table header.
- setOptionsKeys(String[]) - Method in class IMPACT_S.CodemlOptions
-
Set all keys for HashMap instantiation holding content for codeml control file.
Performs initialization of HashMaps for parameters and values and copy of argument.
- setOptionsM03(boolean) - Method in class IMPACT_S.CodemlOptions
-
Instantiate set of DEFAULT options for Models 0 and 3.
- setOptionsM12(boolean) - Method in class IMPACT_S.CodemlOptions
-
Instantiate set of DEFAULT options for Models 1 and 2.
- setOptionsM78(boolean) - Method in class IMPACT_S.CodemlOptions
-
Instantiate set of DEFAULT options for Models 7 and 8.
- setOptionsOther(boolean) - Method in class IMPACT_S.CodemlOptions
-
Instantiate set of user selected options directly from GUI.
- setOptionsParameters(String[]) - Method in class IMPACT_S.CodemlOptions
-
Set all parameters for codeml control file.
- setOptionsValues(String[]) - Method in class IMPACT_S.CodemlOptions
-
Set all values for codeml parameters.
- setOutputFile(String) - Method in class IMPACT_S.FileFormat
-
Set output file for saving data.
- setPhylipFormatType(String) - Method in class IMPACT_S.FileFormatConverter
-
Use phylip format type in read/write phylip files.
- setRadical(boolean, boolean, boolean, boolean) - Method in class IMPACT_S.TreeSAAPTP
-
Set if to process data for conservative (1,2,3) columns or radical (6,7,8) columns.
- setRLocations(String, String) - Method in class IMPACT_S.ResultsN3DTP
-
Set value for associated key.
- setSaveFile(String) - Method in class IMPACT_S.GUIFileChooser
-
Presents dialog to choose save file.
- setSelectedSeqName(String) - Method in class IMPACT_S.ProtToSwissModel
-
Set the use of a user selected sequence name.
- setSequence(String, String) - Method in class IMPACT_S.FileFormatReader
-
Set a single sequence with its name.
- setSequenceCount(int) - Method in class IMPACT_S.FileFormatConverter
-
Set number of sequences to value of count.
- setSequences(String[][]) - Method in class IMPACT_S.AlignmentEditor
-
Set new set of alignment sequences.
- setSequences(String[][]) - Method in class IMPACT_S.FileFormatConverter
-
Set sequences to msa value.
- setSequences(String[][], String[]) - Method in class IMPACT_S.FileFormatReader
-
Set a set of sequences with their names in matching order.
- setSequences(String[], String[]) - Method in class IMPACT_S.FileFormatReader
-
Set a set of sequences with their names in matching order.
- setShowPSColors(Color, int, HashMap<String, Color>) - Method in class IMPACT_S.GUIPDBColorSeq
-
Set colors to exhibit in the PDB sequence.
- setSiteCount(int) - Method in class IMPACT_S.FileFormatConverter
-
Set number of sites to value of count.
- setSndFile(String) - Method in class IMPACT_S.ResultsView
-
Instantiate File2.
- setTableColNames(String[]) - Method in class IMPACT_S.AlignmentEditor
-
Use a different naming for table headers.
- setTaxaNames(String[]) - Method in class IMPACT_S.AlignmentEditor
-
Set new sequence descriptions for alignment, only if the number of sequences is the same.
- setTaxaNames(String[]) - Method in class IMPACT_S.FileFormatConverter
-
Set taxa names to names value.
- setTerminalAspect(Color, Color) - Method in class IMPACT_S.GUIProgExecOutput
-
Set terminal aspect.
- setTreeSAAPSchemeOption(int) - Method in class IMPACT_S.GUIColorSchemes
-
Set the Lower limit as the user selected value for the User TreeSAAP coloring scheme.
- setTSLocation(String, String) - Method in class IMPACT_S.TreeSAAPTP
-
Set TreeSAAP location for given key.
- setUseGUIPEO(GUIProgExecOutput) - Method in class IMPACT_S.ProtToSwissModel
-
Set and enable the use of GUIProgExecOuput window (GUIPEO).
- setUseTranslationTable(int, boolean) - Method in class IMPACT_S.SequenceTranslator
-
Choose translation table to use.
Standard table is initialized by default.
- setValueAt(Object, int, int) - Method in class IMPACT_S.CSVTableModel
-
- setValueAt(Object, int, int) - Method in class IMPACT_S.MSATableModel
-
- setValueAt(Object, int, int) - Method in class IMPACT_S.PDBSeqTableModel
-
- setValues(String[]) - Method in class IMPACT_S.CodemlOptions
-
Set gui values for codeml parameters.
- setvisible() - Method in class IMPACT_S.GUIPhyMLOptions
-
Set PhyML options window visible.
- setVisible() - Method in class IMPACT_S.GUIProgExecOutput
-
- showFFC_DSLF(String, String) - Method in class IMPACT_S.GUIDialogs
-
FileFormatConverter class.
DSLF : Error_Message Different Sequence Lengths Found.
- showFFC_FBF(String) - Method in class IMPACT_S.GUIDialogs
-
FileFormatConverter class.
FBF : Error_Message File Bad Format.
- showFFC_FNC() - Method in class IMPACT_S.GUIDialogs
-
FileFormatConverter class.
FNC : Error_Message Format Not Chosen...
- showFFC_RSAOB(String, int, String) - Method in class IMPACT_S.GUIDialogs
-
FileFormatConverter class.
RSAOB : Error_Message Reading Sequence Array Out Of Bounds
- showFFC_VMPF() - Method in class IMPACT_S.GUIDialogs
-
FileFormatConverter class.
VMPF : Error_Message Values Missing in Phylip File first line.
- showGUI_CNSF(String, String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
CNSF : Error_Message Could Not Save File.
- showGUI_CO() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
CO : Warning_Message Codeml about Options.
- showGUI_CONC() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
CONC : Error_Message Codeml Options Not Chosen.
- showGUI_CV(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
CV : Question_Message for Choice Value.
- showGUI_EF(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
EF : Warning_Message Empty Fields.
- showGUI_FAEM(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FAEM : Question_Message File Already Exists Make new?
- showGUI_FBF(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FBF : Error_Message File Bad Format.
- showGUI_FNAN(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FNAN : Error_Message for Found Not A Number.
- showGUI_FNE(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FNE : Error_Message for File does Not Exist.
- showGUI_FNE(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FNE : Error_Message for File does Not Exist.
- showGUI_FNO(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FNO : Error_Message File Not Opened.
- showGUI_FVR(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
FVR : Error_Message Fields Violating Rules.
- showGUI_GEM(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
GEM : Information_Message Generic Error Message.
- showGUI_GIM(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
GIM : Information_Message Generic Information Message.
- showGUI_GWM(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
GWM : Warning_Message Generic Warning Message.
- showGUI_IFPSV(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
IFPSV : Error_Message Incorrect File for Program Stat Values.
- showGUI_IV(String, String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
IV : Question_Message for Insert Value.
- showGUI_NAN(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
NAN : Error_Message for Not A Number.
- showGUI_NPPF(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
NPPF : Error_Message Not Proper PDB File.
- showGUI_OCCF(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
OCCF : Warning_Message Overwrite Codeml Control File.
- showGUI_PVCF() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
PVCF : Information_Message Please Verify Correct Format field.
- showGUI_RCSC() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
RCSC : Warning_Message Run Codeml without Save Changes
- showGUI_RE() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
RE : Question_Message Really Exit.
- showGUI_RETR() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
RETR : Question_Message Really Exit Tasks Running.
- showGUI_RETRW() - Method in class IMPACT_S.GUIDialogs
-
GUIProtToSwissModel class.
RETRW : Question_Message Really Exit Task Running on Window.
- showGUI_REWO() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
REWO : Question_Message Really Exit Windows Open.
- showGUI_SFC() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
SFC : Question_Message Set File as Current ?
- showGUI_UNMA() - Method in class IMPACT_S.GUIDialogs
-
GUI class.
UNMA : Question_Message Use New MSA File also?
- showGUI_VC(String, String, Object[], Object) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
VC : Question_Message for Value Choice.
- showGUI_VE(String, String, Object) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
VE : Question_Message for Value Edition.
- showGUI_VP(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
VP : Information_Message Viewing Property name.
- showGUI_WD(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
WD : Information_Message Wrong Directory name.
- showGUI_WF(String) - Method in class IMPACT_S.GUIDialogs
-
GUI class.
WF : Information_Message Wrong File name.
- showGUIAE_CFF(String[], int) - Method in class IMPACT_S.GUIDialogs
-
GUIAlignmentEditor class.
CFF : Question_Message Choose File Format.
- showGUIAE_FAEO(String) - Method in class IMPACT_S.GUIDialogs
-
GUIAlignmentEditor class.
FAEO : Question_Message File Already Exists Overwrite?
- showGUIAE_FENF(String) - Method in class IMPACT_S.GUIDialogs
-
GUIAlignmentEditor class.
FENF : Error_Message File Extension Not Found.
- showGUIAE_FS(String) - Method in class IMPACT_S.GUIDialogs
-
GUIAlignmentEditor class.
FS : Information_Message File Saved.
- showGUIAE_PONC() - Method in class IMPACT_S.GUIDialogs
-
GUIAlignmentEditor class.
PONC : Error_Message PhyML Options Not Chosen.
- showGUIAE_RPSC() - Method in class IMPACT_S.GUIDialogs
-
GUIAlignmentEditor class.
RPSC : Warning_Message Run PhyML without Save Changes
- showGUICP_DC(String) - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
DC : Information_Message Directory Created.
- showGUICP_IURL(String) - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
IURL : Error_Message Invalid URL.
- showGUICP_NPAF() - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
NPAF : Error_Message Not Proper AAIndex1 file.
- showGUICP_OS() - Method in class IMPACT_S.GUIDialogs
-
GUIPreferences class.
OS : Information_Message Options Saved.
- showGUICP_PW() - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
PW : Plain_Message Please Wait.
- showGUICP_UOK(String) - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
UOK : Information_Message URL OK.
- showGUICP_URNA() - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
URNA : ERROR_Message URL Resource does Not seem to be Available.
- showGUICP_URNE() - Method in class IMPACT_S.GUIDialogs
-
GUIConfPreferences class.
URNE : ERROR_Message URL Resource does Not Exist.
- showGUIFFC_CPFT(String[]) - Method in class IMPACT_S.GUIDialogs
-
GUIFileFormatConverter class.
CPFT : Question_Message Choose Phylip Format Type
- showGUIRS_NSS(String) - Method in class IMPACT_S.GUIDialogs
-
ResultsSummary class.
NSS : Warning_Message No Selected Sequences.
- showRS_FBF() - Method in class IMPACT_S.GUIDialogs
-
ResultsSummary class.
FBF : Error_Message File Bad Format.
- showRS_SCNF() - Method in class IMPACT_S.GUIDialogs
-
ResultsSummary class.
SCNF : Error_Message Selected Column Not Found.
- showRV_RCAOB(String, int, String) - Method in class IMPACT_S.GUIDialogs
-
ResultsView class.
RCAOB : Error_Message Reading CSV file Array Out Of Bounds
- showTSTP_ATS(int, int) - Method in class IMPACT_S.GUIDialogs
-
AlignmentOperations class.
ATS : Error_Message Alignment Too Short.
- showUTIL_BFF(String, String) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
BFF : Error_Message Bad File Format.
- showUTIL_FEF(String, int) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
FEF: Warning_Message File with Empty Fields.
- showUTIL_FMF(String) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
FMF : Warning_Message File with Missing Fields.
- showUTIL_FNF(String) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
FNF: Warning_Message File Not Found.
- showUTIL_GWL(String) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
GWL : Error_Message GUI in Wrong Location
- showUTIL_IOF() - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
IOF : Error_Message Incorrect Options File syntax.
- showUTIL_MD(String, String) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
MD : Error_Message Missing Directory
- showUTIL_NAF(String) - Method in class IMPACT_S.GUIDialogs
-
Utilities class.
NAF : Error_Message Not an AAIndex1 File.
- SLACFileLocKey - Static variable in class IMPACT_S.DatamonkeyTP
-
SLAC input file key.
- SLACmodel - Static variable in class IMPACT_S.DatamonkeyTP
-
SLAC model code = 0.
- SlidingWindowDN - Static variable in class IMPACT_S.TreeSAAPTP
-
Directory name for Sliding Window
- SlidingWLocKey - Static variable in class IMPACT_S.TreeSAAPTP
-
Location Key for SlidingWindow directory
- SOURCE - Static variable in class IMPACT_S.FileFormat
-
Input files
- startUtilities() - Method in class IMPACT_S.Utilities
-
Start initialization of necessary locations.
- Statistics - Class in IMPACT_S
-
Class implementing some distributions, tests, etc.
- Statistics() - Constructor for class IMPACT_S.Statistics
-
- stop() - Method in class IMPACT_S.CodemlTask
-
Stop Codeml execution.
- stop() - Method in class IMPACT_S.GenericJarTask
-
Stop generic java task.
- stop() - Method in class IMPACT_S.GnuplotTask
-
Stop Gnuplot execution.
- stop() - Method in class IMPACT_S.PhyMLTask
-
Stop PhyML execution.
- studentTConfidenceInterval(int, double, double) - Method in class IMPACT_S.Statistics
-
Computes absolute size of half of a student-t confidence interval
for given degrees of freedom, probability, and observed value.
- submitSeqToSwissModelAlM() - Method in class IMPACT_S.ProtToSwissModel
-
Submit (previously translated) sequences to Swiss Model in Alignment Mode.
- submitSeqToSwissModelAuM() - Method in class IMPACT_S.ProtToSwissModel
-
Submit (previously translated) sequence to Swiss Model in Automatic Mode.
- SubstsDN - Static variable in class IMPACT_S.TreeSAAPTP
-
Directory Name for Substs directory
- SubstsLocKey - Static variable in class IMPACT_S.TreeSAAPTP
-
Location Key for Substs directory
- SynSubsFN - Static variable in class IMPACT_S.TreeSAAPTP
-
File name for SynSubs file
- SynSubsLocKey - Static variable in class IMPACT_S.TreeSAAPTP
-
Location Key for SynSubs file
- SystemKey - Static variable in class IMPACT_S.Utilities
-
GUI directory location