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

S

SAVE - Static variable in class IMPACT.GUIFileChooser

constructor parameter 'mode' value, indicates Save selection.

setAAindex1URL(String) - Method in class IMPACT.Utilities

Set URL value for AAindex1 DB given by user.

setActiveFile(int) - Method in class IMPACT.ResultsView

Set the file1 for use in all methods in this class.

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

Add an extension to file name, according to given format.

setFinal() - Method in class IMPACT.GUIInitializationBox

Finalize procedure.

setFstFile(String) - Method in class IMPACT.ResultsView

Instantiate File1.

setHashTableValueByIndex(char, int, String) - Method in class IMPACT.Utilities

Set hashtable value for specified index and accessTable.

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

Set location value for Locations hashtable, given key field at

setNameFile(String) - Method in class IMPACT.GUIFileChooser

Set new file name, for further operations.

setPhylipFormatType(String) - Method in class IMPACT.FileFormatConverter

Use phylip format type in read/write phylip files.

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

Set option to specified key.

setSaveFile(String) - Method in class IMPACT.GUIFileChooser

Presents dialog to choose save file.

setSequenceCount(int) - Method in class IMPACT.FileFormatConverter

Set number of sequences to value of count.

setSequences(String[][]) - Method in class IMPACT.FileFormatConverter

Set sequences to msa value.

setSiteCount(int) - Method in class IMPACT.FileFormatConverter

Set number of sites to value of count.

setSndFile(String) - Method in class IMPACT.ResultsView

Instantiate File2.

setStatusMessage(String) - Method in class IMPACT.GUIInitializationBox

Set window status message.

setTaxaNames(String[]) - Method in class IMPACT.FileFormatConverter

Set taxa names to names value.

setValueAt(Object, int, int) - Method in class IMPACT.CSVTableModel

setValueAt(Object, int, int) - Method in class IMPACT.MSATableModel

setValueCheckpoint(int) - Method in class IMPACT.GUIInitializationBox

Set progress bar value, by given checkpoint.

setvisible() - Method in class IMPACT.GUIPhyMLOptions

Set PhyML options window visible.

showFFC_DSLF(String, String) - Method in class IMPACT.GUIDialogs

FileFormatConverter class.
DSLF : Error_Message Different Sequence Lengths Found.

showFFC_FBF(String) - Method in class IMPACT.GUIDialogs

FileFormatConverter class.
FBF : Error_Message File Bad Format.

showFFC_FNC() - Method in class IMPACT.GUIDialogs

FileFormatConverter class.
FNC : Error_Message Format Not Chosen...

showFFC_RSAOB(String, int, String) - Method in class IMPACT.GUIDialogs

FileFormatConverter class.
RSAOB : Error_Message Reading Sequence Array Out Of Bounds

showFFC_VMPF() - Method in class IMPACT.GUIDialogs

FileFormatConverter class.
VMPF : Error_Message Values Missing in Phylip File first line.

showGUI_EF(String, String) - Method in class IMPACT.GUIDialogs

GUI class.
EF : Warning_Message Empty Fields.

showGUI_FAEM(String) - Method in class IMPACT.GUIDialogs

GUI class.
FAEM : Question_Message File Already Exists Make new?

showGUI_FNE(String) - Method in class IMPACT.GUIDialogs

GUI class.
FNE : Error_Message for File does Not Exist.

showGUI_FNE(String, String) - Method in class IMPACT.GUIDialogs

GUI class.
FNE : Error_Message for File does Not Exist.

showGUI_FNO(String) - Method in class IMPACT.GUIDialogs

GUI class.
FNO : Error_Message File Not Opened.

showGUI_IFPSV(String, String) - Method in class IMPACT.GUIDialogs

GUI class.
PVENCF : Error_Message Incorrect File for Program Stat Values.

showGUI_PVCF() - Method in class IMPACT.GUIDialogs

GUI class.
PVCF : Information_Message Please Verify Correct Format field.

showGUI_RCSC() - Method in class IMPACT.GUIDialogs

GUI class.
RCSC : Warning_Message Run ConTest without Save Changes

showGUI_RE() - Method in class IMPACT.GUIDialogs

GUI class.
RE : Question_Message Really Exit.

showGUI_RETR() - Method in class IMPACT.GUIDialogs

GUI class.
REFQ : Question_Message Really Exit Tasks Running.

showGUI_REWO() - Method in class IMPACT.GUIDialogs

GUI class.
REFQ : Question_Message Really Exit Windows Open.

showGUI_SFC() - Method in class IMPACT.GUIDialogs

GUI class.
SFC : Question_Message Set File as Current ?

showGUI_UNMA() - Method in class IMPACT.GUIDialogs

GUI class.

showGUIAE_CFF(String[], int) - Method in class IMPACT.GUIDialogs

GUIAlignmentEditor class.
CFF : Question_Message Choose File Format.

showGUIAE_FAEO(String) - Method in class IMPACT.GUIDialogs

GUIAlignmentEditor class.
FAEO : Question_Message File Already Exists Overwrite?

showGUIAE_FENF(String) - Method in class IMPACT.GUIDialogs

GUIAlignmentEditor class.
FENF : Error_Message File Extension Not Found.

showGUIAE_FS(String) - Method in class IMPACT.GUIDialogs

GUIAlignmentEditor class.
FS : Information_Message File Saved.

showGUIAE_PONC() - Method in class IMPACT.GUIDialogs

GUIAlignmentEditor class.
PONC : Error_Message PhyML Options Not Chosen.

showGUIAE_RPSC() - Method in class IMPACT.GUIDialogs

GUIAlignmentEditor class.
RPSC : Warning_Message Run PhyML without Save Changes

showGUICP_DC(String) - Method in class IMPACT.GUIDialogs

GUIConfPreferences class.
DC : Information_Message Directory Created.

showGUICP_IURL(String) - Method in class IMPACT.GUIDialogs

GUIConfPreferences class.
IURL : Error_Message Invalid URL.

showGUICP_NPAF() - Method in class IMPACT.GUIDialogs

GUIConfPreferences class.
NPAF : Error_Message Not Propert AAIndex1 file.

showGUICP_PW() - Method in class IMPACT.GUIDialogs

GUIConfPreferences class.
PW : Plain_Message Please Wait.

showGUICP_UOK(String) - Method in class IMPACT.GUIDialogs

GUIConfPreferences class.
UOK : Information_Message URL OK.

showGUICP_URNE() - Method in class IMPACT.GUIDialogs

GUIConfPreferences class.
URNE : ERROR_Message URL Resource does Not Exist.

showGUIFFC_CPFT(String[]) - Method in class IMPACT.GUIDialogs

GUIFileFormatConverter class.
CPFT : Question_Message Choose Phylip Format Type

showGUIRS_NSS(String) - Method in class IMPACT.GUIDialogs

ResultsSummary class.
NSS : Warning_Message No Selected Sequences.

showRS_FBF() - Method in class IMPACT.GUIDialogs

ResultsSummary class.
FBF : Error_Message File Bad Format.

showRS_SCNF() - Method in class IMPACT.GUIDialogs

ResultsSummary class.
SCNF : Error_Message Selected Column Not Found.

showRV_RCAOB(String, int, String) - Method in class IMPACT.GUIDialogs

ResultsView class.
RCAOB : Error_Message Reading CSV file Array Out Of Bounds

showUTIL_BFF(String, String) - Method in class IMPACT.GUIDialogs

Utilities class.
BFF : Error_Message Bad File Format.

showUTIL_FEF(String, int) - Method in class IMPACT.GUIDialogs

Utilities class.
FEF: Warning_Message File with Empty Fields.

showUTIL_FMF(String) - Method in class IMPACT.GUIDialogs

Utilities class.
FMF : Warning_Message File with Missing Fields.

showUTIL_FNF(String) - Method in class IMPACT.GUIDialogs

Utilities class.
FNF: Warning_Message File Not Found.

showUTIL_GWL(String) - Method in class IMPACT.GUIDialogs

Utilities class.
GWL : Error_Message GUI in Wrong Location

showUTIL_IOF() - Method in class IMPACT.GUIDialogs

Utilities class.
COF : Error_Message Incorrect Options File syntax.

showUTIL_NAF(String) - Method in class IMPACT.GUIDialogs

Utilities class.
NAF : Error_Message Not an AAIndex1 File.

SOURCE - Static variable in class IMPACT.FileFormatConverter

Input files

stop() - Method in class IMPACT.ConTestTask

Stop ConTest execution.

stop() - Method in class IMPACT.GenericJarTask

Stop generic java task.

stop() - Method in class IMPACT.PhyMLTask

Stop PhyML execution.

stop() - Method in class IMPACT.RSoftwareTask

Stop R Scripts execution.

stop() - Method in class IMPACT.ViewerTask

Stop viewer task.

summaryToFile() - Method in class IMPACT.ResultsSummary

Write Summary to file.
Also creates a companion file for this file with extension '.rs.info', which provides the information used to build the summary.