Serialized Form

Package IMPACT_S

Class IMPACT_S.CSVTableModel extends javax.swing.table.AbstractTableModel implements Serializable
- Serialized Fields
  - columnNames
```
java.lang.String[] columnNames
```
  - data
```
java.lang.Object[][] data
```
  - types
```
java.lang.Class<T>[] types
```
  - canEdit
```
boolean[] canEdit
```

Class IMPACT_S.GUI extends javax.swing.JFrame implements Serializable

Serialized Fields

extrZsigPropFl
```
java.lang.String extrZsigPropFl
```
Extracted TreeSAAP Z-SigProp file
openedZSP
```
java.lang.String openedZSP
```
TreeSAAP opened Z-SigProp file
openedSWD
```
java.lang.String openedSWD
```
TreeSAAP opened sliding window directory
openedNSS
```
java.lang.String openedNSS
```
TreeSAAP opened NSynSubs file
openedSS
```
java.lang.String openedSS
```
TreeSAAP opened SynSubs file
dialog
```
GUIDialogs dialog
```
i
```
GUIINFO i
```
guirv
```
GUIResultsView guirv
```
tsres
```
TreeSAAPTP tsres
```
cdlres
```
CodemlTP cdlres
```
stat
```
Statistics stat
```
results3d
```
ResultsN3DTP results3d
```
copts
```
CodemlOptions copts
```
guijs
```
GUIColorSchemes guijs
```
jmolTask
```
GenericJarTask jmolTask
```
atvTask
```
GenericJarTask atvTask
```
treesaapTask
```
GenericJarTask treesaapTask
```
codemlcompleted
```
boolean codemlcompleted
```
codeml_output
```
java.lang.String codeml_output
```
pm
```
javax.swing.ProgressMonitor pm
```
codemlTask
```
CodemlTask codemlTask
```
timer
```
javax.swing.Timer timer
```
ctaskRunning
```
boolean ctaskRunning
```
ffcformat
```
java.lang.String ffcformat
```
tslowerlimit
```
int tslowerlimit
```
lhvma
```
java.awt.Color lhvma
```
lhvmb
```
java.awt.Color lhvmb
```
lrtm
```
java.awt.Color lrtm
```
gnupo
```
GUIGnuplotOptions gnupo
```
guiae
```
GUIAlignmentEditor guiae
```
selectedcodonsTS
```
int[] selectedcodonsTS
```
selectedcodonsDM
```
int[] selectedcodonsDM
```
DNAdata
```
boolean DNAdata
```
guipdbs
```
GUIPDBColorSeq guipdbs
```
guipeo
```
GUIProgExecOutput guipeo
```
dmres
```
DatamonkeyTP dmres
```
guiaf
```
GUIAlignmentFiltering guiaf
```
alops
```
AlignmentOperations alops
```
retrievedModels
```
boolean[] retrievedModels
```
TSres
```
boolean TSres
```
DMres
```
boolean DMres
```
PAMLres
```
boolean PAMLres
```
i2once
```
boolean i2once
```
AboutMI
```
javax.swing.JMenuItem AboutMI
```
AlignmentEditorMI
```
javax.swing.JMenuItem AlignmentEditorMI
```
AlignmentFilterBUT
```
javax.swing.JButton AlignmentFilterBUT
```
AlignmentFilterMI
```
javax.swing.JMenuItem AlignmentFilterMI
```

AlignmentFilteringBUT

javax.swing.JButton AlignmentFilteringBUT

BEBResultsFile1BrowseBUT

javax.swing.JButton BEBResultsFile1BrowseBUT

BEBResultsFile1Lbl
```
javax.swing.JLabel BEBResultsFile1Lbl
```

BEBResultsFile1RB

javax.swing.JRadioButton BEBResultsFile1RB

BEBResultsFile1TF

javax.swing.JTextField BEBResultsFile1TF

BEBResultsFile1ViewBUT

javax.swing.JButton BEBResultsFile1ViewBUT

BEBResultsFile2BrowseBUT

javax.swing.JButton BEBResultsFile2BrowseBUT

BEBResultsFile2Lbl
```
javax.swing.JLabel BEBResultsFile2Lbl
```

BEBResultsFile2RB

javax.swing.JRadioButton BEBResultsFile2RB

BEBResultsFile2TF

javax.swing.JTextField BEBResultsFile2TF

BackPanel
```
javax.swing.JPanel BackPanel
```
BackupPanel
```
javax.swing.JPanel BackupPanel
```
C12CkBox
```
javax.swing.JCheckBox C12CkBox
```
C12SCkBox
```
javax.swing.JCheckBox C12SCkBox
```
C78CkBox
```
javax.swing.JCheckBox C78CkBox
```
C78SCkBox
```
javax.swing.JCheckBox C78SCkBox
```
CSVViewerMI
```
javax.swing.JMenuItem CSVViewerMI
```

ChooseMergeFileBrowseBUT

javax.swing.JButton ChooseMergeFileBrowseBUT

ChooseMergeFileLbl
```
javax.swing.JLabel ChooseMergeFileLbl
```

ChooseMergeFileTF

javax.swing.JTextField ChooseMergeFileTF

ChooseModelsLbl
```
javax.swing.JLabel ChooseModelsLbl
```
ChooseToModelBUT
```
javax.swing.JButton ChooseToModelBUT
```
CodemlPanel
```
javax.swing.JPanel CodemlPanel
```
CodemlResultsPanel
```
javax.swing.JPanel CodemlResultsPanel
```
CodemlRunPanel
```
javax.swing.JPanel CodemlRunPanel
```

ColorSchemesHelpMI

javax.swing.JMenuItem ColorSchemesHelpMI

CombineResPanel
```
javax.swing.JPanel CombineResPanel
```
CombineSelModels
```
javax.swing.JButton CombineSelModels
```

CommonSitesChangeBUT

javax.swing.JButton CommonSitesChangeBUT

CommonSitesLbl
```
javax.swing.JLabel CommonSitesLbl
```
CommonSitesRB
```
javax.swing.JRadioButton CommonSitesRB
```
CommonSitesTF
```
javax.swing.JTextField CommonSitesTF
```
CommonSitesViewBUT
```
javax.swing.JButton CommonSitesViewBUT
```
ConservativeRB
```
javax.swing.JRadioButton ConservativeRB
```

ConservativeSRB

javax.swing.JRadioButton ConservativeSRB

ControlFileRB
```
javax.swing.JRadioButton ControlFileRB
```
DMCkBox
```
javax.swing.JCheckBox DMCkBox
```
DMDataChoicePanel
```
javax.swing.JPanel DMDataChoicePanel
```

DMMethodsTabbedPanel

javax.swing.JTabbedPane DMMethodsTabbedPanel

DMOptionsPanel
```
javax.swing.JPanel DMOptionsPanel
```
DOptions03RB
```
javax.swing.JRadioButton DOptions03RB
```
DOptions12RB
```
javax.swing.JRadioButton DOptions12RB
```
DOptions78RB
```
javax.swing.JRadioButton DOptions78RB
```
DatamonkeyPanel
```
javax.swing.JPanel DatamonkeyPanel
```

DatamonkeySitesBrowseBUT

javax.swing.JButton DatamonkeySitesBrowseBUT

DatamonkeySitesLbl
```
javax.swing.JLabel DatamonkeySitesLbl
```

DatamonkeySitesTF

javax.swing.JTextField DatamonkeySitesTF

DatamonkeySitesViewBUT

javax.swing.JButton DatamonkeySitesViewBUT

EditMenu
```
javax.swing.JMenu EditMenu
```
EvpthwyBrowseBUT
```
javax.swing.JButton EvpthwyBrowseBUT
```
EvpthwyLbl
```
javax.swing.JLabel EvpthwyLbl
```
EvpthwyTF
```
javax.swing.JTextField EvpthwyTF
```

ExtractBEBToFlChooseBUT

javax.swing.JButton ExtractBEBToFlChooseBUT

ExtractBEBToFlLbl
```
javax.swing.JLabel ExtractBEBToFlLbl
```
ExtractBEBToFlTF
```
javax.swing.JTextField ExtractBEBToFlTF
```

ExtractBEBToFlViewBUT

javax.swing.JButton ExtractBEBToFlViewBUT

ExtractbebBUT
```
javax.swing.JButton ExtractbebBUT
```
FELCSVFileBrowseBUT
```
javax.swing.JButton FELCSVFileBrowseBUT
```
FELCSVFileLbl
```
javax.swing.JLabel FELCSVFileLbl
```
FELCSVFileTF
```
javax.swing.JTextField FELCSVFileTF
```
FELCSVFileViewBUT
```
javax.swing.JButton FELCSVFileViewBUT
```
FELCkBox
```
javax.swing.JCheckBox FELCkBox
```
FELNegSelChangeBUT
```
javax.swing.JButton FELNegSelChangeBUT
```
FELNegSelLbl
```
javax.swing.JLabel FELNegSelLbl
```
FELNegSelTF
```
javax.swing.JTextField FELNegSelTF
```
FELPanel
```
javax.swing.JPanel FELPanel
```
FELPosNegSelViewBUT
```
javax.swing.JButton FELPosNegSelViewBUT
```
FELPosSelChangeBUT
```
javax.swing.JButton FELPosSelChangeBUT
```
FELPosSelLbl
```
javax.swing.JLabel FELPosSelLbl
```
FELPosSelTF
```
javax.swing.JTextField FELPosSelTF
```
FELRB
```
javax.swing.JRadioButton FELRB
```

FELSignifLevelCBox

javax.swing.JComboBox<E> FELSignifLevelCBox

FELSignifLevelLbl
```
javax.swing.JLabel FELSignifLevelLbl
```

FELSignifLevelRetrieveBUT

javax.swing.JButton FELSignifLevelRetrieveBUT

FUBARCSVFileBrowseBUT

javax.swing.JButton FUBARCSVFileBrowseBUT

FUBARCSVFileLbl
```
javax.swing.JLabel FUBARCSVFileLbl
```
FUBARCSVFileTF
```
javax.swing.JTextField FUBARCSVFileTF
```
FUBARCSVFileViewBUT
```
javax.swing.JButton FUBARCSVFileViewBUT
```
FUBARCkBox
```
javax.swing.JCheckBox FUBARCkBox
```

FUBARNegSelChangeBUT

javax.swing.JButton FUBARNegSelChangeBUT

FUBARNegSelLbl
```
javax.swing.JLabel FUBARNegSelLbl
```
FUBARNegSelTF
```
javax.swing.JTextField FUBARNegSelTF
```
FUBARPanel
```
javax.swing.JPanel FUBARPanel
```

FUBARPosNegSelViewBUT

javax.swing.JButton FUBARPosNegSelViewBUT

FUBARPosSelChangeBUT

javax.swing.JButton FUBARPosSelChangeBUT

FUBARPosSelLbl
```
javax.swing.JLabel FUBARPosSelLbl
```
FUBARPosSelTF
```
javax.swing.JTextField FUBARPosSelTF
```

FUBARPosteriorProbCBox

javax.swing.JComboBox<E> FUBARPosteriorProbCBox

FUBARPosteriorProbLbl

javax.swing.JLabel FUBARPosteriorProbLbl

FUBARPosteriorProbRetrieveBUT

javax.swing.JButton FUBARPosteriorProbRetrieveBUT

FUBARRB
```
javax.swing.JRadioButton FUBARRB
```
FileBranchStatBUT
```
javax.swing.JButton FileBranchStatBUT
```
FileMenu
```
javax.swing.JMenu FileMenu
```
FileStatBUT
```
javax.swing.JButton FileStatBUT
```

FilterAlignmentSitesBUT

javax.swing.JButton FilterAlignmentSitesBUT

FormatConverterMI
```
javax.swing.JMenuItem FormatConverterMI
```
GetMergedResultsBUT
```
javax.swing.JButton GetMergedResultsBUT
```
GetPDBFileBUT
```
javax.swing.JButton GetPDBFileBUT
```
GetPropsByRangeBUT
```
javax.swing.JButton GetPropsByRangeBUT
```
GnuplotMI
```
javax.swing.JMenuItem GnuplotMI
```
HelpMenu
```
javax.swing.JMenu HelpMenu
```
INFO1TogBUT
```
javax.swing.JToggleButton INFO1TogBUT
```
INFO2TogBUT
```
javax.swing.JToggleButton INFO2TogBUT
```
INFOTogBUT
```
javax.swing.JToggleButton INFOTogBUT
```
IncBranchesCkBox
```
javax.swing.JCheckBox IncBranchesCkBox
```
IncCodAACkBox
```
javax.swing.JCheckBox IncCodAACkBox
```
IncludeColsInfoLbl
```
javax.swing.JLabel IncludeColsInfoLbl
```
JmolOptionsLbl
```
javax.swing.JLabel JmolOptionsLbl
```

JmolScriptCreationPanel

javax.swing.JPanel JmolScriptCreationPanel

KaiSquareLbl
```
javax.swing.JLabel KaiSquareLbl
```
KaiSquareLst
```
javax.swing.JList<E> KaiSquareLst
```
KaiSquareSP
```
javax.swing.JScrollPane KaiSquareSP
```
LHValuesPanel
```
javax.swing.JPanel LHValuesPanel
```
LRTBothModelsLbl
```
javax.swing.JLabel LRTBothModelsLbl
```
LRTBothModelsTF
```
javax.swing.JTextField LRTBothModelsTF
```

LabelResiduesCkBox

javax.swing.JCheckBox LabelResiduesCkBox

LhVModelATF
```
javax.swing.JTextField LhVModelATF
```
LhVModelBTF
```
javax.swing.JTextField LhVModelBTF
```
LikelihoodValuesLbl
```
javax.swing.JLabel LikelihoodValuesLbl
```
LnLTableChangeBUT
```
javax.swing.JButton LnLTableChangeBUT
```
LnLTableLbl
```
javax.swing.JLabel LnLTableLbl
```
LnLTableTF
```
javax.swing.JTextField LnLTableTF
```

MEMECSVFileBrowseBUT

javax.swing.JButton MEMECSVFileBrowseBUT

MEMECSVFileLbl
```
javax.swing.JLabel MEMECSVFileLbl
```
MEMECSVFileTF
```
javax.swing.JTextField MEMECSVFileTF
```
MEMECSVFileViewBUT
```
javax.swing.JButton MEMECSVFileViewBUT
```
MEMECkBox
```
javax.swing.JCheckBox MEMECkBox
```
MEMENegSelChangeBUT
```
javax.swing.JButton MEMENegSelChangeBUT
```
MEMENegSelLbl
```
javax.swing.JLabel MEMENegSelLbl
```
MEMENegSelTF
```
javax.swing.JTextField MEMENegSelTF
```
MEMEPanel
```
javax.swing.JPanel MEMEPanel
```

MEMEPosNegSelViewBUT

javax.swing.JButton MEMEPosNegSelViewBUT

MEMEPosSelChangeBUT
```
javax.swing.JButton MEMEPosSelChangeBUT
```
MEMEPosSelLbl
```
javax.swing.JLabel MEMEPosSelLbl
```
MEMEPosSelTF
```
javax.swing.JTextField MEMEPosSelTF
```
MEMERB
```
javax.swing.JRadioButton MEMERB
```

MEMESignifLevelCBox

javax.swing.JComboBox<E> MEMESignifLevelCBox

MEMESignifLevelLbl
```
javax.swing.JLabel MEMESignifLevelLbl
```

MEMESignifLevelRetrieveBUT

javax.swing.JButton MEMESignifLevelRetrieveBUT

MRFilterAlignmentBUT

javax.swing.JButton MRFilterAlignmentBUT

MROptionsPanel
```
javax.swing.JPanel MROptionsPanel
```
MRangeFromLbl
```
javax.swing.JLabel MRangeFromLbl
```
MRangeFromTF
```
javax.swing.JTextField MRangeFromTF
```
MRangeToLbl
```
javax.swing.JLabel MRangeToLbl
```
MRangeToTF
```
javax.swing.JTextField MRangeToTF
```
MSAFileBrowseBUT
```
javax.swing.JButton MSAFileBrowseBUT
```
MSAFileLbl
```
javax.swing.JLabel MSAFileLbl
```
MSAFileTF
```
javax.swing.JTextField MSAFileTF
```
MSAFileViewBUT
```
javax.swing.JButton MSAFileViewBUT
```
MSNSynSubsChangeBUT
```
javax.swing.JButton MSNSynSubsChangeBUT
```
MSNSynSubsLbl
```
javax.swing.JLabel MSNSynSubsLbl
```

MSNSynSubsRetrieveBUT

javax.swing.JButton MSNSynSubsRetrieveBUT

MSNSynSubsTF
```
javax.swing.JTextField MSNSynSubsTF
```
MSNSynSubsViewBUT
```
javax.swing.JButton MSNSynSubsViewBUT
```

MSignNegValuesCkBox

javax.swing.JCheckBox MSignNegValuesCkBox

MSignNegValuesSCkBox

javax.swing.JCheckBox MSignNegValuesSCkBox

MSignPosValuesCkBox

javax.swing.JCheckBox MSignPosValuesCkBox

MSignPosValuesSCkBox

javax.swing.JCheckBox MSignPosValuesSCkBox

MakePlotCkBox
```
javax.swing.JCheckBox MakePlotCkBox
```
MenuBar
```
javax.swing.JMenuBar MenuBar
```
MergePanel
```
javax.swing.JPanel MergePanel
```
ModelledRangeLbl
```
javax.swing.JLabel ModelledRangeLbl
```

NSynSubsFileBrowseBUT

javax.swing.JButton NSynSubsFileBrowseBUT

NSynSubsFileLbl
```
javax.swing.JLabel NSynSubsFileLbl
```
NSynSubsFileTF
```
javax.swing.JTextField NSynSubsFileTF
```
NSynSubsFileViewBUT
```
javax.swing.JButton NSynSubsFileViewBUT
```
NegativeRB
```
javax.swing.JRadioButton NegativeRB
```
NegativeSelRB
```
javax.swing.JRadioButton NegativeSelRB
```
OptionsAllRB
```
javax.swing.JRadioButton OptionsAllRB
```
OptionsChooseBUT
```
javax.swing.JButton OptionsChooseBUT
```
OptionsLbl
```
javax.swing.JLabel OptionsLbl
```
OptionsM03RB
```
javax.swing.JRadioButton OptionsM03RB
```
OptionsM12RB
```
javax.swing.JRadioButton OptionsM12RB
```
OptionsM78RB
```
javax.swing.JRadioButton OptionsM78RB
```
OptionsPanel
```
javax.swing.JPanel OptionsPanel
```
OptionsResLbl
```
javax.swing.JLabel OptionsResLbl
```
OtherOptionsRB
```
javax.swing.JRadioButton OtherOptionsRB
```
OutputFileBrowseBUT
```
javax.swing.JButton OutputFileBrowseBUT
```
OutputFileLbl
```
javax.swing.JLabel OutputFileLbl
```
OutputFileTF
```
javax.swing.JTextField OutputFileTF
```
PAMLCkBox
```
javax.swing.JCheckBox PAMLCkBox
```
PBRTreeSAAPRB
```
javax.swing.JRadioButton PBRTreeSAAPRB
```
PBSTreeSAAPRB
```
javax.swing.JRadioButton PBSTreeSAAPRB
```
PDBDownloaderMI
```
javax.swing.JMenuItem PDBDownloaderMI
```
PDBFileBrowseBUT
```
javax.swing.JButton PDBFileBrowseBUT
```
PDBFileInfoLbl
```
javax.swing.JLabel PDBFileInfoLbl
```
PDBFileLbl
```
javax.swing.JLabel PDBFileLbl
```
PDBFileTF
```
javax.swing.JTextField PDBFileTF
```
PositiveRB
```
javax.swing.JRadioButton PositiveRB
```
PositiveSelRB
```
javax.swing.JRadioButton PositiveSelRB
```
PreferencesMI
```
javax.swing.JMenuItem PreferencesMI
```
PropLstRowNumLbl
```
javax.swing.JLabel PropLstRowNumLbl
```
PropLstRowNumTF
```
javax.swing.JTextField PropLstRowNumTF
```
PropertiesLbl
```
javax.swing.JLabel PropertiesLbl
```
PropertiesLst
```
javax.swing.JList<E> PropertiesLst
```
PropertiesSP
```
javax.swing.JScrollPane PropertiesSP
```
PropertiesViewBUT
```
javax.swing.JButton PropertiesViewBUT
```

PropertiesViewMostSignifBUT

javax.swing.JButton PropertiesViewMostSignifBUT

PropsByRangeBrowseBUT

javax.swing.JButton PropsByRangeBrowseBUT

PropsByRangeChooseBUT

javax.swing.JButton PropsByRangeChooseBUT

PropsByRangeLbl
```
javax.swing.JLabel PropsByRangeLbl
```

PropsByRangeSaveAsLbl

javax.swing.JLabel PropsByRangeSaveAsLbl

PropsByRangeSaveAsTF

javax.swing.JTextField PropsByRangeSaveAsTF

PropsByRangeTF
```
javax.swing.JTextField PropsByRangeTF
```
PropsByRangeViewBUT
```
javax.swing.JButton PropsByRangeViewBUT
```

PropsBySiteBrowseBUT

javax.swing.JButton PropsBySiteBrowseBUT

PropsBySiteLbl
```
javax.swing.JLabel PropsBySiteLbl
```

PropsBySiteRetrieveBUT

javax.swing.JButton PropsBySiteRetrieveBUT

PropsBySiteSaveAsChangeBUT

javax.swing.JButton PropsBySiteSaveAsChangeBUT

PropsBySiteSaveAsLbl
```
javax.swing.JLabel PropsBySiteSaveAsLbl
```

PropsBySiteSaveAsTF

javax.swing.JTextField PropsBySiteSaveAsTF

PropsBySiteSaveAsViewBUT

javax.swing.JButton PropsBySiteSaveAsViewBUT

PropsBySiteTF
```
javax.swing.JTextField PropsBySiteTF
```
ProteinModelerMI
```
javax.swing.JMenuItem ProteinModelerMI
```
QuitMI
```
javax.swing.JMenuItem QuitMI
```
RELCSVFileBrowseBUT
```
javax.swing.JButton RELCSVFileBrowseBUT
```
RELCSVFileLbl
```
javax.swing.JLabel RELCSVFileLbl
```
RELCSVFileTF
```
javax.swing.JTextField RELCSVFileTF
```
RELCSVFileViewBUT
```
javax.swing.JButton RELCSVFileViewBUT
```
RELCkBox
```
javax.swing.JCheckBox RELCkBox
```
RELNegSelChangeBUT
```
javax.swing.JButton RELNegSelChangeBUT
```
RELNegSelLbl
```
javax.swing.JLabel RELNegSelLbl
```
RELNegSelTF
```
javax.swing.JTextField RELNegSelTF
```
RELPanel
```
javax.swing.JPanel RELPanel
```
RELPosNegSelViewBUT
```
javax.swing.JButton RELPosNegSelViewBUT
```
RELPosSelChangeBUT
```
javax.swing.JButton RELPosSelChangeBUT
```
RELPosSelLbl
```
javax.swing.JLabel RELPosSelLbl
```
RELPosSelTF
```
javax.swing.JTextField RELPosSelTF
```
RELRB
```
javax.swing.JRadioButton RELRB
```

RELSignifLevelCBox

javax.swing.JComboBox<E> RELSignifLevelCBox

RELSignifLevelLbl
```
javax.swing.JLabel RELSignifLevelLbl
```

RELSignifLevelRetrieveBUT

javax.swing.JButton RELSignifLevelRetrieveBUT

ROuputFileBrowseBUT
```
javax.swing.JButton ROuputFileBrowseBUT
```
ROutputFileLbl
```
javax.swing.JLabel ROutputFileLbl
```
ROutputFileTF
```
javax.swing.JTextField ROutputFileTF
```
ROutputFileViewBUT
```
javax.swing.JButton ROutputFileViewBUT
```
RadicalRB
```
javax.swing.JRadioButton RadicalRB
```
RadicalSRB
```
javax.swing.JRadioButton RadicalSRB
```

RatiosTableChangeBUT

javax.swing.JButton RatiosTableChangeBUT

RatiosTableLbl
```
javax.swing.JLabel RatiosTableLbl
```
RatiosTableTF
```
javax.swing.JTextField RatiosTableTF
```
ResDatamonkeyPanel
```
javax.swing.JPanel ResDatamonkeyPanel
```
ResPAMLPanel
```
javax.swing.JPanel ResPAMLPanel
```
ResTreeSAAPPanel
```
javax.swing.JPanel ResTreeSAAPPanel
```
Results3DPanel
```
javax.swing.JPanel Results3DPanel
```

ResultsTabbedPanel

javax.swing.JTabbedPane ResultsTabbedPanel

RetrieveAllSelModelsBUT

javax.swing.JButton RetrieveAllSelModelsBUT

RunArchaeopteryxMI

javax.swing.JMenuItem RunArchaeopteryxMI

RunCodemlBUT
```
javax.swing.JButton RunCodemlBUT
```
RunCodemlMI
```
javax.swing.JMenuItem RunCodemlMI
```
RunJmolMI
```
javax.swing.JMenuItem RunJmolMI
```
RunMenu
```
javax.swing.JMenu RunMenu
```
RunTreeSAAPMI
```
javax.swing.JMenuItem RunTreeSAAPMI
```

SLACCSVFileBrowseBUT

javax.swing.JButton SLACCSVFileBrowseBUT

SLACCSVFileLbl
```
javax.swing.JLabel SLACCSVFileLbl
```
SLACCSVFileTF
```
javax.swing.JTextField SLACCSVFileTF
```
SLACCSVFileViewBUT
```
javax.swing.JButton SLACCSVFileViewBUT
```
SLACCkBox
```
javax.swing.JCheckBox SLACCkBox
```
SLACNegSelChangeBUT
```
javax.swing.JButton SLACNegSelChangeBUT
```
SLACNegSelLbl
```
javax.swing.JLabel SLACNegSelLbl
```
SLACNegSelTF
```
javax.swing.JTextField SLACNegSelTF
```
SLACPanel
```
javax.swing.JPanel SLACPanel
```

SLACPosNegSelViewBUT

javax.swing.JButton SLACPosNegSelViewBUT

SLACPosSelChangeBUT
```
javax.swing.JButton SLACPosSelChangeBUT
```
SLACPosSelLbl
```
javax.swing.JLabel SLACPosSelLbl
```
SLACPosSelTF
```
javax.swing.JTextField SLACPosSelTF
```
SLACRB
```
javax.swing.JRadioButton SLACRB
```

SLACSignifLevelCBox

javax.swing.JComboBox<E> SLACSignifLevelCBox

SLACSignifLevelLbl
```
javax.swing.JLabel SLACSignifLevelLbl
```

SLACSignifLevelRetrieveBUT

javax.swing.JButton SLACSignifLevelRetrieveBUT

SelectCBox
```
javax.swing.JComboBox<E> SelectCBox
```

SelectColorSchemeCBox

javax.swing.JComboBox<E> SelectColorSchemeCBox

SelectColorSchemeLbl
```
javax.swing.JLabel SelectColorSchemeLbl
```

SelectFileForMSASitesLbl

javax.swing.JLabel SelectFileForMSASitesLbl

SelectLbl
```
javax.swing.JLabel SelectLbl
```
SelectionLbl
```
javax.swing.JLabel SelectionLbl
```
SendFileToRes3DBUT
```
javax.swing.JButton SendFileToRes3DBUT
```
ShapeCBox
```
javax.swing.JComboBox<E> ShapeCBox
```
ShapeLbl
```
javax.swing.JLabel ShapeLbl
```
ShapeOnlyCkBox
```
javax.swing.JCheckBox ShapeOnlyCkBox
```

ShapeRestrictCkBox

javax.swing.JCheckBox ShapeRestrictCkBox

ShapeRestrictSmallCkBox

javax.swing.JCheckBox ShapeRestrictSmallCkBox

SlidingWindowBrowseBUT

javax.swing.JButton SlidingWindowBrowseBUT

SlidingWindowLbl
```
javax.swing.JLabel SlidingWindowLbl
```
SlidingWindowTF
```
javax.swing.JTextField SlidingWindowTF
```
SubstsBrowseBUT
```
javax.swing.JButton SubstsBrowseBUT
```
SubstsLbl
```
javax.swing.JLabel SubstsLbl
```
SubstsTF
```
javax.swing.JTextField SubstsTF
```

SynSubsFileBrowseBUT

javax.swing.JButton SynSubsFileBrowseBUT

SynSubsFileLbl
```
javax.swing.JLabel SynSubsFileLbl
```
SynSubsFileTF
```
javax.swing.JTextField SynSubsFileTF
```
SynSubsFileViewBUT
```
javax.swing.JButton SynSubsFileViewBUT
```
TDMSAFileBrowseBUT
```
javax.swing.JButton TDMSAFileBrowseBUT
```
TDMSAFileLbl
```
javax.swing.JLabel TDMSAFileLbl
```
TDMSAFileTF
```
javax.swing.JTextField TDMSAFileTF
```
TSCkBox
```
javax.swing.JCheckBox TSCkBox
```
TablesViewBUT
```
javax.swing.JButton TablesViewBUT
```
ThreeDeeViewPanel
```
javax.swing.JPanel ThreeDeeViewPanel
```
ToolsMenu
```
javax.swing.JMenu ToolsMenu
```
TreeFileBrowseBUT
```
javax.swing.JButton TreeFileBrowseBUT
```
TreeFileLbl
```
javax.swing.JLabel TreeFileLbl
```
TreeFileTF
```
javax.swing.JTextField TreeFileTF
```
TreeFileViewBUT
```
javax.swing.JButton TreeFileViewBUT
```

TreeSAAPDataTabbedPanel

javax.swing.JTabbedPane TreeSAAPDataTabbedPanel

TreeSAAPEvpthwyPanel
```
javax.swing.JPanel TreeSAAPEvpthwyPanel
```
TreeSAAPPanel
```
javax.swing.JPanel TreeSAAPPanel
```
TreeSAAPSubstsPanel
```
javax.swing.JPanel TreeSAAPSubstsPanel
```

UseMyOwnJmolScriptBrowseBUT

javax.swing.JButton UseMyOwnJmolScriptBrowseBUT

UseMyOwnJmolScriptLbl

javax.swing.JLabel UseMyOwnJmolScriptLbl

UseMyOwnJmolScriptTF

javax.swing.JTextField UseMyOwnJmolScriptTF

UseMyOwnJmolScriptViewBUT

javax.swing.JButton UseMyOwnJmolScriptViewBUT

UseNewExPDBBUT
```
javax.swing.JButton UseNewExPDBBUT
```
UseNewModPDBBUT
```
javax.swing.JButton UseNewModPDBBUT
```

UseTranslucentOtherCkBox

javax.swing.JCheckBox UseTranslucentOtherCkBox

ViewColorSchemeBUT
```
javax.swing.JButton ViewColorSchemeBUT
```
ViewDetailsBUT
```
javax.swing.JButton ViewDetailsBUT
```
ViewInJmolBUT
```
javax.swing.JButton ViewInJmolBUT
```

ViewMergedResultsBUT

javax.swing.JButton ViewMergedResultsBUT

ViewOptionsBUT
```
javax.swing.JButton ViewOptionsBUT
```
ViewPropsByRangeBUT
```
javax.swing.JButton ViewPropsByRangeBUT
```
ViewYModelFileBUT
```
javax.swing.JButton ViewYModelFileBUT
```
ZSigPropBrowseBUT
```
javax.swing.JButton ZSigPropBrowseBUT
```
ZSigPropLbl
```
javax.swing.JLabel ZSigPropLbl
```
ZSigPropTF
```
javax.swing.JTextField ZSigPropTF
```
ZSigPropViewBUT
```
javax.swing.JButton ZSigPropViewBUT
```

ZSigPropViewMostSignifBUT

javax.swing.JButton ZSigPropViewMostSignifBUT

bebFieldSelectorBGrp

javax.swing.ButtonGroup bebFieldSelectorBGrp

codemlOptionsBGrp

javax.swing.ButtonGroup codemlOptionsBGrp

codemlOptionsResBGrp

javax.swing.ButtonGroup codemlOptionsResBGrp

dmCodonFileSelectorBGrp

javax.swing.ButtonGroup dmCodonFileSelectorBGrp

dmSelectionBGrp
```
javax.swing.ButtonGroup dmSelectionBGrp
```

generateNewFileName1BUT

javax.swing.JButton generateNewFileName1BUT

generateNewFileName1BUT1

javax.swing.JButton generateNewFileName1BUT1

generateNewFileName1BUT2

javax.swing.JButton generateNewFileName1BUT2

generateNewFileName1BUT4

javax.swing.JButton generateNewFileName1BUT4

generateNewFileName2BUT

javax.swing.JButton generateNewFileName2BUT

generateNewFileName3BUT

javax.swing.JButton generateNewFileName3BUT

generateNewFileName4BUT

javax.swing.JButton generateNewFileName4BUT

jSeparator1

javax.swing.JPopupMenu.Separator jSeparator1

jSeparator4

javax.swing.JPopupMenu.Separator jSeparator4

jSeparator5

javax.swing.JPopupMenu.Separator jSeparator5

mainTabbedPanel
```
javax.swing.JTabbedPane mainTabbedPanel
```

pbsrFieldSelectorBGrp

javax.swing.ButtonGroup pbsrFieldSelectorBGrp

posNegSelectionBGrp

javax.swing.ButtonGroup posNegSelectionBGrp

statusMessageLbl
```
javax.swing.JLabel statusMessageLbl
```
tsConsRadEBGrp
```
javax.swing.ButtonGroup tsConsRadEBGrp
```
tsConsRadSBGrp
```
javax.swing.ButtonGroup tsConsRadSBGrp
```

Class IMPACT_S.GUIAboutBox extends javax.swing.JFrame implements Serializable

Serialized Fields

util
```
Utilities util
```
AboutTextSP
```
javax.swing.JScrollPane AboutTextSP
```
AboutTextTA
```
javax.swing.JTextArea AboutTextTA
```
CloseBUT
```
javax.swing.JButton CloseBUT
```
ImageContainerPanel
```
javax.swing.JPanel ImageContainerPanel
```
ImageLbl
```
javax.swing.JLabel ImageLbl
```
ImagePanel
```
javax.swing.JPanel ImagePanel
```

Class IMPACT_S.GUIAlignmentEditor extends javax.swing.JFrame implements Serializable

Serialized Fields

On
```
boolean On
```
Off
```
boolean Off
```
title
```
java.lang.String title
```
DEFLT_PHYML_TREE_FILE
```
java.lang.String DEFLT_PHYML_TREE_FILE
```
dest_tmpfl
```
java.io.File dest_tmpfl
```
msaFileRun
```
java.lang.String msaFileRun
```
msafile
```
java.io.File msafile
```
msaformat
```
java.lang.String msaformat
```
aeditor
```
AlignmentEditor aeditor
```
msaTModel
```
MSATableModel msaTModel
```
util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
phymlopt
```
GUIPhyMLOptions phymlopt
```
phymlTask
```
PhyMLTask phymlTask
```
phymlcompleted
```
boolean phymlcompleted
```
phyOpts
```
boolean phyOpts
```
phyml_output
```
java.lang.String phyml_output
```
newTreeFiles
```
java.lang.String[] newTreeFiles
```
timer
```
javax.swing.Timer timer
```
pm
```
javax.swing.ProgressMonitor pm
```
pmLen
```
int pmLen
```
tableEnabled
```
boolean tableEnabled
```
seqtableView
```
boolean seqtableView
```
True if currently in Sequence view, or; false if in Site view
markUnselSeq
```
boolean[] markUnselSeq
```
markUnselSites
```
boolean[] markUnselSites
```
treeFileName
```
java.lang.String treeFileName
```
treeFilePath
```
java.lang.String treeFilePath
```
fromRow
```
int fromRow
```
toRow
```
int toRow
```
newtableHeader
```
java.lang.String[] newtableHeader
```
lastProtSelSch
```
int lastProtSelSch
```
lastDRNASelSch
```
int lastDRNASelSch
```
colorScheme
```
int colorScheme
```
colors
```
GUIColorSchemes colors
```
selectedSeqC1
```
int selectedSeqC1
```
AlignmentTable
```
javax.swing.JTable AlignmentTable
```

AlignmentTableSP

javax.swing.JScrollPane AlignmentTableSP

AminoColSchRBMI

javax.swing.JRadioButtonMenuItem AminoColSchRBMI

ChooseLocationCkBox

javax.swing.JCheckBox ChooseLocationCkBox

ChooseLocationPanel
```
javax.swing.JPanel ChooseLocationPanel
```
ColorSchemesMenu
```
javax.swing.JMenu ColorSchemesMenu
```

DRNAImpactRBMI

javax.swing.JRadioButtonMenuItem DRNAImpactRBMI

DRNAJalviewRBMI

javax.swing.JRadioButtonMenuItem DRNAJalviewRBMI

DRNAMegaRBMI

javax.swing.JRadioButtonMenuItem DRNAMegaRBMI

DRNASchemesSepMI
```
javax.swing.JMenuItem DRNASchemesSepMI
```

DRNASeaviewRBMI

javax.swing.JRadioButtonMenuItem DRNASeaviewRBMI

DiscardBUT
```
javax.swing.JButton DiscardBUT
```
DiscardMI
```
javax.swing.JMenuItem DiscardMI
```
FileMenu
```
javax.swing.JMenu FileMenu
```
FindReplaceMI
```
javax.swing.JMenuItem FindReplaceMI
```
GUIAEditorMB
```
javax.swing.JMenuBar GUIAEditorMB
```
MSAPanel
```
javax.swing.JPanel MSAPanel
```

MinSizeColsCkBoxMI

javax.swing.JCheckBoxMenuItem MinSizeColsCkBoxMI

MoveSeqDownBUT
```
javax.swing.JButton MoveSeqDownBUT
```
MoveSeqUpBUT
```
javax.swing.JButton MoveSeqUpBUT
```
NewTreeBrowseBUT
```
javax.swing.JButton NewTreeBrowseBUT
```
NewTreeFileLbl
```
javax.swing.JLabel NewTreeFileLbl
```
NewTreeFileTF
```
javax.swing.JTextField NewTreeFileTF
```

OnlySelectedCkBoxMI

javax.swing.JCheckBoxMenuItem OnlySelectedCkBoxMI

OpenMSAMI
```
javax.swing.JMenuItem OpenMSAMI
```
PhyMLMenu
```
javax.swing.JMenu PhyMLMenu
```
PhyMLOptionsBUT
```
javax.swing.JButton PhyMLOptionsBUT
```
PhyMLOptionsMI
```
javax.swing.JMenuItem PhyMLOptionsMI
```
PhyMLPanel
```
javax.swing.JPanel PhyMLPanel
```
ProtSchemesSepMI
```
javax.swing.JMenuItem ProtSchemesSepMI
```
RenameTaxaMI
```
javax.swing.JMenuItem RenameTaxaMI
```
ResetAlignBUT
```
javax.swing.JButton ResetAlignBUT
```
ResetMSAMI
```
javax.swing.JMenuItem ResetMSAMI
```
RunBUT
```
javax.swing.JButton RunBUT
```
RunPhyML_MI
```
javax.swing.JMenuItem RunPhyML_MI
```
SaveAlignAsBUT
```
javax.swing.JButton SaveAlignAsBUT
```
SaveMSAMI
```
javax.swing.JMenuItem SaveMSAMI
```
SaveMSAasMI
```
javax.swing.JMenuItem SaveMSAasMI
```

SeaviewColSchRBMI

javax.swing.JRadioButtonMenuItem SeaviewColSchRBMI

SelAllRBMI

javax.swing.JRadioButtonMenuItem SelAllRBMI

SelNoneRBMI

javax.swing.JRadioButtonMenuItem SelNoneRBMI

SequenceSelecRadioBUT

javax.swing.JRadioButton SequenceSelecRadioBUT

ShapelyColSchRBMI

javax.swing.JRadioButtonMenuItem ShapelyColSchRBMI

ShowGridCkBoxMI

javax.swing.JCheckBoxMenuItem ShowGridCkBoxMI

SideChainsColSchRBMI

javax.swing.JRadioButtonMenuItem SideChainsColSchRBMI

SiteSelecRadioBUT

javax.swing.JRadioButton SiteSelecRadioBUT

TTable10RBMI

javax.swing.JRadioButtonMenuItem TTable10RBMI

TTable11RBMI

javax.swing.JRadioButtonMenuItem TTable11RBMI

TTable12RBMI

javax.swing.JRadioButtonMenuItem TTable12RBMI

TTable13RBMI

javax.swing.JRadioButtonMenuItem TTable13RBMI

TTable14RBMI

javax.swing.JRadioButtonMenuItem TTable14RBMI

TTable15RBMI

javax.swing.JRadioButtonMenuItem TTable15RBMI

TTable16RBMI

javax.swing.JRadioButtonMenuItem TTable16RBMI

TTable1RBMI

javax.swing.JRadioButtonMenuItem TTable1RBMI

TTable21RBMI

javax.swing.JRadioButtonMenuItem TTable21RBMI

TTable22RBMI

javax.swing.JRadioButtonMenuItem TTable22RBMI

TTable23RBMI

javax.swing.JRadioButtonMenuItem TTable23RBMI

TTable2RBMI

javax.swing.JRadioButtonMenuItem TTable2RBMI

TTable3RBMI

javax.swing.JRadioButtonMenuItem TTable3RBMI

TTable4RBMI

javax.swing.JRadioButtonMenuItem TTable4RBMI

TTable5RBMI

javax.swing.JRadioButtonMenuItem TTable5RBMI

TTable6RBMI

javax.swing.JRadioButtonMenuItem TTable6RBMI

TTable9RBMI

javax.swing.JRadioButtonMenuItem TTable9RBMI

TableMenu
```
javax.swing.JMenu TableMenu
```

ViewAsCodonsRBMI

javax.swing.JRadioButtonMenuItem ViewAsCodonsRBMI

ViewAsDNARBMI

javax.swing.JRadioButtonMenuItem ViewAsDNARBMI

ViewAsProteinsMenu
```
javax.swing.JMenu ViewAsProteinsMenu
```
ViewMenu
```
javax.swing.JMenu ViewMenu
```
ViewOnlySelCkBox
```
javax.swing.JCheckBox ViewOnlySelCkBox
```
ViewOutputBUT
```
javax.swing.JButton ViewOutputBUT
```

drnaColorSchemesBGrp

javax.swing.ButtonGroup drnaColorSchemesBGrp

jSeparator1
```
javax.swing.JSeparator jSeparator1
```
jSeparator2
```
javax.swing.JSeparator jSeparator2
```
jSeparator3
```
javax.swing.JSeparator jSeparator3
```

jSeparator4

javax.swing.JPopupMenu.Separator jSeparator4

jSeparator5

javax.swing.JPopupMenu.Separator jSeparator5

jSeparator6

javax.swing.JPopupMenu.Separator jSeparator6

jSeparator7

javax.swing.JPopupMenu.Separator jSeparator7

jSeparator8

javax.swing.JPopupMenu.Separator jSeparator8

progressBar
```
javax.swing.JProgressBar progressBar
```

protColorSchemesBGrp

javax.swing.ButtonGroup protColorSchemesBGrp

protMenuTablesBGrp

javax.swing.ButtonGroup protMenuTablesBGrp

statusMessageLabel
```
javax.swing.JLabel statusMessageLabel
```
statusPanel
```
javax.swing.JPanel statusPanel
```
tableSelBGrp
```
javax.swing.ButtonGroup tableSelBGrp
```
tableViewBGrp
```
javax.swing.ButtonGroup tableViewBGrp
```

viewDataTypeBGrp

javax.swing.ButtonGroup viewDataTypeBGrp

Class IMPACT_S.GUIAlignmentFiltering extends javax.swing.JFrame implements Serializable

Serialized Fields

On
```
boolean On
```
Off
```
boolean Off
```
title0
```
java.lang.String title0
```
util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
guiae
```
GUIAlignmentEditor guiae
```
alops
```
AlignmentOperations alops
```
ffcformat
```
java.lang.String ffcformat
```
selectedcodons
```
int[] selectedcodons
```
sourceLoc
```
java.lang.String sourceLoc
```
codonsTable
```
java.util.HashMap<K,V> codonsTable
```
ActionPanel
```
javax.swing.JPanel ActionPanel
```
AddGapColsCkBox
```
javax.swing.JCheckBox AddGapColsCkBox
```

AlignmentFileBrowseBUT

javax.swing.JButton AlignmentFileBrowseBUT

AlignmentFileLbl
```
javax.swing.JLabel AlignmentFileLbl
```

AlignmentFileSitesViewBUT

javax.swing.JButton AlignmentFileSitesViewBUT

AlignmentFileTF
```
javax.swing.JTextField AlignmentFileTF
```

AlignmentFileViewBUT

javax.swing.JButton AlignmentFileViewBUT

BackPanel
```
javax.swing.JPanel BackPanel
```
CloseBUT
```
javax.swing.JButton CloseBUT
```
CloseMI
```
javax.swing.JMenuItem CloseMI
```
DNAdataRB
```
javax.swing.JRadioButton DNAdataRB
```

MSAlignmentSitesChangeBUT

javax.swing.JButton MSAlignmentSitesChangeBUT

MSAlignmentSitesFilterBUT

javax.swing.JButton MSAlignmentSitesFilterBUT

MSAlignmentSitesLbl
```
javax.swing.JLabel MSAlignmentSitesLbl
```

MSAlignmentSitesTF

javax.swing.JTextField MSAlignmentSitesTF

MSAlignmentSitesViewBUT

javax.swing.JButton MSAlignmentSitesViewBUT

OpenCSVFileMI
```
javax.swing.JMenuItem OpenCSVFileMI
```
OptionsPanel
```
javax.swing.JPanel OptionsPanel
```
ProteindataRB
```
javax.swing.JRadioButton ProteindataRB
```
dataTypeBGrp
```
javax.swing.ButtonGroup dataTypeBGrp
```

generateNewFileName1BUT3

javax.swing.JButton generateNewFileName1BUT3

jMenu1
```
javax.swing.JMenu jMenu1
```
jMenuBar1
```
javax.swing.JMenuBar jMenuBar1
```

jSeparator1

javax.swing.JPopupMenu.Separator jSeparator1

Class IMPACT_S.GUICodemlOptions extends javax.swing.JFrame implements Serializable

Serialized Fields

copts
```
CodemlOptions copts
```
util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
AADistanceCBox
```
javax.swing.JComboBox<E> AADistanceCBox
```
AADistanceLbl
```
javax.swing.JLabel AADistanceLbl
```
AARateFileBrowseBUT
```
javax.swing.JButton AARateFileBrowseBUT
```
AARateFileLbl
```
javax.swing.JLabel AARateFileLbl
```
AARateFileTF
```
javax.swing.JTextField AARateFileTF
```
AcceptBUT
```
javax.swing.JButton AcceptBUT
```
ActionsPanel
```
javax.swing.JPanel ActionsPanel
```
AddNSsitesOptionBUT
```
javax.swing.JButton AddNSsitesOptionBUT
```
AlphaLbl
```
javax.swing.JLabel AlphaLbl
```
AlphaTF
```
javax.swing.JTextField AlphaTF
```
CancelBUT
```
javax.swing.JButton CancelBUT
```
CleandataCBox
```
javax.swing.JComboBox<E> CleandataCBox
```
CleandataLbl
```
javax.swing.JLabel CleandataLbl
```
CleandataPanel
```
javax.swing.JPanel CleandataPanel
```
ClockCBox
```
javax.swing.JComboBox<E> ClockCBox
```
ClockLbl
```
javax.swing.JLabel ClockLbl
```
CodePanel
```
javax.swing.JPanel CodePanel
```
CodemlOptionsPanel
```
javax.swing.JPanel CodemlOptionsPanel
```
CodonFreqCBox
```
javax.swing.JComboBox<E> CodonFreqCBox
```
CodonFreqLbl
```
javax.swing.JLabel CodonFreqLbl
```
EstFreqCBox
```
javax.swing.JComboBox<E> EstFreqCBox
```
EstFreqLbl
```
javax.swing.JLabel EstFreqLbl
```
EstimatesPanel
```
javax.swing.JPanel EstimatesPanel
```
FixAlphaCBox
```
javax.swing.JComboBox<E> FixAlphaCBox
```
FixAlphaIncCkBox
```
javax.swing.JCheckBox FixAlphaIncCkBox
```
FixAlphaLbl
```
javax.swing.JLabel FixAlphaLbl
```
FixBranchCBox
```
javax.swing.JComboBox<E> FixBranchCBox
```
FixBranchLengthsLbl
```
javax.swing.JLabel FixBranchLengthsLbl
```
FixKappaCBox
```
javax.swing.JComboBox<E> FixKappaCBox
```
FixKappaIncCkBox
```
javax.swing.JCheckBox FixKappaIncCkBox
```
FixKappaLbl
```
javax.swing.JLabel FixKappaLbl
```
FixOmegaCBox
```
javax.swing.JComboBox<E> FixOmegaCBox
```
FixOmegaIncCkBox
```
javax.swing.JCheckBox FixOmegaIncCkBox
```
FixOmegaLbl
```
javax.swing.JLabel FixOmegaLbl
```
FixRhoCBox
```
javax.swing.JComboBox<E> FixRhoCBox
```
FixRhoIncCkBox
```
javax.swing.JCheckBox FixRhoIncCkBox
```
FixRhoLbl
```
javax.swing.JLabel FixRhoLbl
```
ICodeCBox
```
javax.swing.JComboBox<E> ICodeCBox
```
ICodeLbl
```
javax.swing.JLabel ICodeLbl
```
KappaLbl
```
javax.swing.JLabel KappaLbl
```
KappaTF
```
javax.swing.JTextField KappaTF
```
MalphaCBox
```
javax.swing.JComboBox<E> MalphaCBox
```
MalphaIncCkBox
```
javax.swing.JCheckBox MalphaIncCkBox
```
MalphaLbl
```
javax.swing.JLabel MalphaLbl
```
MethodCBox
```
javax.swing.JComboBox<E> MethodCBox
```
MethodIncCkBox
```
javax.swing.JCheckBox MethodIncCkBox
```
MethodLbl
```
javax.swing.JLabel MethodLbl
```
MgeneCBox
```
javax.swing.JComboBox<E> MgeneCBox
```
MgeneLbl
```
javax.swing.JLabel MgeneLbl
```
ModelLbl
```
javax.swing.JLabel ModelLbl
```
ModelsAACBox
```
javax.swing.JComboBox<E> ModelsAACBox
```

ModelsCodonCBox

javax.swing.JComboBox<E> ModelsCodonCBox

ModelsPanel
```
javax.swing.JPanel ModelsPanel
```
NSSitesLbl
```
javax.swing.JLabel NSSitesLbl
```
NSsitesCBox
```
javax.swing.JComboBox<E> NSsitesCBox
```
NSsitesTF
```
javax.swing.JTextField NSsitesTF
```
NoisePanel
```
javax.swing.JPanel NoisePanel
```
NoisyCBox
```
javax.swing.JComboBox<E> NoisyCBox
```
NoisyLbl
```
javax.swing.JLabel NoisyLbl
```
OmegaLbl
```
javax.swing.JLabel OmegaLbl
```
OmegaTF
```
javax.swing.JTextField OmegaTF
```

RateAncestorCBox

javax.swing.JComboBox<E> RateAncestorCBox

RateAncestorLbl
```
javax.swing.JLabel RateAncestorLbl
```
RhoLbl
```
javax.swing.JLabel RhoLbl
```
RhoTF
```
javax.swing.JTextField RhoTF
```
RunModeCBox
```
javax.swing.JComboBox<E> RunModeCBox
```
RunModeLbl
```
javax.swing.JLabel RunModeLbl
```
SaveOptionsAsBUT
```
javax.swing.JButton SaveOptionsAsBUT
```
SeqTypeCBox
```
javax.swing.JComboBox<E> SeqTypeCBox
```
SeqTypeLbl
```
javax.swing.JLabel SeqTypeLbl
```
SeqTypePanel
```
javax.swing.JPanel SeqTypePanel
```
SmallDiffLbl
```
javax.swing.JLabel SmallDiffLbl
```
SmallDiffTF
```
javax.swing.JTextField SmallDiffTF
```
StandardErrorPanel
```
javax.swing.JPanel StandardErrorPanel
```
VerboseCBox
```
javax.swing.JComboBox<E> VerboseCBox
```
VerboseLbl
```
javax.swing.JLabel VerboseLbl
```
getSEECBox
```
javax.swing.JComboBox<E> getSEECBox
```
getSEELbl
```
javax.swing.JLabel getSEELbl
```
nCategoriesGLbl
```
javax.swing.JLabel nCategoriesGLbl
```
nCategoriesGTF
```
javax.swing.JTextField nCategoriesGTF
```

Class IMPACT_S.GUIColorSchemes extends javax.swing.JFrame implements Serializable

Serialized Fields

ptitle
```
java.lang.String ptitle
```
treeSAAPScheme
```
java.awt.Color[] treeSAAPScheme
```
treeSAAP123Scheme
```
java.awt.Color[] treeSAAP123Scheme
```
datamonkeyScheme
```
java.awt.Color[] datamonkeyScheme
```
codemlM2M8Scheme
```
java.awt.Color[] codemlM2M8Scheme
```
codemlM282Scheme
```
java.awt.Color[] codemlM282Scheme
```
codemlM283Scheme
```
java.awt.Color[] codemlM283Scheme
```
mergedResultsScheme
```
java.awt.Color[] mergedResultsScheme
```
seaviewScheme
```
java.awt.Color[] seaviewScheme
```
sidechainsScheme
```
java.awt.Color[] sidechainsScheme
```
aminoScheme
```
java.awt.Color[] aminoScheme
```
shapelyScheme
```
java.awt.Color[] shapelyScheme
```
dnarnaScheme
```
java.awt.Color[] dnarnaScheme
```
userScheme
```
java.awt.Color[] userScheme
```
userchoice
```
int userchoice
```
visible
```
boolean visible
```
tf
```
javax.swing.JTextField[] tf
```
lbl
```
javax.swing.JLabel[] lbl
```
chbox
```
javax.swing.JCheckBox[] chbox
```
ColorSchemes
```
java.util.HashMap<K,V> ColorSchemes
```
loadedScheme
```
int loadedScheme
```
wwidth
```
int wwidth
```
wheight
```
int wheight
```
AAcolor
```
java.util.HashMap<K,V> AAcolor
```
DRNAcolor
```
java.util.HashMap<K,V> DRNAcolor
```
usrSelected
```
boolean usrSelected
```
util
```
Utilities util
```
AlaChBox
```
javax.swing.JCheckBox AlaChBox
```
AlaLbl
```
javax.swing.JLabel AlaLbl
```
AlaTF
```
javax.swing.JTextField AlaTF
```
ArgChBox
```
javax.swing.JCheckBox ArgChBox
```
ArgLbl
```
javax.swing.JLabel ArgLbl
```
ArgTF
```
javax.swing.JTextField ArgTF
```
AsnChBox
```
javax.swing.JCheckBox AsnChBox
```
AsnLbl
```
javax.swing.JLabel AsnLbl
```
AsnTF
```
javax.swing.JTextField AsnTF
```
AspChBox
```
javax.swing.JCheckBox AspChBox
```
AspLbl
```
javax.swing.JLabel AspLbl
```
AspTF
```
javax.swing.JTextField AspTF
```
AsxChBox
```
javax.swing.JCheckBox AsxChBox
```
AsxLbl
```
javax.swing.JLabel AsxLbl
```
AsxTF
```
javax.swing.JTextField AsxTF
```
CloseMI
```
javax.swing.JMenuItem CloseMI
```
CysChBox
```
javax.swing.JCheckBox CysChBox
```
CysLbl
```
javax.swing.JLabel CysLbl
```
CysTF
```
javax.swing.JTextField CysTF
```
GlnChBox
```
javax.swing.JCheckBox GlnChBox
```
GlnLbl
```
javax.swing.JLabel GlnLbl
```
GlnTF
```
javax.swing.JTextField GlnTF
```
GluChBox
```
javax.swing.JCheckBox GluChBox
```
GluLbl
```
javax.swing.JLabel GluLbl
```
GluTF
```
javax.swing.JTextField GluTF
```
GlxChBox
```
javax.swing.JCheckBox GlxChBox
```
GlxLbl
```
javax.swing.JLabel GlxLbl
```
GlxTF
```
javax.swing.JTextField GlxTF
```
GlyChBox
```
javax.swing.JCheckBox GlyChBox
```
GlyLbl
```
javax.swing.JLabel GlyLbl
```
GlyTF
```
javax.swing.JTextField GlyTF
```
HisChBox
```
javax.swing.JCheckBox HisChBox
```
HisLbl
```
javax.swing.JLabel HisLbl
```
HisTF
```
javax.swing.JTextField HisTF
```
IleChBox
```
javax.swing.JCheckBox IleChBox
```
IleLbl
```
javax.swing.JLabel IleLbl
```
IleTF
```
javax.swing.JTextField IleTF
```
JmolSchemePanel
```
javax.swing.JPanel JmolSchemePanel
```
JmolSchemeSP
```
javax.swing.JScrollPane JmolSchemeSP
```
LeuChBox
```
javax.swing.JCheckBox LeuChBox
```
LeuLbl
```
javax.swing.JLabel LeuLbl
```
LeuTF
```
javax.swing.JTextField LeuTF
```
LysChBox
```
javax.swing.JCheckBox LysChBox
```
LysLbl
```
javax.swing.JLabel LysLbl
```
LysTF
```
javax.swing.JTextField LysTF
```
MetChBox
```
javax.swing.JCheckBox MetChBox
```
MetLbl
```
javax.swing.JLabel MetLbl
```
MetTF
```
javax.swing.JTextField MetTF
```
OtherChBox
```
javax.swing.JCheckBox OtherChBox
```
OtherLbl
```
javax.swing.JLabel OtherLbl
```
OtherTF
```
javax.swing.JTextField OtherTF
```
PheChBox
```
javax.swing.JCheckBox PheChBox
```
PheLbl
```
javax.swing.JLabel PheLbl
```
PheTF
```
javax.swing.JTextField PheTF
```
ProChBox
```
javax.swing.JCheckBox ProChBox
```
ProLbl
```
javax.swing.JLabel ProLbl
```
ProTF
```
javax.swing.JTextField ProTF
```
ResetMI
```
javax.swing.JMenuItem ResetMI
```
SelAllMI
```
javax.swing.JMenuItem SelAllMI
```
SelNoneMI
```
javax.swing.JMenuItem SelNoneMI
```
SelectMenu
```
javax.swing.JMenu SelectMenu
```
SerChBox
```
javax.swing.JCheckBox SerChBox
```
SerLbl
```
javax.swing.JLabel SerLbl
```
SerTF
```
javax.swing.JTextField SerTF
```
ThrChBox
```
javax.swing.JCheckBox ThrChBox
```
ThrLbl
```
javax.swing.JLabel ThrLbl
```
ThrTF
```
javax.swing.JTextField ThrTF
```
TrpChBox
```
javax.swing.JCheckBox TrpChBox
```
TrpLbl
```
javax.swing.JLabel TrpLbl
```
TrpTF
```
javax.swing.JTextField TrpTF
```
TyrChBox
```
javax.swing.JCheckBox TyrChBox
```
TyrLbl
```
javax.swing.JLabel TyrLbl
```
TyrTF
```
javax.swing.JTextField TyrTF
```
ValChBox
```
javax.swing.JCheckBox ValChBox
```
ValLbl
```
javax.swing.JLabel ValLbl
```
ValTF
```
javax.swing.JTextField ValTF
```
WindowMenu
```
javax.swing.JMenu WindowMenu
```
jmolSchemesMB
```
javax.swing.JMenuBar jmolSchemesMB
```

Class IMPACT_S.GUIDialogs extends javax.swing.JFrame implements Serializable
- Serialized Fields
  - programName
```
java.lang.String programName
```
  - Question0
```
java.lang.String Question0
```
  - Question1
```
java.lang.String Question1
```
  - Question2
```
java.lang.String Question2
```
  - parentComp
```
java.awt.Component parentComp
```
Class IMPACT_S.GUIFileChooser extends javax.swing.JFrame implements Serializable
- Serialized Fields
  - fileName
```
java.lang.String fileName
```
  - fileDir
```
java.lang.String fileDir
```
  - title
```
java.lang.String title
```
  - FileChooser
```
javax.swing.JFileChooser FileChooser
```

Class IMPACT_S.GUIFileFormatConverter extends javax.swing.JFrame implements Serializable

Serialized Fields

title
```
java.lang.String title
```
FORMATS
```
java.lang.String[] FORMATS
```
msafile
```
java.lang.String msafile
```
usedSetLoc
```
boolean usedSetLoc
```
fileconv
```
FileFormatConverter fileconv
```
util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
BackgroundPanel
```
javax.swing.JPanel BackgroundPanel
```
CancelBUT
```
javax.swing.JButton CancelBUT
```

ChooseLocationCkBox

javax.swing.JCheckBox ChooseLocationCkBox

CloseMI
```
javax.swing.JMenuItem CloseMI
```
ConvertBUT
```
javax.swing.JButton ConvertBUT
```
ConvertFileMI
```
javax.swing.JMenuItem ConvertFileMI
```
FileConverterMB
```
javax.swing.JMenuBar FileConverterMB
```
FileMenu
```
javax.swing.JMenu FileMenu
```
FromCBox
```
javax.swing.JComboBox<E> FromCBox
```
FromLbl
```
javax.swing.JLabel FromLbl
```
InputFileBrowseBUT
```
javax.swing.JButton InputFileBrowseBUT
```
InputFileLbl
```
javax.swing.JLabel InputFileLbl
```
InputFileTF
```
javax.swing.JTextField InputFileTF
```
OpenFileMI
```
javax.swing.JMenuItem OpenFileMI
```

SetLocationBrowseBUT

javax.swing.JButton SetLocationBrowseBUT

SetLocationPanel
```
javax.swing.JPanel SetLocationPanel
```
SetLocationTF
```
javax.swing.JTextField SetLocationTF
```
StatusTF
```
javax.swing.JTextField StatusTF
```
ToCBox
```
javax.swing.JComboBox<E> ToCBox
```
ToLbl
```
javax.swing.JLabel ToLbl
```
jCheckBox1
```
javax.swing.JCheckBox jCheckBox1
```
jSeparator1
```
javax.swing.JSeparator jSeparator1
```

Class IMPACT_S.GUIGnuplotOptions extends javax.swing.JFrame implements Serializable

Serialized Fields

On
```
boolean On
```
Off
```
boolean Off
```
title
```
java.lang.String title
```
util
```
Utilities util
```
df
```
java.lang.String df
```
gpltscript
```
java.lang.String gpltscript
```
gpltscriptloc
```
java.lang.String gpltscriptloc
```
guid
```
GUIDialogs guid
```
ts
```
TreeSAAPTP ts
```
plottask
```
GnuplotTask plottask
```
ActionPanel
```
javax.swing.JPanel ActionPanel
```
BothThreshRB
```
javax.swing.JRadioButton BothThreshRB
```
CloseBUT
```
javax.swing.JButton CloseBUT
```
CloseMI
```
javax.swing.JMenuItem CloseMI
```
ColorG1BUT
```
javax.swing.JButton ColorG1BUT
```
ColorG2BUT
```
javax.swing.JButton ColorG2BUT
```
ColorG3BUT
```
javax.swing.JButton ColorG3BUT
```
DataColumnPanel
```
javax.swing.JPanel DataColumnPanel
```
DataFileLbl
```
javax.swing.JLabel DataFileLbl
```
DataFileTF
```
javax.swing.JTextField DataFileTF
```
DataPanel
```
javax.swing.JPanel DataPanel
```
FileMenu
```
javax.swing.JMenu FileMenu
```
GnuplotMB
```
javax.swing.JMenuBar GnuplotMB
```
GraphColorPanel
```
javax.swing.JPanel GraphColorPanel
```
GraphLegendPanel
```
javax.swing.JPanel GraphLegendPanel
```
GraphStylePanel
```
javax.swing.JPanel GraphStylePanel
```
LegG1TF
```
javax.swing.JTextField LegG1TF
```
LegG2TF
```
javax.swing.JTextField LegG2TF
```
LegG3TF
```
javax.swing.JTextField LegG3TF
```
NegThreshRB
```
javax.swing.JRadioButton NegThreshRB
```
NoThreshRB
```
javax.swing.JRadioButton NoThreshRB
```
OpenDataFileMI
```
javax.swing.JMenuItem OpenDataFileMI
```
OptionsPanel
```
javax.swing.JPanel OptionsPanel
```
OtherOptionsPanel
```
javax.swing.JPanel OtherOptionsPanel
```
PlotGraphBUT
```
javax.swing.JButton PlotGraphBUT
```
PosThreshRB
```
javax.swing.JRadioButton PosThreshRB
```
SelDataG1CBox
```
javax.swing.JComboBox<E> SelDataG1CBox
```
SelDataG2CBox
```
javax.swing.JComboBox<E> SelDataG2CBox
```
SelDataG3CBox
```
javax.swing.JComboBox<E> SelDataG3CBox
```
SelG1CkBox
```
javax.swing.JCheckBox SelG1CkBox
```
SelG2CkBox
```
javax.swing.JCheckBox SelG2CkBox
```
SelG3CkBox
```
javax.swing.JCheckBox SelG3CkBox
```
SelectPanel
```
javax.swing.JPanel SelectPanel
```
StyleG1CBox
```
javax.swing.JComboBox<E> StyleG1CBox
```
StyleG2CBox
```
javax.swing.JComboBox<E> StyleG2CBox
```
StyleG3CBox
```
javax.swing.JComboBox<E> StyleG3CBox
```
ThreshValLbl
```
javax.swing.JLabel ThreshValLbl
```
ThreshValTF
```
javax.swing.JTextField ThreshValTF
```
ThresholdsBGrp
```
javax.swing.ButtonGroup ThresholdsBGrp
```
ViewBUT
```
javax.swing.JButton ViewBUT
```
XarLbl
```
javax.swing.JLabel XarLbl
```
XarMaxTF
```
javax.swing.JTextField XarMaxTF
```
XarMinTF
```
javax.swing.JTextField XarMinTF
```
YarLbl
```
javax.swing.JLabel YarLbl
```
YarMaxTF
```
javax.swing.JTextField YarMaxTF
```
YarMinTF
```
javax.swing.JTextField YarMinTF
```
infoLbl
```
javax.swing.JLabel infoLbl
```

jSeparator1

javax.swing.JPopupMenu.Separator jSeparator1

xtoLbl
```
javax.swing.JLabel xtoLbl
```
ytoLbl
```
javax.swing.JLabel ytoLbl
```

Class IMPACT_S.GUIINFO extends javax.swing.JFrame implements Serializable
- Serialized Fields
  - INFOtitleLbl
```
javax.swing.JLabel INFOtitleLbl
```
  - messagePanel
```
javax.swing.JPanel messagePanel
```
  - messageTA
```
javax.swing.JTextArea messageTA
```

Class IMPACT_S.GUIInitBox extends javax.swing.JFrame implements Serializable

Serialized Fields

On
```
boolean On
```
Off
```
boolean Off
```
timer
```
javax.swing.Timer timer
```
counter
```
int counter
```
ONE_SECOND
```
int ONE_SECOND
```
util
```
Utilities util
```
AuthorsLbl
```
javax.swing.JLabel AuthorsLbl
```
ImageLbl
```
javax.swing.JLabel ImageLbl
```
InitPanel
```
javax.swing.JPanel InitPanel
```
LicenseLbl
```
javax.swing.JLabel LicenseLbl
```
ProgramTitleLbl
```
javax.swing.JLabel ProgramTitleLbl
```
SinceLbl
```
javax.swing.JLabel SinceLbl
```
StatusLbl
```
javax.swing.JLabel StatusLbl
```
VersionLbl
```
javax.swing.JLabel VersionLbl
```
jLabel2
```
javax.swing.JLabel jLabel2
```

Class IMPACT_S.GUIPDBColorSeq extends javax.swing.JFrame implements Serializable

Serialized Fields

On
```
boolean On
```
Off
```
boolean Off
```
title
```
java.lang.String title
```
pdbsequence
```
java.lang.String pdbsequence
```
resRange
```
int[] resRange
```
pdbstm
```
PDBSeqTableModel pdbstm
```
colNames
```
java.lang.String[] colNames
```
pdbseq
```
java.lang.String[][] pdbseq
```
colorsPerSite
```
java.awt.Color[] colorsPerSite
```
dialog
```
GUIDialogs dialog
```
util
```
Utilities util
```
startcol
```
int startcol
```
endcol
```
int endcol
```
startrow
```
int startrow
```
ActionPanel
```
javax.swing.JPanel ActionPanel
```
CloseBUT
```
javax.swing.JButton CloseBUT
```
LastColorLbl
```
javax.swing.JLabel LastColorLbl
```
LastColorTF
```
javax.swing.JTextField LastColorTF
```
MinSizeColsCkBox
```
javax.swing.JCheckBox MinSizeColsCkBox
```
PDBSeqPanel
```
javax.swing.JPanel PDBSeqPanel
```
PDBSeqSP
```
javax.swing.JScrollPane PDBSeqSP
```
PDBSeqTable
```
javax.swing.JTable PDBSeqTable
```
ResRangeLbl
```
javax.swing.JLabel ResRangeLbl
```
ResetBUT
```
javax.swing.JButton ResetBUT
```
SelBgColorLbl
```
javax.swing.JLabel SelBgColorLbl
```
SelBgColorTF
```
javax.swing.JTextField SelBgColorTF
```

Class IMPACT_S.GUIPDBTool extends javax.swing.JFrame implements Serializable

Serialized Fields

util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
ptsm
```
ProtToSwissModel ptsm
```
rcsbtool
```
RCSBTools rcsbtool
```
ffr
```
FileFormatReader ffr
```
results3d
```
ResultsN3DTP results3d
```
rcsbpath
```
java.lang.String rcsbpath
```
User selected path for RCSB PDB file
rcsbspath
```
java.lang.String rcsbspath
```
User selected path for RCSB PDB FASTA file
expdbpath
```
java.lang.String expdbpath
```
User selected path for Swiss Model PDB file
rcsbURL
```
java.lang.String rcsbURL
```
Final direct url to RCSB to use for download of PDB file.
rcsbsURL
```
java.lang.String rcsbsURL
```
Final direct url to RCSB to use for download of PDB FASTA file.
expdbURL
```
java.lang.String expdbURL
```
Final direct url to Swiss Model to use for download of PDB file.
pdbcode
```
java.lang.String pdbcode
```
Concatenated pdbcode from Swiss Model Tab (Tab 1)
dpdbfile
```
java.lang.String dpdbfile
```
Downloaded PDB file location

AvailablePDBSeqsLst

javax.swing.JList<E> AvailablePDBSeqsLst

AvailablePDBSeqsSP

javax.swing.JScrollPane AvailablePDBSeqsSP

AvailablePDBSeqsSpPane

javax.swing.JSplitPane AvailablePDBSeqsSpPane

CloseBUT
```
javax.swing.JButton CloseBUT
```
DownloadBUT
```
javax.swing.JButton DownloadBUT
```
DownloadFromTP
```
javax.swing.JTabbedPane DownloadFromTP
```
DownloadPanel
```
javax.swing.JPanel DownloadPanel
```
ExPDBPanel
```
javax.swing.JPanel ExPDBPanel
```
ExPDBTabPanel
```
javax.swing.JPanel ExPDBTabPanel
```
PDBSeqSizeLbl
```
javax.swing.JLabel PDBSeqSizeLbl
```
PDBSeqSizeTF
```
javax.swing.JTextField PDBSeqSizeTF
```
RCSBPanel
```
javax.swing.JPanel RCSBPanel
```
RCSBTabPanel
```
javax.swing.JPanel RCSBTabPanel
```

SavePDBFileAsChangeBUT

javax.swing.JButton SavePDBFileAsChangeBUT

SavePDBFileAsLbl
```
javax.swing.JLabel SavePDBFileAsLbl
```
SavePDBFileAsTF
```
javax.swing.JTextField SavePDBFileAsTF
```

SaveSelectedSeqAsBUT

javax.swing.JButton SaveSelectedSeqAsBUT

SelectedSeqDisplaySP

javax.swing.JScrollPane SelectedSeqDisplaySP

SelectedSeqDisplayTA

javax.swing.JTextArea SelectedSeqDisplayTA

StatusMessageLbl
```
javax.swing.JLabel StatusMessageLbl
```

UsePDBIDChainForExPDBBUT

javax.swing.JButton UsePDBIDChainForExPDBBUT

downloadPDBFileCkBox

javax.swing.JCheckBox downloadPDBFileCkBox

downloadPDBSeqsFileCkBox

javax.swing.JCheckBox downloadPDBSeqsFileCkBox

downloadedPDBFileChangeBUT

javax.swing.JButton downloadedPDBFileChangeBUT

downloadedPDBFileLbl
```
javax.swing.JLabel downloadedPDBFileLbl
```

downloadedPDBFileTF

javax.swing.JTextField downloadedPDBFileTF

downloadedPDBFileViewBUT

javax.swing.JButton downloadedPDBFileViewBUT

downloadedPDBSeqsFileChangeBUT

javax.swing.JButton downloadedPDBSeqsFileChangeBUT

downloadedPDBSeqsFileLbl

javax.swing.JLabel downloadedPDBSeqsFileLbl

downloadedPDBSeqsFileTF

javax.swing.JTextField downloadedPDBSeqsFileTF

requiredChainIDLbl
```
javax.swing.JLabel requiredChainIDLbl
```

requiredChainIDTF1

javax.swing.JTextField requiredChainIDTF1

requiredPDBIDLbl
```
javax.swing.JLabel requiredPDBIDLbl
```
requiredPDBIDLbl1
```
javax.swing.JLabel requiredPDBIDLbl1
```
requiredPDBIDTF
```
javax.swing.JTextField requiredPDBIDTF
```
requiredPDBIDTF1
```
javax.swing.JTextField requiredPDBIDTF1
```

Class IMPACT_S.GUIPhyMLOptions extends javax.swing.JFrame implements Serializable

Serialized Fields

title
```
java.lang.String title
```
DNASubstModels
```
java.lang.String[] DNASubstModels
```
AASubstModels
```
java.lang.String[] AASubstModels
```
options
```
java.lang.String options
```
util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
AcceptBUT
```
javax.swing.JButton AcceptBUT
```
AcceptCancelPanel
```
javax.swing.JPanel AcceptCancelPanel
```
CancelBUT
```
javax.swing.JButton CancelBUT
```
DataTypeCbox
```
javax.swing.JComboBox<E> DataTypeCbox
```
DataTypeLbl
```
javax.swing.JLabel DataTypeLbl
```

GammaDistrRParamCBox

javax.swing.JComboBox<E> GammaDistrRParamCBox

GammaDistrRParamTF

javax.swing.JTextField GammaDistrRParamTF

GammaDistrRateParamLbl

javax.swing.JLabel GammaDistrRateParamLbl

NBootstrapDSLbl
```
javax.swing.JLabel NBootstrapDSLbl
```
NBootstrapDSTF
```
javax.swing.JTextField NBootstrapDSTF
```
NSubstRateCategLbl
```
javax.swing.JLabel NSubstRateCategLbl
```
NumDataSetsLbl
```
javax.swing.JLabel NumDataSetsLbl
```
NumDataSetsTF
```
javax.swing.JTextField NumDataSetsTF
```
NumRateCategTF
```
javax.swing.JTextField NumRateCategTF
```

OptimizeBLandRPCBox

javax.swing.JComboBox<E> OptimizeBLandRPCBox

OptimizeBLandRPLbl
```
javax.swing.JLabel OptimizeBLandRPLbl
```

OptimizeTreeTopolCBox

javax.swing.JComboBox<E> OptimizeTreeTopolCBox

OptimizeTreeTopolLbl
```
javax.swing.JLabel OptimizeTreeTopolLbl
```

PerformBootstrapCkBox

javax.swing.JCheckBox PerformBootstrapCkBox

PhyMLOptionsPanel
```
javax.swing.JPanel PhyMLOptionsPanel
```
PhyMLOptionsSP
```
javax.swing.JScrollPane PhyMLOptionsSP
```

ProportionInvSitesCBox

javax.swing.JComboBox<E> ProportionInvSitesCBox

ProportionInvSitesLbl

javax.swing.JLabel ProportionInvSitesLbl

ProportionInvSitesTF

javax.swing.JTextField ProportionInvSitesTF

SeqFileCBox
```
javax.swing.JComboBox<E> SeqFileCBox
```
SequenceFileLbl
```
javax.swing.JLabel SequenceFileLbl
```
SubstModelCBox
```
javax.swing.JComboBox<E> SubstModelCBox
```
SubstModelLbl
```
javax.swing.JLabel SubstModelLbl
```
TransRatioCBox
```
javax.swing.JComboBox<E> TransRatioCBox
```
TransRatioLbl
```
javax.swing.JLabel TransRatioLbl
```
TransRatioTF
```
javax.swing.JTextField TransRatioTF
```
TreeTopolBrowseBUT
```
javax.swing.JButton TreeTopolBrowseBUT
```
TreeTopolCbox
```
javax.swing.JComboBox<E> TreeTopolCbox
```
TreeTopolLbl
```
javax.swing.JLabel TreeTopolLbl
```
TreeTopolTF
```
javax.swing.JTextField TreeTopolTF
```

Class IMPACT_S.GUIPreferences extends javax.swing.JFrame implements Serializable

Serialized Fields

util
```
Utilities util
```
dialog
```
GUIDialogs dialog
```
myDefltDSName
```
java.lang.String myDefltDSName
```
ATVExeLocBrowseBUT
```
javax.swing.JButton ATVExeLocBrowseBUT
```
ATVExeLocLbl
```
javax.swing.JLabel ATVExeLocLbl
```
ATVExeLocTF
```
javax.swing.JTextField ATVExeLocTF
```
ActionsPanel
```
javax.swing.JPanel ActionsPanel
```
BaseLocLbl
```
javax.swing.JLabel BaseLocLbl
```
BaseLocTF
```
javax.swing.JTextField BaseLocTF
```
CancelBUT
```
javax.swing.JButton CancelBUT
```

CodemlExeLocBrowseBUT

javax.swing.JButton CodemlExeLocBrowseBUT

CodemlExeLocLbl
```
javax.swing.JLabel CodemlExeLocLbl
```
CodemlExeLocTF
```
javax.swing.JTextField CodemlExeLocTF
```
CreateLocationsBUT
```
javax.swing.JButton CreateLocationsBUT
```

DataSetBaseLocBrowseBUT

javax.swing.JButton DataSetBaseLocBrowseBUT

DataSetBaseLocLbl
```
javax.swing.JLabel DataSetBaseLocLbl
```
DataSetBaseLocTF
```
javax.swing.JTextField DataSetBaseLocTF
```

DataSetsPreferencesPanel

javax.swing.JPanel DataSetsPreferencesPanel

DatamonkeyTabDSLocBrowseBUT

javax.swing.JButton DatamonkeyTabDSLocBrowseBUT

DatamonkeyTabDSLocLbl

javax.swing.JLabel DatamonkeyTabDSLocLbl

DatamonkeyTabDSLocTF

javax.swing.JTextField DatamonkeyTabDSLocTF

GUILocLbl
```
javax.swing.JLabel GUILocLbl
```
GUILocTF
```
javax.swing.JTextField GUILocTF
```
GUIPreferencesPanel
```
javax.swing.JPanel GUIPreferencesPanel
```

GnuplotExeLocBrowseBUT

javax.swing.JButton GnuplotExeLocBrowseBUT

GnuplotExeLocLbl
```
javax.swing.JLabel GnuplotExeLocLbl
```
GnuplotExeLocTF
```
javax.swing.JTextField GnuplotExeLocTF
```
JmolExeLocBrowseBUT
```
javax.swing.JButton JmolExeLocBrowseBUT
```
JmolExeLocLbl
```
javax.swing.JLabel JmolExeLocLbl
```
JmolExeLocTF
```
javax.swing.JTextField JmolExeLocTF
```

PAMLTabDSLocBrowseBUT

javax.swing.JButton PAMLTabDSLocBrowseBUT

PAMLTabDSLocLbl
```
javax.swing.JLabel PAMLTabDSLocLbl
```
PAMLTabDSLocTF
```
javax.swing.JTextField PAMLTabDSLocTF
```

PhyMLExeLocBrowseBUT

javax.swing.JButton PhyMLExeLocBrowseBUT

PhyMLExeLocLbl
```
javax.swing.JLabel PhyMLExeLocLbl
```
PhyMLExeLocTF
```
javax.swing.JTextField PhyMLExeLocTF
```
PreferencesTP
```
javax.swing.JTabbedPane PreferencesTP
```
ProgramsBaseLocLbl
```
javax.swing.JLabel ProgramsBaseLocLbl
```

ProgramsBaseLocTF

javax.swing.JTextField ProgramsBaseLocTF

ProgramsPreferencesPanel

javax.swing.JPanel ProgramsPreferencesPanel

ResultsTabDSLocBrowseBUT

javax.swing.JButton ResultsTabDSLocBrowseBUT

ResultsTabDSLocLbl
```
javax.swing.JLabel ResultsTabDSLocLbl
```

ResultsTabDSLocTF

javax.swing.JTextField ResultsTabDSLocTF

SaveBUT
```
javax.swing.JButton SaveBUT
```
TreeSAAPExeLocLbl
```
javax.swing.JLabel TreeSAAPExeLocLbl
```
TreeSAAPExeLocTF
```
javax.swing.JTextField TreeSAAPExeLocTF
```

TreeSAAPTabDSLocBrowseBUT

javax.swing.JButton TreeSAAPTabDSLocBrowseBUT

TreeSAAPTabDSLocLbl
```
javax.swing.JLabel TreeSAAPTabDSLocLbl
```

TreeSAAPTabDSLocTF

javax.swing.JTextField TreeSAAPTabDSLocTF

TryDSSuggestionCkBox

javax.swing.JCheckBox TryDSSuggestionCkBox

UseDSLocationsCkBox

javax.swing.JCheckBox UseDSLocationsCkBox

jLabel1
```
javax.swing.JLabel jLabel1
```
jPanel1
```
javax.swing.JPanel jPanel1
```

Class IMPACT_S.GUIProgExecOutput extends javax.swing.JFrame implements Serializable
- Serialized Fields
  - CloseBUT
```
javax.swing.JButton CloseBUT
```
  - ClosePanel
```
javax.swing.JPanel ClosePanel
```
  - OutputSP
```
javax.swing.JScrollPane OutputSP
```
  - OutputTA
```
javax.swing.JTextArea OutputTA
```

Class IMPACT_S.GUIProtToSwissModel extends javax.swing.JFrame implements Serializable

Serialized Fields

util
```
Utilities util
```
ptsm
```
ProtToSwissModel ptsm
```
ffc
```
FileFormatConverter ffc
```
seqtrans
```
SequenceTranslator seqtrans
```
results3d
```
ResultsN3DTP results3d
```
sw
```
javax.swing.SwingWorker<T,V> sw
```
guipeo
```
GUIProgExecOutput guipeo
```
dialog
```
GUIDialogs dialog
```
selSeqName
```
java.lang.String selSeqName
```
selSeqNameT
```
java.lang.String selSeqNameT
```
selSeqNameP
```
java.lang.String selSeqNameP
```
savedseq
```
java.lang.String savedseq
```
savedseqT
```
java.lang.String savedseqT
```
savedseqP
```
java.lang.String savedseqP
```
translated
```
boolean translated
```
translatedT
```
boolean translatedT
```
translatedP
```
boolean translatedP
```
translateStateT
```
boolean translateStateT
```
translateStateP
```
boolean translateStateP
```
selSeqIndexT
```
int selSeqIndexT
```
selSeqIndexP
```
int selSeqIndexP
```
selTransIndexT
```
int selTransIndexT
```
selTransIndexP
```
int selTransIndexP
```

AlMWhichSequenceBGrp

javax.swing.ButtonGroup AlMWhichSequenceBGrp

AlignmentModePanel
```
javax.swing.JPanel AlignmentModePanel
```

AuMWhichTemplateBGrp

javax.swing.ButtonGroup AuMWhichTemplateBGrp

AutomatedModePanel
```
javax.swing.JPanel AutomatedModePanel
```

ChooseTranslTableCBox

javax.swing.JComboBox<E> ChooseTranslTableCBox

ChooseTranslTableCBox1

javax.swing.JComboBox<E> ChooseTranslTableCBox1

ChooseTranslTableLbl
```
javax.swing.JLabel ChooseTranslTableLbl
```

ChooseTranslTableLbl1

javax.swing.JLabel ChooseTranslTableLbl1

CloseBUT
```
javax.swing.JButton CloseBUT
```
CloseMI
```
javax.swing.JMenuItem CloseMI
```
EditMenu
```
javax.swing.JMenu EditMenu
```
FileMenu
```
javax.swing.JMenu FileMenu
```
KeepGapsChBox
```
javax.swing.JCheckBox KeepGapsChBox
```
KeepGapsChBox1
```
javax.swing.JCheckBox KeepGapsChBox1
```
MSANamesLst
```
javax.swing.JList<E> MSANamesLst
```
MSANamesLst1
```
javax.swing.JList<E> MSANamesLst1
```
MSANamesSP
```
javax.swing.JScrollPane MSANamesSP
```
MSANamesSP1
```
javax.swing.JScrollPane MSANamesSP1
```
OpenMSAFileMI
```
javax.swing.JMenuItem OpenMSAFileMI
```
PDBSLengthLbl
```
javax.swing.JLabel PDBSLengthLbl
```
PDBSLengthTF
```
javax.swing.JTextField PDBSLengthTF
```
PDBSequenceRB
```
javax.swing.JRadioButton PDBSequenceRB
```
PDBSequenceSP
```
javax.swing.JScrollPane PDBSequenceSP
```
PDBSequenceTA
```
javax.swing.JTextArea PDBSequenceTA
```

ProteinAlignmentCkBox

javax.swing.JCheckBox ProteinAlignmentCkBox

ProteinAlignmentCkBox1

javax.swing.JCheckBox ProteinAlignmentCkBox1

ProteinModelerMenuBar

javax.swing.JMenuBar ProteinModelerMenuBar

SMProjectModesTP

javax.swing.JTabbedPane SMProjectModesTP

SMProjectTitleLbl
```
javax.swing.JLabel SMProjectTitleLbl
```
SMProjectTitleLbl1
```
javax.swing.JLabel SMProjectTitleLbl1
```
SMProjectTitleTF
```
javax.swing.JTextField SMProjectTitleTF
```

SMProjectTitleTF1

javax.swing.JTextField SMProjectTitleTF1

SMSubmitPanel
```
javax.swing.JPanel SMSubmitPanel
```

SMUseDefaultValuesChBox

javax.swing.JCheckBox SMUseDefaultValuesChBox

SMUseDefaultValuesChBox1

javax.swing.JCheckBox SMUseDefaultValuesChBox1

SMYourEmailLbl
```
javax.swing.JLabel SMYourEmailLbl
```
SMYourEmailLbl1
```
javax.swing.JLabel SMYourEmailLbl1
```
SMYourEmailTF
```
javax.swing.JTextField SMYourEmailTF
```
SMYourEmailTF1
```
javax.swing.JTextField SMYourEmailTF1
```

SaveTranslatedSeqAsMI

javax.swing.JMenuItem SaveTranslatedSeqAsMI

SelSequencesSPane

javax.swing.JSplitPane SelSequencesSPane

SelectedSeqSP
```
javax.swing.JScrollPane SelectedSeqSP
```
SelectedSeqTA
```
javax.swing.JTextArea SelectedSeqTA
```
SeqLengthLbl
```
javax.swing.JLabel SeqLengthLbl
```
SeqLengthTF
```
javax.swing.JTextField SeqLengthTF
```
SeqSemaphoreTF
```
javax.swing.JTextField SeqSemaphoreTF
```

SetEditableSeqsMI

javax.swing.JCheckBoxMenuItem SetEditableSeqsMI

SubmitSwissModelBUT
```
javax.swing.JButton SubmitSwissModelBUT
```
SwissModelAlMPanel
```
javax.swing.JPanel SwissModelAlMPanel
```
SwissModelAuMPanel
```
javax.swing.JPanel SwissModelAuMPanel
```
TargetSLengthLbl
```
javax.swing.JLabel TargetSLengthLbl
```
TargetSLengthTF
```
javax.swing.JTextField TargetSLengthTF
```

TargetSequenceRB

javax.swing.JRadioButton TargetSequenceRB

TargetSequenceSP

javax.swing.JScrollPane TargetSequenceSP

TargetSequenceTA
```
javax.swing.JTextArea TargetSequenceTA
```
TemplateChainIDLbl1
```
javax.swing.JLabel TemplateChainIDLbl1
```

TemplateChainIDTF1

javax.swing.JTextField TemplateChainIDTF1

TemplateChainLbl
```
javax.swing.JLabel TemplateChainLbl
```
TemplateChainTF
```
javax.swing.JTextField TemplateChainTF
```

TemplateFileBrowseBUT

javax.swing.JButton TemplateFileBrowseBUT

TemplateFileTF
```
javax.swing.JTextField TemplateFileTF
```
TemplateLbl
```
javax.swing.JLabel TemplateLbl
```
TemplatePDBIDLbl
```
javax.swing.JLabel TemplatePDBIDLbl
```
TemplatePDBIDLbl1
```
javax.swing.JLabel TemplatePDBIDLbl1
```
TemplatePDBIDTF
```
javax.swing.JTextField TemplatePDBIDTF
```
TemplatePDBIDTF1
```
javax.swing.JTextField TemplatePDBIDTF1
```
TransSeqPanel
```
javax.swing.JPanel TransSeqPanel
```
TransSeqPanel1
```
javax.swing.JPanel TransSeqPanel1
```

TranslateAndSaveMSAFileMI

javax.swing.JMenuItem TranslateAndSaveMSAFileMI

TranslateBUT
```
javax.swing.JButton TranslateBUT
```
TranslateBUT1
```
javax.swing.JButton TranslateBUT1
```
ViewYModelBUT
```
javax.swing.JButton ViewYModelBUT
```

jSeparator1

javax.swing.JPopupMenu.Separator jSeparator1

jSeparator2

javax.swing.JPopupMenu.Separator jSeparator2

pdbIDChainRB
```
javax.swing.JRadioButton pdbIDChainRB
```
seqLengthInfoPanel
```
javax.swing.JPanel seqLengthInfoPanel
```
swissModelOptsPanel
```
javax.swing.JPanel swissModelOptsPanel
```
templateFileRB
```
javax.swing.JRadioButton templateFileRB
```

Class IMPACT_S.GUIResultsView extends javax.swing.JFrame implements Serializable

Serialized Fields

title
```
java.lang.String title
```
file0
```
java.lang.String file0
```
file1
```
java.lang.String file1
```
tableColNamesF0
```
java.lang.String[] tableColNamesF0
```
tableColNamesF1
```
java.lang.String[] tableColNamesF1
```
tableDataValuesF0
```
java.lang.Object[][] tableDataValuesF0
```
tableDataValuesF1
```
java.lang.Object[][] tableDataValuesF1
```
util
```
Utilities util
```
resView
```
ResultsView resView
```
csvModel
```
CSVTableModel csvModel
```
dialog
```
GUIDialogs dialog
```
emptyModel
```
java.lang.String[] emptyModel
```
loadedFile0
```
boolean loadedFile0
```
inputOutput
```
java.lang.String inputOutput
```
tableClicked
```
boolean tableClicked
```
startSelRowF0
```
int startSelRowF0
```
startSelColF0
```
int startSelColF0
```
startSelRowF1
```
int startSelRowF1
```
startSelColF1
```
int startSelColF1
```
endSelRowF0
```
int endSelRowF0
```
endSelColF0
```
int endSelColF0
```
endSelRowF1
```
int endSelRowF1
```
endSelColF1
```
int endSelColF1
```
file0read
```
boolean file0read
```
file1read
```
boolean file1read
```
both
```
boolean both
```
selectedColF0
```
int selectedColF0
```
selectedColF1
```
int selectedColF1
```
savedAsFile
```
java.lang.String savedAsFile
```
CSVViewerMB
```
javax.swing.JMenuBar CSVViewerMB
```
CSVViewerSP
```
javax.swing.JScrollPane CSVViewerSP
```
CSVViewerTable
```
javax.swing.JTable CSVViewerTable
```
CloseBUT
```
javax.swing.JButton CloseBUT
```

ColFixedSizeMI

javax.swing.JCheckBoxMenuItem ColFixedSizeMI

ColMaxSizeMI

javax.swing.JCheckBoxMenuItem ColMaxSizeMI

ColMinSizeMI

javax.swing.JCheckBoxMenuItem ColMinSizeMI

ColumnsCountLbl
```
javax.swing.JLabel ColumnsCountLbl
```
ColumnsCountTF
```
javax.swing.JTextField ColumnsCountTF
```
ExitMI
```
javax.swing.JMenuItem ExitMI
```
File01Panel
```
javax.swing.JPanel File01Panel
```
File1NWinMI
```
javax.swing.JMenuItem File1NWinMI
```
File1n2NWinMI
```
javax.swing.JMenuItem File1n2NWinMI
```
File2NWinMI
```
javax.swing.JMenuItem File2NWinMI
```
FileMenu
```
javax.swing.JMenu FileMenu
```
FileViewCBox
```
javax.swing.JComboBox<E> FileViewCBox
```
NewWindowMenu
```
javax.swing.JMenu NewWindowMenu
```
OpenCSVFile0MI
```
javax.swing.JMenuItem OpenCSVFile0MI
```
OpenCSVFile1MI
```
javax.swing.JMenuItem OpenCSVFile1MI
```
ResizeMenu
```
javax.swing.JMenu ResizeMenu
```
RowsCountLbl
```
javax.swing.JLabel RowsCountLbl
```
RowsCountTF
```
javax.swing.JTextField RowsCountTF
```
SSClosePanel
```
javax.swing.JPanel SSClosePanel
```
SaveAsMI
```
javax.swing.JMenuItem SaveAsMI
```
SelectFileLbl
```
javax.swing.JLabel SelectFileLbl
```
TablePanel
```
javax.swing.JPanel TablePanel
```
ViewMenu
```
javax.swing.JMenu ViewMenu
```

ViewResultsFile0RadioMI

javax.swing.JRadioButtonMenuItem ViewResultsFile0RadioMI

ViewResultsFile1RadioMI

javax.swing.JRadioButtonMenuItem ViewResultsFile1RadioMI

jSeparator1
```
javax.swing.JSeparator jSeparator1
```
jSeparator2
```
javax.swing.JSeparator jSeparator2
```

jSeparator3

javax.swing.JPopupMenu.Separator jSeparator3

statusMsgLbl
```
javax.swing.JLabel statusMsgLbl
```

Class IMPACT_S.MSAColumnColorRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
- Serialized Fields
  - bkgndColor
```
java.awt.Color bkgndColor
```
  - fgndColor
```
java.awt.Color fgndColor
```
  - selBg
```
java.awt.Color selBg
```
  - selFg
```
java.awt.Color selFg
```
  - datatype
```
int datatype
```
  - datacolors
```
java.util.HashMap<K,V> datacolors
```
Class IMPACT_S.MSATableModel extends javax.swing.table.AbstractTableModel implements Serializable
- Serialized Fields
  - columnNames
```
java.lang.String[] columnNames
```
  - data
```
java.lang.Object[][] data
```
  - types
```
java.lang.Class<T>[] types
```
  - canEdit
```
boolean[] canEdit
```
Class IMPACT_S.PDBSeqColClrRenderer extends javax.swing.table.DefaultTableCellRenderer implements Serializable
- Serialized Fields
  - bkgndColor
```
java.awt.Color bkgndColor
```
  - fgndColor
```
java.awt.Color fgndColor
```
  - selBg
```
java.awt.Color selBg
```
  - selFg
```
java.awt.Color selFg
```
Class IMPACT_S.PDBSeqTableModel extends javax.swing.table.AbstractTableModel implements Serializable
- Serialized Fields
  - columnNames
```
java.lang.String[] columnNames
```
  - data
```
java.lang.Object[][] data
```
  - types
```
java.lang.Class<T>[] types
```
  - canEdit
```
boolean[] canEdit
```

Serialized Form

Package IMPACT_S

Class IMPACT_S.CSVTableModel extends javax.swing.table.AbstractTableModel implements Serializable

Serialized Fields

columnNames

data

types

canEdit

Class IMPACT_S.GUI extends javax.swing.JFrame implements Serializable

Serialized Fields

extrZsigPropFl

openedZSP

openedSWD

openedNSS

openedSS

dialog

i

guirv

tsres

cdlres

stat

results3d

copts

guijs

jmolTask

atvTask

treesaapTask

codemlcompleted

codeml_output

pm

codemlTask

timer

ctaskRunning

ffcformat

tslowerlimit

lhvma

lhvmb

lrtm

gnupo

guiae

selectedcodonsTS

selectedcodonsDM

DNAdata

guipdbs

guipeo

dmres

guiaf

alops

retrievedModels

TSres

DMres

PAMLres

i2once

AboutMI

AlignmentEditorMI

AlignmentFilterBUT

AlignmentFilterMI

AlignmentFilteringBUT

BEBResultsFile1BrowseBUT

BEBResultsFile1Lbl

BEBResultsFile1RB

BEBResultsFile1TF

BEBResultsFile1ViewBUT

BEBResultsFile2BrowseBUT

BEBResultsFile2Lbl

BEBResultsFile2RB

BEBResultsFile2TF

BackPanel

BackupPanel

C12CkBox

C12SCkBox

C78CkBox

C78SCkBox

CSVViewerMI

ChooseMergeFileBrowseBUT

ChooseMergeFileLbl

ChooseMergeFileTF

ChooseModelsLbl

ChooseToModelBUT

CodemlPanel