Serialized Form
columnNames
java.lang.String[] columnNames
data
java.lang.Object[][] data
types
java.lang.Class<T>[] types
canEdit
boolean[] canEdit
|
Class IMPACT.GUI extends javax.swing.JFrame implements Serializable |
On
boolean On
Off
boolean Off
title
java.lang.String title
titleName
java.lang.String titleName
windowDCO
boolean windowDCO
aai1bg
java.awt.Color aai1bg
gvbg
java.awt.Color gvbg
gpbg
java.awt.Color gpbg
chbg
java.awt.Color chbg
selectedProp
boolean[] selectedProp
properties
java.lang.String[] properties
propertyNum
int propertyNum
aai1TF
java.lang.String aai1TF
pamlTF
java.lang.String pamlTF
optionsFilePathIn
java.lang.String optionsFilePathIn
optionsFilePathOut
java.lang.String optionsFilePathOut
focus
boolean focus
fileopened
boolean fileopened
initializing
boolean initializing
panelChosen
char panelChosen
dialog
GUIDialogs dialog
guiprefs
GUIConfPreferences guiprefs
guiae
GUIAlignmentEditor guiae
guipeo
GUIProgExecOutput guipeo
guirvCT
GUIResultsView guirvCT
guirvR
GUIResultsView guirvR
guirvRS
GUIResultsView guirvRS
guiffc
GUIFileFormatConverter guiffc
guirs
GUIResultsSummary guirs
guiabout
GUIAboutBox guiabout
contestTask
ConTestTask contestTask
statRTask
RSoftwareTask statRTask
pdfviewerTask
ViewerTask pdfviewerTask
psviewerTask
ViewerTask psviewerTask
jmolTask
GenericJarTask jmolTask
atvTask
GenericJarTask atvTask
timerC
javax.swing.Timer timerC
timerR
javax.swing.Timer timerR
pm
javax.swing.ProgressMonitor pm
pmLen
int pmLen
contest_output
java.lang.String contest_output
cttaskRunning
boolean cttaskRunning
editorUsed
boolean editorUsed
emptyModel
java.lang.String[] emptyModel
optionsR
java.lang.String optionsR
r_output
java.lang.String r_output
rtaskRunning
boolean rtaskRunning
selectedValues
java.lang.String[] selectedValues
unselectedList
boolean unselectedList
selectedList
boolean selectedList
useLastCreatedTree
java.lang.String useLastCreatedTree
useLastCreatedStatfl
java.lang.String useLastCreatedStatfl
AAindex1CkBox
javax.swing.JCheckBox AAindex1CkBox
AAindex1FileViewBUT
javax.swing.JButton AAindex1FileViewBUT
AAindex1PropSplitPane
javax.swing.JSplitPane AAindex1PropSplitPane
ASeqFileBrowseBUT
javax.swing.JButton ASeqFileBrowseBUT
ASeqFileEditBUT
javax.swing.JButton ASeqFileEditBUT
ASequenceFileLbl
javax.swing.JLabel ASequenceFileLbl
ASequenceFileTF
javax.swing.JTextField ASequenceFileTF
AboutMI
javax.swing.JMenuItem AboutMI
AlphabetCBox
javax.swing.JComboBox AlphabetCBox
AlphabetLbl
javax.swing.JLabel AlphabetLbl
BPViewRadioMI
javax.swing.JRadioButtonMenuItem BPViewRadioMI
BiochemPropToglBut
javax.swing.JToggleButton BiochemPropToglBut
BiochemicalPropertiesPanel
javax.swing.JPanel BiochemicalPropertiesPanel
BonferroniCorrectCBox
javax.swing.JComboBox BonferroniCorrectCBox
BonferroniCorrectLbl
javax.swing.JLabel BonferroniCorrectLbl
CPULbl
javax.swing.JLabel CPULbl
CPUTF
javax.swing.JTextField CPUTF
CSVViewerMI
javax.swing.JMenuItem CSVViewerMI
ChargeCkBox
javax.swing.JCheckBox ChargeCkBox
ChoosePropertiesLbl
javax.swing.JLabel ChoosePropertiesLbl
ClearValuesAl_MI
javax.swing.JMenuItem ClearValuesAl_MI
ClearValuesBP_MI
javax.swing.JMenuItem ClearValuesBP_MI
ClearValuesDL_MI
javax.swing.JMenuItem ClearValuesDL_MI
ClearValuesMS_MI
javax.swing.JMenuItem ClearValuesMS_MI
ClearValuesMenu
javax.swing.JMenu ClearValuesMenu
ClearValuesOT_MI
javax.swing.JMenuItem ClearValuesOT_MI
ConTestOutFileBrowseBUT
javax.swing.JButton ConTestOutFileBrowseBUT
ConTestOutFileLbl
javax.swing.JLabel ConTestOutFileLbl
ConTestOutFileTF
javax.swing.JTextField ConTestOutFileTF
ConTestOutFilesViewBUT
javax.swing.JButton ConTestOutFilesViewBUT
ConTestSimulOutFileBrowseBUT
javax.swing.JButton ConTestSimulOutFileBrowseBUT
ConTestSimulOutFileLbl
javax.swing.JLabel ConTestSimulOutFileLbl
ConTestSimulOutFileTF
javax.swing.JTextField ConTestSimulOutFileTF
ConfigTabPanel
javax.swing.JPanel ConfigTabPanel
DLViewRadioMI
javax.swing.JRadioButtonMenuItem DLViewRadioMI
DataFileNameBrowseBUT
javax.swing.JButton DataFileNameBrowseBUT
DataFileNameLbl
javax.swing.JLabel DataFileNameLbl
DataFileNameTF
javax.swing.JTextField DataFileNameTF
DataLoadToglBut
javax.swing.JToggleButton DataLoadToglBut
DataLoadingPanel
javax.swing.JPanel DataLoadingPanel
DataSetNameLbl
javax.swing.JLabel DataSetNameLbl
DataSetNameTF
javax.swing.JTextField DataSetNameTF
DeselectPropBUT
javax.swing.JButton DeselectPropBUT
DetectionLevelExampleLbl
javax.swing.JLabel DetectionLevelExampleLbl
DetectionLevelLbl
javax.swing.JLabel DetectionLevelLbl
DetectionLevelTF
javax.swing.JTextField DetectionLevelTF
EditMenu
javax.swing.JMenu EditMenu
ExecuteRStatBUT
javax.swing.JButton ExecuteRStatBUT
FDRCorrectCBox
javax.swing.JComboBox FDRCorrectCBox
FDRCorrectLbl
javax.swing.JLabel FDRCorrectLbl
FileFormatCBox
javax.swing.JComboBox FileFormatCBox
FileFormatLbl
javax.swing.JLabel FileFormatLbl
FileMenu
javax.swing.JMenu FileMenu
FormatTypeCBox
javax.swing.JComboBox FormatTypeCBox
FormatTypeLbl
javax.swing.JLabel FormatTypeLbl
GPolarityCkBox
javax.swing.JCheckBox GPolarityCkBox
GVolumeCkBox
javax.swing.JCheckBox GVolumeCkBox
HelpMenu
javax.swing.JMenu HelpMenu
InputPanel
javax.swing.JPanel InputPanel
InsertFromFilePanel
javax.swing.JPanel InsertFromFilePanel
InsertValuesFromProgBUT
javax.swing.JButton InsertValuesFromProgBUT
InternalParamsMenu
javax.swing.JMenu InternalParamsMenu
JMolMI
javax.swing.JMenuItem JMolMI
LabelsPanel
javax.swing.JPanel LabelsPanel
LowerPanel
javax.swing.JPanel LowerPanel
MLProgramCBox
javax.swing.JComboBox MLProgramCBox
MSAEditorMI
javax.swing.JMenuItem MSAEditorMI
MSAFileConvertMI
javax.swing.JMenuItem MSAFileConvertMI
MSViewRadioMI
javax.swing.JRadioButtonMenuItem MSViewRadioMI
MaseFormatPanel
javax.swing.JPanel MaseFormatPanel
MaxGapAllwLbl
javax.swing.JLabel MaxGapAllwLbl
MaxGapAllwTF
javax.swing.JTextField MaxGapAllwTF
MiddlePanel
javax.swing.JPanel MiddlePanel
ModelCBox
javax.swing.JComboBox ModelCBox
ModelLbl
javax.swing.JLabel ModelLbl
ModelSpecToglBut
javax.swing.JToggleButton ModelSpecToglBut
ModelSpecificationPanel
javax.swing.JPanel ModelSpecificationPanel
NameForSiteLbl
javax.swing.JLabel NameForSiteLbl
NameForSiteTF
javax.swing.JTextField NameForSiteTF
NumberCategoriesLbl
javax.swing.JLabel NumberCategoriesLbl
NumberCategoriesTF
javax.swing.JTextField NumberCategoriesTF
NumberOfPropertiesLbl
javax.swing.JLabel NumberOfPropertiesLbl
NumberOfPropertiesTF
javax.swing.JTextField NumberOfPropertiesTF
OTViewRadioMI
javax.swing.JRadioButtonMenuItem OTViewRadioMI
OldFormatCBox
javax.swing.JComboBox OldFormatCBox
OldFormatLbl
javax.swing.JLabel OldFormatLbl
OpenFileMI
javax.swing.JMenuItem OpenFileMI
OpenROptFileMI
javax.swing.JMenuItem OpenROptFileMI
OutputPanel
javax.swing.JPanel OutputPanel
OutputToglBut
javax.swing.JToggleButton OutputToglBut
PhylipFormatPanel
javax.swing.JPanel PhylipFormatPanel
PosSelecDetecCkBox
javax.swing.JCheckBox PosSelecDetecCkBox
PreferencesMI
javax.swing.JMenuItem PreferencesMI
PreviewOptionsBUT
javax.swing.JButton PreviewOptionsBUT
PrintToFileMI
javax.swing.JMenuItem PrintToFileMI
QuitMI
javax.swing.JMenuItem QuitMI
RAMLbl
javax.swing.JLabel RAMLbl
RAMTF
javax.swing.JTextField RAMTF
RExecutionPanel
javax.swing.JPanel RExecutionPanel
RGraphicsBrowseBUT
javax.swing.JButton RGraphicsBrowseBUT
RGraphicsCBox
javax.swing.JComboBox RGraphicsCBox
RGraphicsLbl
javax.swing.JLabel RGraphicsLbl
RGraphicsPanel
javax.swing.JPanel RGraphicsPanel
RGraphicsViewBUT
javax.swing.JButton RGraphicsViewBUT
ROptionsPanel
javax.swing.JPanel ROptionsPanel
RPosSelectionFileBrowseBUT
javax.swing.JButton RPosSelectionFileBrowseBUT
RPosSelectionLbl
javax.swing.JLabel RPosSelectionLbl
RPosSelectionTF
javax.swing.JTextField RPosSelectionTF
RResFilesViewBUT
javax.swing.JButton RResFilesViewBUT
RStatResFileBrowseBUT
javax.swing.JButton RStatResFileBrowseBUT
RStatResFileLbl
javax.swing.JLabel RStatResFileLbl
RStatResFileTF
javax.swing.JTextField RStatResFileTF
RStatSaveAsBUT
javax.swing.JButton RStatSaveAsBUT
RamxCpuLbl
javax.swing.JLabel RamxCpuLbl
RateAcrossSitesVarCBox
javax.swing.JComboBox RateAcrossSitesVarCBox
RateAcrossSitesVarLbl
javax.swing.JLabel RateAcrossSitesVarLbl
RateDistribPanel
javax.swing.JPanel RateDistribPanel
ReloadValuesAll_MI
javax.swing.JMenuItem ReloadValuesAll_MI
ReloadValuesBP_MI
javax.swing.JMenuItem ReloadValuesBP_MI
ReloadValuesDL_MI
javax.swing.JMenuItem ReloadValuesDL_MI
ReloadValuesMS_MI
javax.swing.JMenuItem ReloadValuesMS_MI
ReloadValuesMenu
javax.swing.JMenu ReloadValuesMenu
ReloadValuesOT_MI
javax.swing.JMenuItem ReloadValuesOT_MI
ResetPropListsBUT
javax.swing.JButton ResetPropListsBUT
ResultsTabPanel
javax.swing.JPanel ResultsTabPanel
RunATVMI
javax.swing.JMenuItem RunATVMI
RunConTestBUT
javax.swing.JButton RunConTestBUT
RunConTestMI
javax.swing.JMenuItem RunConTestMI
RunMenu
javax.swing.JMenu RunMenu
RunRScritpsMI
javax.swing.JMenuItem RunRScritpsMI
SaveOptsAsMI
javax.swing.JMenuItem SaveOptsAsMI
SaveOptsMI
javax.swing.JMenuItem SaveOptsMI
SearchListLbl
javax.swing.JLabel SearchListLbl
SearchListTF
javax.swing.JTextField SearchListTF
SearchResultsNumTF
javax.swing.JTextField SearchResultsNumTF
SelectPropBUT
javax.swing.JButton SelectPropBUT
SelectedList
javax.swing.JList SelectedList
SelectedPropsLbl
javax.swing.JLabel SelectedPropsLbl
SelectedPropsTF
javax.swing.JTextField SelectedPropsTF
ShapeParameterExampleLbl
javax.swing.JLabel ShapeParameterExampleLbl
ShapeParameterLbl
javax.swing.JLabel ShapeParameterLbl
ShapeParameterTF
javax.swing.JTextField ShapeParameterTF
SimulationFileNameBrowseBUT
javax.swing.JButton SimulationFileNameBrowseBUT
SimulationFileNameLbl
javax.swing.JLabel SimulationFileNameLbl
SimulationFileNameTF
javax.swing.JTextField SimulationFileNameTF
SitesToUseCBox
javax.swing.JComboBox SitesToUseCBox
SitesToUseLbl
javax.swing.JLabel SitesToUseLbl
SpecificModelPanel
javax.swing.JPanel SpecificModelPanel
SpecificPropertiesPanel
javax.swing.JPanel SpecificPropertiesPanel
StructureVisualizationBrowseBUT
javax.swing.JButton StructureVisualizationBrowseBUT
StructureVisualizationLbl
javax.swing.JLabel StructureVisualizationLbl
StructureVisualizationTF
javax.swing.JTextField StructureVisualizationTF
StructureVisualizationViewBUT
javax.swing.JButton StructureVisualizationViewBUT
SummaryFileBrowseBUT
javax.swing.JButton SummaryFileBrowseBUT
SummaryFileLbl
javax.swing.JLabel SummaryFileLbl
SummaryFileTF
javax.swing.JTextField SummaryFileTF
SummaryFileViewBUT
javax.swing.JButton SummaryFileViewBUT
TabbedPane
javax.swing.JTabbedPane TabbedPane
ToglButtonsPanel
javax.swing.JPanel ToglButtonsPanel
ToolsMenu
javax.swing.JMenu ToolsMenu
TotalNumberSimulationLbl
javax.swing.JLabel TotalNumberSimulationLbl
TreeFileBrowseBUT
javax.swing.JButton TreeFileBrowseBUT
TreeFileLbl
javax.swing.JLabel TreeFileLbl
TreeFileTF
javax.swing.JTextField TreeFileTF
TreeFileViewBUT
javax.swing.JButton TreeFileViewBUT
UnselectedList
javax.swing.JList UnselectedList
UpperPanel
javax.swing.JPanel UpperPanel
UseAnotherModelBrowseBUT
javax.swing.JButton UseAnotherModelBrowseBUT
UseAnotherModelLbl
javax.swing.JLabel UseAnotherModelLbl
UseAnotherModelTF
javax.swing.JTextField UseAnotherModelTF
UseNDiscGammaCBox
javax.swing.JComboBox UseNDiscGammaCBox
UseNDiscGammaLbl
javax.swing.JLabel UseNDiscGammaLbl
UseNewTreeBUT
javax.swing.JButton UseNewTreeBUT
UseObsFreqCBox
javax.swing.JComboBox UseObsFreqCBox
UseObsFreqLbl
javax.swing.JLabel UseObsFreqLbl
ViewMenu
javax.swing.JMenu ViewMenu
ViewOutputBUT
javax.swing.JButton ViewOutputBUT
ViewR_OutputBUT
javax.swing.JButton ViewR_OutputBUT
ViewWindowMI
javax.swing.JMenuItem ViewWindowMI
jLabel1
javax.swing.JLabel jLabel1
jPanel1
javax.swing.JPanel jPanel1
jPanel2
javax.swing.JPanel jPanel2
jScrollPane1
javax.swing.JScrollPane jScrollPane1
jScrollPane2
javax.swing.JScrollPane jScrollPane2
jSeparator1
javax.swing.JSeparator jSeparator1
jSeparator2
javax.swing.JSeparator jSeparator2
jSeparator3
javax.swing.JSeparator jSeparator3
jSeparator4
javax.swing.JSeparator jSeparator4
jSeparator5
javax.swing.JSeparator jSeparator5
jSeparator6
javax.swing.JSeparator jSeparator6
jSeparator7
javax.swing.JSeparator jSeparator7
jSeparator8
javax.swing.JSeparator jSeparator8
mainMB
javax.swing.JMenuBar mainMB
mainPanel
javax.swing.JPanel mainPanel
progressBar
javax.swing.JProgressBar progressBar
statusMessageLabel
javax.swing.JLabel statusMessageLabel
statusPanel
javax.swing.JPanel statusPanel
util
Utilities util
ciimarTxtLbl
javax.swing.JLabel ciimarTxtLbl
ciimarWebLbl
javax.swing.JLabel ciimarWebLbl
closeBUT
javax.swing.JButton closeBUT
closePanel
javax.swing.JPanel closePanel
developed1ByLbl
javax.swing.JLabel developed1ByLbl
developedByLbl
javax.swing.JLabel developedByLbl
headerDP
javax.swing.JDesktopPane headerDP
infoPanel
javax.swing.JPanel infoPanel
infoSP
javax.swing.JScrollPane infoSP
infoTA
javax.swing.JTextArea infoTA
legeImgLbl
javax.swing.JLabel legeImgLbl
legeTxtLbl
javax.swing.JLabel legeTxtLbl
yearLbl
javax.swing.JLabel yearLbl
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
markUnselSeq
boolean[] markUnselSeq
markUnselSites
boolean[] markUnselSites
treeFileName
java.lang.String treeFileName
treeFilePath
java.lang.String treeFilePath
AlignmentTable
javax.swing.JTable AlignmentTable
AlignmentTableSP
javax.swing.JScrollPane AlignmentTableSP
ChooseLocationCkBox
javax.swing.JCheckBox ChooseLocationCkBox
ChooseLocationPanel
javax.swing.JPanel ChooseLocationPanel
DiscardBUT
javax.swing.JButton DiscardBUT
DiscardMI
javax.swing.JMenuItem DiscardMI
FileMenu
javax.swing.JMenu FileMenu
GUIAEditorMB
javax.swing.JMenuBar GUIAEditorMB
MSAPanel
javax.swing.JPanel MSAPanel
NewTreeBrowseBUT
javax.swing.JButton NewTreeBrowseBUT
NewTreeFileLbl
javax.swing.JLabel NewTreeFileLbl
NewTreeFileTF
javax.swing.JTextField NewTreeFileTF
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
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
SequenceSelecRadioBUT
javax.swing.JRadioButton SequenceSelecRadioBUT
SiteSelecRadioBUT
javax.swing.JRadioButton SiteSelecRadioBUT
ViewOnlySelCkBox
javax.swing.JCheckBox ViewOnlySelCkBox
ViewOutputBUT
javax.swing.JButton ViewOutputBUT
jSeparator1
javax.swing.JSeparator jSeparator1
jSeparator2
javax.swing.JSeparator jSeparator2
jSeparator3
javax.swing.JSeparator jSeparator3
progressBar
javax.swing.JProgressBar progressBar
statusMessageLabel
javax.swing.JLabel statusMessageLabel
statusPanel
javax.swing.JPanel statusPanel
On
boolean On
Off
boolean Off
util
Utilities util
dialog
GUIDialogs dialog
verified
boolean verified
textChanged
boolean textChanged
AAindex1URLLbl
javax.swing.JLabel AAindex1URLLbl
AAindex1URLTF
javax.swing.JTextField AAindex1URLTF
AAindex1VerifyURLBUT
javax.swing.JButton AAindex1VerifyURLBUT
ATVBrowseBUT
javax.swing.JButton ATVBrowseBUT
ATVLbl
javax.swing.JLabel ATVLbl
ATVTF
javax.swing.JTextField ATVTF
AcceptBUT
javax.swing.JButton AcceptBUT
BasePathBrowseBUT
javax.swing.JButton BasePathBrowseBUT
BasePathLbl
javax.swing.JLabel BasePathLbl
BasePathTF
javax.swing.JTextField BasePathTF
CancelBUT
javax.swing.JButton CancelBUT
ConTestExeBrowseBUT
javax.swing.JButton ConTestExeBrowseBUT
ConTestExeLbl
javax.swing.JLabel ConTestExeLbl
ConTestExeTF
javax.swing.JTextField ConTestExeTF
ConTestGUIBrowseBUT
javax.swing.JButton ConTestGUIBrowseBUT
ConTestGUILbl
javax.swing.JLabel ConTestGUILbl
ConTestGUITF
javax.swing.JTextField ConTestGUITF
ConTestPanel
javax.swing.JPanel ConTestPanel
DSConTestBrowseBUT
javax.swing.JButton DSConTestBrowseBUT
DSConTestLbl
javax.swing.JLabel DSConTestLbl
DSConTestTF
javax.swing.JTextField DSConTestTF
DSPhylogBrowseBUT
javax.swing.JButton DSPhylogBrowseBUT
DSPhylogLbl
javax.swing.JLabel DSPhylogLbl
DSPhylogTF
javax.swing.JTextField DSPhylogTF
DSResultsBrowseBUT
javax.swing.JButton DSResultsBrowseBUT
DSResultsLbl
javax.swing.JLabel DSResultsLbl
DSResultsLbl1
javax.swing.JLabel DSResultsLbl1
DSResultsLbl2
javax.swing.JLabel DSResultsLbl2
DSResultsTF
javax.swing.JTextField DSResultsTF
DSSequencesBrowseBUT
javax.swing.JButton DSSequencesBrowseBUT
DSSequencesTF
javax.swing.JTextField DSSequencesTF
DSStructureBrowseBUT
javax.swing.JButton DSStructureBrowseBUT
DSStructureTF
javax.swing.JTextField DSStructureTF
DataSetBasePathBrowseBUT
javax.swing.JButton DataSetBasePathBrowseBUT
DataSetBasePathLbl
javax.swing.JLabel DataSetBasePathLbl
DataSetBasePathTF
javax.swing.JTextField DataSetBasePathTF
DataSetNamePathBrowseBUT
javax.swing.JButton DataSetNamePathBrowseBUT
DataSetNamePathLbl
javax.swing.JLabel DataSetNamePathLbl
DataSetNamePathTF
javax.swing.JTextField DataSetNamePathTF
DataSetsPanel
javax.swing.JPanel DataSetsPanel
ExecutablesPanel
javax.swing.JPanel ExecutablesPanel
ExternProgramsBrowseBUT
javax.swing.JButton ExternProgramsBrowseBUT
ExternProgramsLbl
javax.swing.JLabel ExternProgramsLbl
ExternProgramsTF
javax.swing.JTextField ExternProgramsTF
JMolBrowseBUT
javax.swing.JButton JMolBrowseBUT
JMolExeLbl
javax.swing.JLabel JMolExeLbl
JMolExeTF
javax.swing.JTextField JMolExeTF
OtherExecutablesPanel
javax.swing.JPanel OtherExecutablesPanel
PDFViewerBrowseBUT
javax.swing.JButton PDFViewerBrowseBUT
PDFViewerLbl
javax.swing.JLabel PDFViewerLbl
PDFViewerTF
javax.swing.JTextField PDFViewerTF
PSViewerBrowseBUT
javax.swing.JButton PSViewerBrowseBUT
PSViewerLbl
javax.swing.JLabel PSViewerLbl
PSViewerTF
javax.swing.JTextField PSViewerTF
PhyMLExeBrowseBUT
javax.swing.JButton PhyMLExeBrowseBUT
PhyMLExeLbl
javax.swing.JLabel PhyMLExeLbl
PhyMLExeTF
javax.swing.JTextField PhyMLExeTF
PreferencesTP
javax.swing.JTabbedPane PreferencesTP
RExecutablePathBrowseBUT
javax.swing.JButton RExecutablePathBrowseBUT
RExecutablePathLbl
javax.swing.JLabel RExecutablePathLbl
RExecutablePathTF
javax.swing.JTextField RExecutablePathTF
RMainScriptBrowseBUT
javax.swing.JButton RMainScriptBrowseBUT
RMainScriptLbl
javax.swing.JLabel RMainScriptLbl
RMainScriptTF
javax.swing.JTextField RMainScriptTF
SetDefaultsBUT
javax.swing.JButton SetDefaultsBUT
StatusLbl
javax.swing.JLabel StatusLbl
jPanel1
javax.swing.JPanel jPanel1
jSeparator1
javax.swing.JSeparator jSeparator1
Question0
java.lang.String Question0
Question1
java.lang.String Question1
parentComp
java.awt.Component parentComp
ptitle
java.lang.String ptitle
fileName
java.lang.String fileName
fileDir
java.lang.String fileDir
title
java.lang.String title
FileChooser
javax.swing.JFileChooser FileChooser
On
boolean On
Off
boolean Off
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 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 ToCBox
ToLbl
javax.swing.JLabel ToLbl
jCheckBox1
javax.swing.JCheckBox jCheckBox1
jSeparator1
javax.swing.JSeparator jSeparator1
On
boolean On
Off
boolean Off
max
int max
ncheckpoints
int ncheckpoints
moreDim
java.awt.Dimension moreDim
lessDim
java.awt.Dimension lessDim
timer
javax.swing.Timer timer
ONE_SECOND
int ONE_SECOND
counter
int counter
start
java.awt.Point start
tlcorner
java.awt.Point tlcorner
CloseBUT
javax.swing.JButton CloseBUT
MaxMinimizeToglBut
javax.swing.JToggleButton MaxMinimizeToglBut
MoreToglBut
javax.swing.JToggleButton MoreToglBut
OutputSP
javax.swing.JScrollPane OutputSP
OutputTA
javax.swing.JTextArea OutputTA
TTipToglBut
javax.swing.JToggleButton TTipToglBut
basePanel
javax.swing.JPanel basePanel
iconCT
javax.swing.JLabel iconCT
nameLbl
javax.swing.JLabel nameLbl
outPanel
javax.swing.JPanel outPanel
progressBar
javax.swing.JProgressBar progressBar
statusLbl
javax.swing.JLabel statusLbl
topPanel
javax.swing.JPanel topPanel
On
boolean On
Off
boolean Off
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 DataTypeCbox
DataTypeLbl
javax.swing.JLabel DataTypeLbl
GammaDistrRParamCBox
javax.swing.JComboBox 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 OptimizeBLandRPCBox
OptimizeBLandRPLbl
javax.swing.JLabel OptimizeBLandRPLbl
OptimizeTreeTopolCBox
javax.swing.JComboBox 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 ProportionInvSitesCBox
ProportionInvSitesLbl
javax.swing.JLabel ProportionInvSitesLbl
ProportionInvSitesTF
javax.swing.JTextField ProportionInvSitesTF
SeqFileCBox
javax.swing.JComboBox SeqFileCBox
SequenceFileLbl
javax.swing.JLabel SequenceFileLbl
SubstModelCBox
javax.swing.JComboBox SubstModelCBox
SubstModelLbl
javax.swing.JLabel SubstModelLbl
TransRatioCBox
javax.swing.JComboBox TransRatioCBox
TransRatioLbl
javax.swing.JLabel TransRatioLbl
TransRatioTF
javax.swing.JTextField TransRatioTF
TreeTopolBrowseBUT
javax.swing.JButton TreeTopolBrowseBUT
TreeTopolCbox
javax.swing.JComboBox TreeTopolCbox
TreeTopolLbl
javax.swing.JLabel TreeTopolLbl
TreeTopolTF
javax.swing.JTextField TreeTopolTF
CloseBUT
javax.swing.JButton CloseBUT
ClosePanel
javax.swing.JPanel ClosePanel
OutputSP
javax.swing.JScrollPane OutputSP
OutputTA
javax.swing.JTextArea OutputTA
On
boolean On
Off
boolean Off
title
java.lang.String title
util
Utilities util
rsum
ResultsSummary rsum
guirv
GUIResultsView guirv
msaTable
MSATableModel msaTable
msa_File
java.lang.String msa_File
msa_Format
java.lang.String msa_Format
csv_RFile
java.lang.String csv_RFile
residLoc
java.lang.String residLoc
outputFile
java.lang.String outputFile
colnames
java.lang.String[] colnames
dialog
GUIDialogs dialog
selectedSeq
boolean[] selectedSeq
numTaxa
int numTaxa
AcceptPanel
javax.swing.JPanel AcceptPanel
Add3DBrowseBUT
javax.swing.JButton Add3DBrowseBUT
Add3DCkBox
javax.swing.JCheckBox Add3DCkBox
Add3DTF
javax.swing.JTextField Add3DTF
CancelBUT
javax.swing.JButton CancelBUT
Info3DFormatBUT
javax.swing.JButton Info3DFormatBUT
LeaveWinOpenCkBox
javax.swing.JCheckBox LeaveWinOpenCkBox
LevelcodeCBox
javax.swing.JComboBox LevelcodeCBox
LevelcodeLbl
javax.swing.JLabel LevelcodeLbl
OutputPanel
javax.swing.JPanel OutputPanel
OutputSumFileBrowseBUT
javax.swing.JButton OutputSumFileBrowseBUT
OutputSumFileTF
javax.swing.JTextField OutputSumFileTF
RColumnCBox
javax.swing.JComboBox RColumnCBox
RColumnLbl
javax.swing.JLabel RColumnLbl
RResultsFileBrowseBUT
javax.swing.JButton RResultsFileBrowseBUT
RResultsFileTF
javax.swing.JTextField RResultsFileTF
RResultsPanel
javax.swing.JPanel RResultsPanel
SelectAllBUT
javax.swing.JButton SelectAllBUT
SelectLbl
javax.swing.JLabel SelectLbl
SelectNoneBUT
javax.swing.JButton SelectNoneBUT
StructurePanel
javax.swing.JPanel StructurePanel
TaxaCounterTF
javax.swing.JTextField TaxaCounterTF
TaxaNamesBrowseBUT
javax.swing.JButton TaxaNamesBrowseBUT
TaxaNamesPanel
javax.swing.JPanel TaxaNamesPanel
TaxaNamesSP
javax.swing.JScrollPane TaxaNamesSP
TaxaNamesTF
javax.swing.JTextField TaxaNamesTF
TaxaNamesTable
javax.swing.JTable TaxaNamesTable
ViewSummaryBUT
javax.swing.JButton ViewSummaryBUT
On
boolean On
Off
boolean Off
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
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 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
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
statusMsgLbl
javax.swing.JLabel statusMsgLbl
bkgndColor
java.awt.Color bkgndColor
fgndColor
java.awt.Color fgndColor
selBg
java.awt.Color selBg
selFg
java.awt.Color selFg
columnNames
java.lang.String[] columnNames
data
java.lang.Object[][] data
types
java.lang.Class<T>[] types
canEdit
boolean[] canEdit