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AliView-master
src
main
java
aliview
AliView.java
AliViewExtraNexusUtilities.java
AliViewWindow.java
AminoAcid.java
Base.java
BrowserUtils.java
EmptyUndoControler.java
GeneticCode.java
HelpUtils.java
LimitedStack.java
LoggingOutputStream.java
MemoryUtils.java
NucleotideUtilities.java
PrintUtils.java
UndoControler.java
UndoList.java
aligner
AliItemPanel.java
AlignemtItem.java
Aligner.java
AlignerADDItemsFrame.java
AlignerADDItemsPanel.java
AlignerALLItemsFrame.java
AlignerALLItemsPanel.java
MuscleWrapper.java
alignment
AAHistogram.java
AliHistogram.java
Alignment.java
AlignmentEvent.java
AlignmentFile.java
AlignmentListener.java
AlignmentMeta.java
NotUsed_AASequenceTranslator.java
NotUsed_AATranslator.java
NucleotideHistogram.java
color
AACompColorThreshold.java
ClustalXColorScheme.java
ColorScheme.java
ColorSchemeFactory.java
ColorThreshold.java
ColorUtils.java
DefaultColorScheme.java
DefaultColorSchemeFast.java
SeaViewColorScheme.java
exporter
ImageExporter.java
externalcommands
CmdItemPanel.java
CmdItemsPanel.java
CommandItem.java
ExternalCommandExecutor.java
gui
AliToolBar.java
AliViewJMenuBar.java
AliViewJMenuBarFactory.java
AlignmentPopupMenu.java
AppIcons.java
GlassPaneKeyListener.java
GlassPaneMouseListener.java
ListTopOffsetJPanel.java
MessageLogFrame.java
NoneSelectedButtonGroup.java
RepeatingKeyEventsFixer.java
ScrollBarModelSyncChangeListener.java
ScrollPaneSyncKeyAndMouseWheelListener.java
SearchPanel.java
StatusPanel.java
TextEditDialog.java
TextEditFrame.java
TextEditPanel.java
TextEditPanelCharsets.java
TranslationToolPanel.java
pane
AACharPixelsContainer.java
AlignmentPane.java
CharPixels.java
CharPixelsBothNucAndAA.java
CharPixelsContainer.java
CompoundCharPixelsContainer.java
ImageUtils.java
InvalidAlignmentPositionException.java
NotUsed_AlignmentPane_Orig.java
RGBArray.java
SequencePainter.java
SequencePainterAminoAcid.java
SequencePainterAminoAcidTranslated.java
SequencePainterAminoAcidTranslatedIgnoreGap.java
SequencePainterNucleotide.java
SequencePainterNucleotideTranslatedShowNucAndAcid.java
TranslationCharPixelsContainer.java
TranslationCharPixelsContainerShowBoth.java
importer
AlignmentFactory.java
AlignmentImportException.java
ByteBufferAutogrow.java
ClustalFileIndexer.java
ClustalImporter.java
FastFastaImporter.java
FastFastaImporterSlow.java
FastNexusImporterSlow.java
FastaFileIndexer.java
FileFormat.java
FileImportUtils.java
FileIndexer.java
MSFFileIndexer.java
MSFImporter.java
MappedBuffReaderHelper.java
NexusFileIndexer.java
NotUsed_IndexFileReader.java
PhylipFileIndexer.java
PhylipImporter.java
ReaderHelper.java
SequencesFactory.java
messenges
JOptionPaneWithCheckbox.java
Messenger.java
TipPanel.java
not_used
hacks
FilePreferences.java
FilePreferencesFactory.java
old
AlignerItemPanel.java
CommandItemPanel.java
ExternalCmdFrame.java
InfoLabel.java
MyChangeListener2.java
MyScrollPane.java
phenotype2genotype
Image2AscII.java
Phenotype2Genootype.java
primer
ComponentCellRenderer.java
Dimer.java
OligoCalc.java
Primer.java
PrimerDetailFrame.java
PrimerDisplay.java
PrimerPanel.java
PrimerPanelCellRenderer.java
PrimerResultTableRow.java
PrimerResultsFrame.java
PrimerResultsPopup.java
sequencelist
AlignmentDataEvent.java
AlignmentDataListener.java
AlignmentListModel.java
AlignmentSelectionEvent.java
AlignmentSelectionListener.java
AlignmentSelectionModel.java
FasterTextCellRenderer.java
FilePage.java
FileSequenceAlignmentListModel.java
FileSequenceLoadListener.java
FindObject.java
Interval.java
MemoryMappedSequencesFile.java
MemorySequenceAlignmentListModel.java
MyDropTarget.java
MyOtherDropTarget.java
NotUsedRubberBandListener.java
NotUsedSequenceListMouseListener2.java
NotUsedSequenceListSelectionListener.java
NotUsedTextCellRenderer.java
NotUsed_AlignmentDataAndSelectionListener.java
SequenceJList.java
SequenceListMouseListener.java
SequenceListMouseWheelListener.java
SequenceListSelectionModel.java
SequencePositionComparator.java
SequenceTransferHandler.java
sequenceold
OldFileSequenceList.java
sequences
AminoAcidAndPosition.java
Bases.java
BasicSequence.java
ClustalFileSequence.java
ClustalSequence.java
ConvertedJEBLSequence.java
DefaultBases.java
DefaultSequenceSelectionModel.java
EditableSequence.java
EmptySelectionModel.java
FastFastaSequence.java
FastaFileSequence.java
FileSequence.java
FileSequenceBases.java
InMemorySequence.java
MSFFileSequence.java
MSFSequence.java
NexusFileSequence.java
NexusSequence.java
PhylipFileSequence.java
PhylipSequence.java
PositionToPointer.java
PositionsToPointer.java
PositionsToPointerFileSequence.java
PositionsToPointerFileSequenceBases.java
Sequence.java
SequenceSelectionModel.java
SequenceUtils.java
TranslatedBases.java
settings
GeneralSettingsPanel.java
MemorySettingsPanel.java
PrimerSettingsPanel.java
RegexInputVerifier.java
SettingValue.java
Settings.java
SettingsFrame.java
SettingsListener.java
ViewSettingsPanel.java
subprocesses
SubProcessWindow.java
SubThreadProgressWindow.java
test
CreateColorChooserDialog.java
DragDropList.java
DropDemo.java
FastFastaFileTest.java
ListModelExample.java
PanelLayouts.java
RegexTest.java
RubberBandingListener.java
ScrollBarSynchronizer.java
Test.java
panel.java
undo
UndoSavedState.java
UndoSavedStateEditedSequences.java
UndoSavedStateEverything.java
UndoSavedStateMetaOnly.java
UndoSavedStateSequenceOrder.java
UndoableEverything.java
UndoableReorder.java
utils
ArrayUtilities.java
FileDrop.java
NotUsedReorderListener.java
Utils.java
it
unimi
dsi
fastutil
Arrays.java
Hash.java
Swapper.java
booleans
BooleanArrays.java
BooleanComparator.java
ints
IntComparator.java
io
MeasurableInputStream.java
MeasurableOutputStream.java
MeasurableStream.java
RepositionableStream.java
io
ByteBufferInpStream.java
org
bitbucket
kienerj
io
OptimizedRandomAccessFile.java
simplericity
macify
eawt
Application.java
ApplicationAdapter.java
ApplicationEvent.java
ApplicationListener.java
DefaultApplication.java
utils
DialogUtils.java
FileUtilities.java
ListUtils.java
MacAdapter.java
MyStringUtils.java
MyUtils.java
OSNativeUtils.java
RangeUtils.java
StringParser.java
Utilities.java
WebUtilities.java
nexus
CharSet.java
CharSets.java
CodonPos.java
CodonPositions.java
CodonRange.java
CodonRanges.java
Excludes.java
NexusAlignmentImportException.java
NexusBoolArray.java
NexusParser.java
NexusRange.java
NexusRangesTranslator.java
NexusUtilities.java
Not_used_PositionsArray.java
Range.java
Ranges.java
TaxSet.java
TranslatedAminoAcidPositions.java
test
java
aliview
AlignmentTest.java
settings
SettingsTest.java
package aliview.importer; public interface FileIndexer { }