Overview
Package
Class
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Help
'STRAP:
multiple sequence alignments
'
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All Classes
Hierarchy For Package charite.christo.strap
Package Hierarchies:
All Packages
Class Hierarchy
java.lang.Object
charite.christo.strap.
AbstractAlignAndCompare
(implements charite.christo.
Disposable
, charite.christo.
HasControlPanel
, charite.christo.
HasModiCount
, charite.christo.
HasSharedControlPanel
, charite.christo.strap.
ProteinProteinValue
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
AbstractAligner
(implements charite.christo.
CanBeStopped
, charite.christo.
Disposable
, charite.christo.
HasControlPanel
, charite.christo.
HasNativeExec
, charite.christo.
HasPropertyMap
, charite.christo.
IsEnabled
)
charite.christo.strap.
AbstractAlignmentProject.Alignment
(implements java.awt.event.ActionListener)
javax.swing.border.AbstractBorder (implements javax.swing.border.Border, java.io.Serializable)
charite.christo.
ChRenderer
(implements javax.swing.ListCellRenderer, charite.christo.
PaintHook
, charite.christo.
ProcessEv
, javax.swing.table.TableCellEditor, javax.swing.table.TableCellRenderer, javax.swing.tree.TreeCellRenderer)
charite.christo.strap.
StrapDAS
(implements charite.christo.
ChRunnable
, charite.christo.
ProcessEv
)
javax.swing.AbstractListModel (implements javax.swing.ListModel, java.io.Serializable)
javax.swing.DefaultComboBoxModel (implements javax.swing.MutableComboBoxModel, java.io.Serializable)
charite.christo.strap.
ComboKeys
charite.christo.strap.
V3dListModel
charite.christo.
AbstractProxy
(implements charite.christo.
HasPropertyMap
)
charite.christo.strap.
AbstractAlignerProxy
javax.swing.table.AbstractTableModel (implements java.io.Serializable, javax.swing.table.TableModel)
javax.swing.table.DefaultTableModel (implements java.io.Serializable)
charite.christo.strap.
DialogAlignOneToAllResult
(implements charite.christo.
Disposable
, charite.christo.
ProcessEv
, java.lang.Runnable)
charite.christo.strap.
EditDnaTable
(implements java.awt.event.ActionListener, charite.christo.protein.
StrapListener
)
charite.christo.strap.
ResidueAnnotationView
(implements charite.christo.
ChRunnable
, charite.christo.
Disposable
, charite.christo.
HasPanel
, javax.swing.ListCellRenderer, charite.christo.
ProcessEv
, charite.christo.protein.
StrapListener
, javax.swing.table.TableCellEditor, javax.swing.table.TableCellRenderer)
charite.christo.strap.
SequenceFeatures
(implements charite.christo.
ChRunnable
, java.util.Comparator<T>, charite.christo.
ProcessEv
, charite.christo.
TooltipProvider
)
charite.christo.protein.
AbstractVisibleIn123
(implements charite.christo.
HasImage
, charite.christo.
HasPropertyMap
, charite.christo.
HasWeakRef
, charite.christo.protein.
VisibleIn123
)
charite.christo.protein.
BasicResidueSelection
(implements charite.christo.
HasName
, charite.christo.
HasRenderer
, charite.christo.protein.
ResidueSelection
)
charite.christo.strap.
Distance3DToCursor
(implements javax.swing.event.ChangeListener, charite.christo.
HasImage
, charite.christo.
HasSharedControlPanel
, charite.christo.
IsEnabled
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
AcceptAlignment2
charite.christo.strap.
Aligner3D
(implements java.awt.event.ActionListener, charite.christo.
CanBeStopped
, charite.christo.
HasControlPanel
, charite.christo.
HasSharedControlPanel
, charite.christo.protein.
NeedsProteins
, charite.christo.protein.
SequenceAlignerSorting
)
com.apple.eawt.ApplicationAdapter (implements com.apple.eawt.ApplicationListener)
charite.christo.strap.
StrapMacApplicationListener
java.awt.Component (implements java.awt.image.ImageObserver, java.awt.MenuContainer, java.io.Serializable)
java.awt.Container
javax.swing.JComponent (implements java.io.Serializable)
javax.swing.Box (implements javax.accessibility.Accessible)
charite.christo.strap.
TexshadeGraph
(implements java.awt.event.ActionListener, charite.christo.
IsEnabled
)
charite.christo.strap.
DialogResidueAnnotationList
(implements charite.christo.
ProcessEv
)
javax.swing.JComboBox (implements javax.accessibility.Accessible, java.awt.event.ActionListener, java.awt.ItemSelectable, javax.swing.event.ListDataListener)
charite.christo.
ChCombo
(implements charite.christo.
HasModiCount
, charite.christo.
IsEnabled
, charite.christo.
ProcessEv
, java.lang.Runnable)
charite.christo.strap.
ProteinCombo
(implements charite.christo.protein.
HasProtein
)
javax.swing.JList (implements javax.accessibility.Accessible, javax.swing.Scrollable)
charite.christo.
ChJList
(implements charite.christo.
HasModiCount
, charite.christo.
IsEnabled
, charite.christo.
ProcessEv
)
charite.christo.strap.
ProteinList
javax.swing.JPanel (implements javax.accessibility.Accessible)
charite.christo.strap.
AddAnnotation
(implements java.awt.event.ActionListener, javax.swing.ListCellRenderer)
charite.christo.
ChPanel
(implements javax.swing.Scrollable)
charite.christo.strap.
AbstractDialogJPanel
(implements charite.christo.
Disposable
)
charite.christo.strap.
AbstractAlignmentProject
(implements java.awt.event.ActionListener)
charite.christo.strap.
Dialog3DViewer
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogBarChart
(implements java.awt.event.ActionListener, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogCopyAnnotations
(implements java.lang.Runnable)
charite.christo.strap.
DialogDotPlot
(implements charite.christo.
Disposable
, charite.christo.
HasControlPanel
, charite.christo.
PaintHook
, charite.christo.
ProcessEv
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogExportProteins
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogHighlightPattern
(implements java.awt.event.ActionListener, charite.christo.
Disposable
, java.lang.Runnable, charite.christo.protein.
StrapListener
, javax.swing.table.TableModel)
charite.christo.strap.
DialogInferCDS
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogNeighborsResult
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogNewProtein
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogPhylogeneticTree
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
)
charite.christo.strap.
DialogProteinList
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogPublishAlignment
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogResidueAnnotationChanges
(implements charite.christo.
ProcessEv
, java.lang.Runnable, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogRestoreFromBackup
(implements java.awt.event.ActionListener, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogSelectionOfResidues
(implements java.awt.event.ActionListener, charite.christo.
IsEnabled
)
charite.christo.strap.
DialogSortProteins
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
)
charite.christo.strap.
EditDna
(implements java.awt.event.ActionListener)
charite.christo.strap.
FilesFetchedFromServer
(implements charite.christo.
ChRunnable
, charite.christo.
ProcessEv
)
charite.christo.strap.
ActivateDeactivate
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogAlignResult
(implements charite.christo.
Disposable
, charite.christo.
PaintHook
, charite.christo.
ProcessEv
, java.lang.Runnable)
charite.christo.strap.
DialogSimilarStructureResult
(implements java.awt.event.ActionListener, charite.christo.
Disposable
)
charite.christo.strap.
DialogDotPlot_Sequence
(implements java.awt.event.ActionListener, java.lang.Runnable)
charite.christo.strap.
DialogSuperimpose3DResult
(implements java.awt.event.ActionListener, charite.christo.
Disposable
, charite.christo.
PaintHook
, java.lang.Runnable, charite.christo.protein.
StrapListener
)
charite.christo.strap.
IntermediateSeqPair
(implements java.awt.event.ActionListener, charite.christo.
Disposable
, charite.christo.
HasControlPanel
, java.awt.event.MouseWheelListener, charite.christo.
PaintHook
, charite.christo.
PreferredSize
, java.lang.Runnable)
javax.swing.JScrollBar (implements javax.accessibility.Accessible, java.awt.Adjustable)
charite.christo.
ChScrollBar
charite.christo.strap.
HScrollBar
javax.swing.JTabbedPane (implements javax.accessibility.Accessible, java.io.Serializable, javax.swing.SwingConstants)
charite.christo.strap.
AbstractDialogJTabbedPane
(implements charite.christo.
Disposable
)
charite.christo.strap.
AbstractDialogPredict
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogPredictCoiledCoil
charite.christo.strap.
DialogPredictSecondaryStructures
charite.christo.strap.
DialogPredictTmHelices2
charite.christo.strap.
DialogPredictTmHelicesMulti
(implements charite.christo.protein.
StrapListener
)
charite.christo.strap.
Dialog_bl2seq
(implements java.lang.Runnable)
charite.christo.strap.
DialogAlign
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogAlignOneToAll
(implements java.awt.event.ActionListener, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogBlast
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
)
charite.christo.strap.
DialogCompareProteins
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogDifferentResidues
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogExportAlignment
(implements java.lang.Runnable)
charite.christo.strap.
DialogExportWord
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogFetchPdb
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogFetchSRS
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogGenbank
(implements java.awt.event.ActionListener, charite.christo.protein.
NeedsProteins
, java.lang.Runnable)
charite.christo.strap.
DialogImportMFA
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogNeighbors
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogNonRedundantSequenceSet
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogPlot
(implements java.awt.event.ActionListener, charite.christo.
HasModiCount
, charite.christo.
IsEnabled
, charite.christo.protein.
ResidueSelection
, charite.christo.protein.
StrapListener
, charite.christo.strap.
ValueOfAlignPosition
, charite.christo.protein.
ValueOfResidue
, charite.christo.protein.
VisibleIn123
)
charite.christo.strap.
DialogSelectionOfResiduesMain
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogSimilarStructure
(implements java.awt.event.ActionListener, java.lang.Runnable, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogSubcellularLocalization
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
DialogSuperimpose3D
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
)
charite.christo.strap.
IntermediateSeq
(implements charite.christo.
ChRunnable
, charite.christo.
Disposable
, charite.christo.
HasControlPanel
, charite.christo.
ProcessEv
, charite.christo.protein.
StrapListener
)
charite.christo.strap.
Texshade
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.
Disposable
, charite.christo.protein.
NeedsProteins
, charite.christo.protein.
StrapListener
)
javax.swing.JTree (implements javax.accessibility.Accessible, javax.swing.Scrollable)
charite.christo.
ChJTree
(implements charite.christo.
HasWeakRef
)
charite.christo.strap.
StrapTree
(implements charite.christo.
ChRunnable
, charite.christo.
ProcessEv
)
charite.christo.strap.
ContextObjects
charite.christo.strap.
CsaWeb
charite.christo.strap.
DialogManyInOneRow
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogPredictTexshade
(implements java.awt.event.ActionListener)
charite.christo.strap.
DialogRenameProteins
(implements java.awt.event.ActionListener, java.lang.Runnable)
charite.christo.strap.
DnaExonStart
charite.christo.strap.
DrawGappedSequence
charite.christo.strap.
ExpasyGff
charite.christo.strap.
Export2Jalview
charite.christo.strap.
ExportAlignment
(implements charite.christo.strap.
AlignmentWriter
, java.util.Comparator<T>)
charite.christo.strap.
HeteroPopup
(implements java.awt.event.ActionListener, charite.christo.
IsEnabled
)
charite.christo.strap.
NextAndPrevSelection
charite.christo.strap.
ProteinComboModel
(implements javax.swing.ComboBoxModel, charite.christo.
HasModiCount
)
charite.christo.strap.
ProteinPopup
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.
IsEnabled
)
charite.christo.strap.
ProteinViewerPopup
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.
IsEnabled
)
charite.christo.strap.
ResidueAnnotation
(implements charite.christo.
ChRunnable
, charite.christo.
Colored
, charite.christo.
Disposable
, charite.christo.
HasImage
, charite.christo.
HasModiCount
, charite.christo.
HasName
, charite.christo.
HasPropertyMap
, charite.christo.
HasRendererModiCount
, charite.christo.
HasWeakRef
, charite.christo.protein.
ResidueSelection
, charite.christo.protein.
SelectorOfNucleotides
, charite.christo.protein.
VisibleIn123
)
charite.christo.strap.
ResidueAnnotation.Entry
(implements charite.christo.
ChRunnable
, charite.christo.
HasRenderer
)
charite.christo.strap.
ResidueSelectionPopup
(implements java.awt.event.ActionListener, charite.christo.
IsEnabled
)
charite.christo.strap.
ResSelUtils
(implements charite.christo.
ChRunnable
, java.util.Comparator<T>)
charite.christo.strap.
SPUtils
(implements charite.christo.
ChRunnable
, java.util.Comparator<T>)
charite.christo.strap.
Strap
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
)
charite.christo.strap.
StrapAlign
(implements charite.christo.
ChRunnable
, java.awt.dnd.DropTargetListener, charite.christo.
ProcessEv
, charite.christo.protein.
ProteinAlignment
)
charite.christo.strap.
StrapHotswap
(implements charite.christo.
ChRunnable
, charite.christo.
HasPanel
, charite.christo.
PaintHook
, charite.christo.
ProcessEv
)
charite.christo.strap.
StrapKeyStroke
charite.christo.strap.
StrapPlugin
(implements charite.christo.
HasRenderer
)
charite.christo.strap.
StrapPlugins
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
)
charite.christo.strap.
StrapScriptInterpreter
(implements charite.christo.
ChRunnable
)
charite.christo.strap.
StrapUtils
charite.christo.strap.
StrapView
(implements java.awt.event.ActionListener, charite.christo.
ChRunnable
, charite.christo.
Disposable
, charite.christo.
PaintHook
, charite.christo.
PreferredSize
, charite.christo.
ProcessEv
, charite.christo.protein.
StrapListener
, charite.christo.
TooltipProvider
)
charite.christo.strap.
Tutorials
(implements charite.christo.
ChRunnable
, charite.christo.
ProcessEv
)
charite.christo.strap.
V3dUtils
(implements charite.christo.
ChRunnable
, charite.christo.
PaintHook
, charite.christo.
ProcessEv
, charite.christo.
TooltipProvider
)
Interface Hierarchy
charite.christo.strap.
AlignmentWriter
charite.christo.
HasModiCount
charite.christo.strap.
ProteinProteinValue
(also extends charite.christo.protein.
ValueOfProtein
)
charite.christo.strap.
ProteinProteinDistance
charite.christo.strap.
ProteinProteinSimilarity
charite.christo.strap.
ValueOfAlignPosition
charite.christo.protein.
ValueOfProtein
(also extends charite.christo.protein.
HasProtein
)
charite.christo.strap.
ProteinProteinValue
(also extends charite.christo.
HasModiCount
)
charite.christo.strap.
ProteinProteinDistance
charite.christo.strap.
ProteinProteinSimilarity
charite.christo.protein.
HasProtein
charite.christo.protein.
ValueOfProtein
(also extends charite.christo.
HasModiCount
)
charite.christo.strap.
ProteinProteinValue
(also extends charite.christo.
HasModiCount
)
charite.christo.strap.
ProteinProteinDistance
charite.christo.strap.
ProteinProteinSimilarity
charite.christo.strap.
ProteinsSorter
charite.christo.protein.
StrapListener
charite.christo.strap.
StrapExtension
Overview
Package
Class
Tree
Deprecated
Index
Help
'STRAP:
multiple sequence alignments
'
PREV
NEXT
FRAMES
NO FRAMES
All Classes
'The most important classes are StrapAlign, Protein and StrapEvent.'