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Class Summary |
| AlignmentViewer |
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| AlignmentViewerRowHeader |
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| AnnotationAlignmentRenderer |
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| AnnotationChangeCoalescer |
The AnnotationChangeCoalescer holds all the AnnotationChangeEvents for
the current edit along with a representation of the
feature tree before the edit began. |
| AnnotationChangeLog |
Logs AnnotationChangeEvents which are fired when edits occur. |
| AnnotationEditor |
A class for performing edits on the annotations. |
| ApolloAdapterChooser |
This nullifies choosers output reference, preventing a java1.3.1 ui mem leak
dangling down to the curation set - i think this mem leak is fixed in 1.4
and if so this class can be discarded, cant make inner class cos inner class
keeps ref to outer class |
| ApolloFrame |
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| ApolloMetalScrollBarUI |
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| ApolloRunner |
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| ApolloScrollBar |
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| Arrays |
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| AttributedCharacterIterator |
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| AutoSaveThread |
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| BlankIcon |
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| ChromosomeDrawer |
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| ChromosomeField |
Chromsome field is either a combo box or text field depending on if config
has a chromosome vector |
| ChromosomePanel |
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| CompositeApolloFrame |
The synteny panels need to display many stranded-zoomable-apollo-panels at once,
(unlike the standard apollo frame). |
| Config |
A class with static data members and static methods for setting and
retrieving configuration information for the apollo gui. |
| ControlledPanel |
An extension of JPanel to make automatic Controller window management possible. |
| ControlledWindow |
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| Controller |
An event controller forwarding multiple types of event to registered listeners. |
| ControllerDebugListener |
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| DataLoader |
This class handles loading of data into Apollo. |
| DetailInfo |
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| DetailRange |
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| DisabledEditor |
A TableCellEditor which disables edits in the cells. |
| EvidencePanel |
A panel containing a table of selected result feature sets. |
| EvidenceSelectionSet |
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| FeatureTree |
A tree to hold a representation of the structure of the feature tree. |
| FeatureTreeNode |
A node in the FeatureTree representation of the FeatureSet tree. |
| FeatureTreePanel |
A scrollpane containing a SWING tree of the annotations (not related to the
FeatureTree or FeatureTreeNode). |
| FeatureTreeVector |
Part of the FeatureTree set of classes for creating a representation of the
structure of a FeatureSet tree. |
| FindPanel |
A ControlledPanel which displays the find dialog
(for name, base position and sequence). |
| FullEnsJDBCSyntenyPanel |
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| FullSyntenyPanel |
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| GCScoreCalculator |
changed long positions to int positions to be consistent with rest of apollo
using ints for positions, hope this is ok |
| GenericFileAdapterGUI |
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| LoadUtil |
LoadUtil calls DataLoader to do loading, puts up progress, catches exceptions
and puts up popups, and adds data. |
| MultiController |
An event controller forwarding multiple types of event to registered listeners. |
| NonWindowControlledObject |
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| NumberColumnHeader |
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| PeptideStatus |
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| PlainSequenceRenderer |
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| PreferencesDialog |
A dialog to let the user change the style parameters. |
| PrefsPanel |
PrefsPanel goes inside a PreferencesDialog window |
| ProgressFrame |
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| PropertyPanel |
A panel which renders a single type row in the TypePanel. |
| ProxyDialog |
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| RawResultViewer |
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| ResultAlignmentRenderer |
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| ScoreCalculator |
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| Selection |
Manages a selection of objects(a vector of SelectionItems),
and for SelectableI's controls their selection
state. |
| SelectionItem |
A holder for a selected object, which also records the objects source. |
| SelectionManager |
Controller for selection. |
| SelectionSet |
This is a convienience class for determining and making easily available which sets,
transcripts and genes a group of features come from. |
| SelectionType |
A class holding selection type information - whether the selection was made at
the feature level, the feature set level (eg by clicking on an intron) or some
other way. |
| SeqMatchPanel |
A Panel to display sequence matches from the find panel. |
| SeqSelectorTable |
CallsSeqSelector on separate thread and populates table with
results |
| SequenceSelector |
Searches for and maintains a list of matches of a search sequence in a SequenceI. |
| SequenceTextPanel |
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| SetDetailPanel |
A panel to show a table of the individual features in a single feature set. |
| SliderWindow |
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| StatusBar |
Shows the status bar at the bottom of the main display. |
| StatusPane |
Class defining a status bar (modified from "Beginning Java 2"). |
| Style |
A Style is basically config options for a particular data adapter |
| SwingWorker |
This is the 3rd version of SwingWorker (also known as
SwingWorker 3), an abstract class that you subclass to
perform GUI-related work in a dedicated thread. |
| SwingWorker.ThreadVar |
Class to maintain reference to current worker thread
under separate synchronization control. |
| SyntenyLayout |
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| SyntenyLinkPanel |
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| SyntenyLinkPolygon |
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| SyntenyPanel |
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| TablePanel |
A panel to show a table of the individual features in a single feature set. |
| Tier |
Judging from the methods here a Tier has drawing space, text end(?),
it might have a label, a non modifiable gap space of 1, and char space. |
| TierManager |
The base abstract TierManager class to organise a set of data into several
tiers. |
| Transformer |
A class to perform coordinate transformations between pixel and user coordinates. |
| TreeIcon |
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| TypePanel |
A panel to show and allow edits to FeatureProperties. |
| TypesObserver |
Registers as an observer for a FeatureTierss object
and relays changes in the PropertyScheme
to TypesChangedListeners registered with a particular controller. |
| URLQueryGenerator |
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| WindowScoreCalculator |
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