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•	apollo.analysis.* (17)	•	apollo.dataadapter.* (153)	•	apollo.datamodel.* (48)	•	apollo.gui.* (229)
•	apollo.io.* (1)	•	apollo.seq.* (4)	•	apollo.test.* (4)	•	apollo.util.* (17)

Package Samples:

• apollo.dataadapter.das.simple: Defines the interfaces to support the reading of DAS datasources by Apollo.  
• apollo.datamodel
• apollo.seq
• apollo.seq.io
• apollo.gui
• apollo.test
• apollo.util
• apollo.dataadapter
• apollo.dataadapter.otter.parser
• apollo.dataadapter.otter
• apollo.dataadapter.das
• apollo.dataadapter.mysql
• apollo.dataadapter.genbank
• apollo.dataadapter.ensj
• apollo.dataadapter.debug
• apollo.dataadapter.synteny
• apollo.dataadapter.gbrowse
• apollo.dataadapter.organism
• apollo.analysis
• apollo.gui.event

Classes:

• AnnotationEditor: A class for performing edits on the annotations. How to use the editor: Using the AnnotationEditor is a two step process: 1. call setSelections with the current selections. 2. call the method for the edit you want. How it works: setSelections creates a group of SelectionSets. These contain the data selected by the Selection and the data selected under the cursor. Some processing is done on the basic selected features to allow easy access to the true (non Drawable) features, the Transcripts, and the Genes in the selection. The data selected by the Selection is also divided into subsets containing ...
• AnnotationChangeCoalescer: The AnnotationChangeCoalescer holds all the AnnotationChangeEvents for the current edit along with a representation of the feature tree before the edit began. NOTE: THIS CLASS IS NOT FULLY IMPLEMENTED. As edits are added to the AnnotationChangeCoalescer it checks to see if they can be coalesced - for example if you delete all the exons in a transcript and then delete the transcript the edit can be coalesced into a delete transcript - all the delete exon AnnotationChangeEvents can be removed from the changes vector. A new AnnotationChangeCoalescer should be created at the start of each edit in the ...
• SelectionManager: Controller for selection. This is only partially implemented at this point. The idea would be that this would be the controller for selection, replacing Controller for just selection (not everything else it controls. SelectionManager deals with selection and deselection where Controller only passes along selects and does not deal with deselecting when new selects come in. When SelectionManager gets a new select it does the appropriate deselecting to accompnay this. note from cvs notes that i thought would be clariflying to put here: Fixed slowness of selection in the views. When i changed selection ...
• ScrollableTierView: This class is the base class for FeatureView and SequenceView. It is abstract because it doesn't implement getTierData() and would be non functional even if it did because it doesn't create the stacker object anywhere. The reason it has been separated from FeatureView is to enable the use of the Scrolling and Tier functionality in the SequenceView, which although different to the FeatureView is basically a TierView where each tier is a piece of the sequence, so we can use the Tier and Scroll functionality and just change the meaning of tiers by creating a new TierManager and changing all the draw ...
• MouseButtonEvent: Static methods for determining whether certain mouse button events have taken place. This class hides the messiness of checking mouse events on Mac, where the swing utilities are buggy. On a ONE-button Mac: - ctrl-click and option(alt)-click both answer true to isMiddleButton. I interpret this as a RIGHT mouse event (pop up menu). - apple(cloverleaf)-click answers true to isRightButton. I interpret this as a MIDDLE mouse event (center the display). On a FIVE-button Mac: - The right of the middle three buttons answers false to isRightButton and true to isMiddleButton. I interpret this as a RIGHT ...
• Config: A class with static data members and static methods for setting and retrieving configuration information for the apollo gui. from apollo.ebi email: createStyle(...) is used to create a new style that is coming in from the apollo.cfg DataAdapterInstall line as you've probably seen: DataAdapterInstall "apollo.dataadapter.EnsCGIAdapter" "ensembl.style" Config sees this line and installs a new Style whose settings are in ensembl.style and will get associated with the EnsCGIAdapter. This will NOT then become the present style. apollo.cfg can specify many DataAdapters with styles, and styles can be shared. ...
• AbstractApolloAdapter: All the dataadapters now subclass AbstractApolloAdapter, which new data adapters should do as well. In AbstractApolloAdapter.getCurationSet() apollo.gui.Config.newDataAdapter(this) is called. This sets up the new style before the data loads. So all the subclasses have to call super.getCurationSet() at the start of their getCurationSet() method. A data adapter has to subclass AbstactApolloAdapter and call super.getCurationSet(). (AAA.getCS() also clears out all the old data that is still lingering). I know this is a bit of an awkward requirement and is easy to miss on coding a new data adapter. ...
• SimpleDASServer: I am a lightweight implementation of a DAS Server which doesn't use external code (apart from a general SAX-parser). I perform client-side assembly of all nested features from a das 'features' call, as well as ensuring that the features are presented in the highest-level (entry-point) coordinate system (typically this are chromosome coords). I should be instantiated with the URL of the datasource, for example http://servlet.sanger.ac.uk:8080/das http://genome.cse.ucsc.edu/cgi-bin/das Calls to me after I've been instantiated are stateless - typically you call getDSNs to isolate a single DSN to study, ...
• FeatureSet: what is a FeatureSet - does it have biological meaning it seems to have biological methods - is it a scandal to use a FeatureSet to hold a bunch of graphical features - meaning like a set of features held together because they are all visible and on the same row - not necasarily having the whole gene as a normal FeatureSet might - should there be a superclass and subclass - FeatureSet, GeneFeatureSet? Yes! FeatureSet should just be an object that holds Features, GeneFeatureSet should subclass that and adds all the gene functions (eg setTranslationStart, setTranslationEnd...) I'm a little scared ...
• CompositeApolloFrame: The synteny panels need to display many stranded-zoomable-apollo-panels at once, (unlike the standard apollo frame). However apollo's menus are very aware of apollo frames...this subclass is an attempt to circumvent these issues without having to rewrite lots of the apollo menu-handling code to support synteny viewing. The idea is: to hold many copies of the instance variables that an Apollo frame usually holds (one for each browsed species). When the user their switches between different species, each copy of these instance variables is, in turn, switched over to the set specific to that species. ...
• DASFeatureContentHandler: I am the ContentHandler used when SimpleDASServer parses the result of a 'features' call to a das data source (with a specified dsn and segment). I am DAS 1.0 compliant. During the parse, I create a list, stored on myself, of the returned features. This list is retrieved by calling getFeaturess after the parse is complete If any of the features retrieved during my run contain subparts or are reference features (have children), then I store them away. When I am done with my parse, I re-invoke the SimpleDASServer with another getFeatures call, passing in all the segments that have children. which ...
• SequenceSelector: Searches for and maintains a list of matches of a search sequence in a SequenceI. The class handles reverse complement by reverse complementing the search sequence so that the whole SequenceI object sequence does not have to be reverse complemented - that could use a lot of memory. Coordinate conversions are done within the class to generate correct coordinates. The matches to the search SequenceI are generated when the object is created. They can be accessed one at a time using the getNextAsSeqFeature() and getNextAsLong(). areMoreMatches() indicates if there are more matches to get. moveToSeqPosition() ...
• SiteCodon: SiteCodon is a class to accomodate the optimizations in SiteView and Sites. SiteView no longer uses DrawableTerminalCodon to do its drawing. But it needs to send DrawwableSeqFeatures for the findDrawablesAt method. And it needs to be aware of the selection of the DrwableSeqFeatures that it sends out but does not draw. SiteCodon is a DrawableSeqFeature used by Sites that never gets drawn but notifies its Sites object of any selections it receives. This class will also probably be needed to deal with dragging which is currently not implemented with the SiteView optimizations. I didnt call it DrawableSiteCodon ...
• CompositeDataSourceConfigurationPanel: This is a panel which composes a number of the standard DataSourceConfiguration panels - one for the results, one for variations, one for sequences. The point is to allow the user to gracefully enter configuration for all of these different databases. Which database the user is configuring is determined by a drop-down at the top of the panel, which determines which one of the set of configuration panels is visible. The set/getProperties reads the properties of ALL the panels, prefacing the properties of all except the "default" panel with a string, like "sequence:" or "default:". This should allow ...
• EnsJAdapterGUI: Configuration GUI for the EnsJAdapter class. It enables the user to specify: a region of a chromosome to retrieve data, or a clone fragment (contig accesion/stable ID). Ensj-driver settings. Where to get data from. Logging configuration for ensj-core. This class interacts with the Apollo history framework by getting and setting various history parameters. Usage: the user should add the line DataAdapterInstall "apollo.dataadapter.ensj.EnsJAdapter" to her apollo.cfg file. The Adaptor and this GUI will then be made available from the initial apollo screen. Originally based on EnsCGIAdaptorGUI.
• ExampleFileFilter: A convenience implementation of FileFilter that filters out all files except for those type extensions that it knows about. Extensions are of the type ".foo", which is typically found on Windows and Unix boxes, but not on Macinthosh. Case is ignored. Example - create a new filter that filerts out all files but gif and jpg image files: JFileChooser chooser = new JFileChooser(); ExampleFileFilter filter = new ExampleFileFilter( new String{"gif", "jpg"}, "JPEG & GIF Images") chooser.addChoosableFileFilter(filter); chooser.showOpenDialog(this);
• DrawableFeatureSet: A drawable for drawing a feature set. It implements FeatureSetI. While this can be convenient, it is also inconvienient because it blurs model and view. When you have a FeatureSetI, you dont know if its in fact a DrawableFeatureSet or a FeatureSet from the datamodel. One has to do instanceof's to figure this out. My suggestion would be to remove DrawableFeatureSet implementing FeatureSetI to have a cleaner split between model and view. Other opinions? It can still retain all the wrapped functions if thats handy, it just wouldnt parade as a FeatureSetI any longer.
• CurationSet: I am the central holder of renderable data - results, annotations etc. I am a composite - I can contain instances of myself. In this case, these "child" curation sets can be retrieved by name. This is the way that the species-specific (and compara-) curation sets are passed around for the Synteny case. In the case that I have no children, my get... methods will act on the (only) Results, Annotations etc that I have. If I _do_ have children, then the get... methods will blow up when invoked.
• SeqFeature: A class to represent a basic sequence feature, such as a result span. This is also the base class for the FeatureSet and FeaturePair classes: FeatureSet should NOT subclass SeqFeature. SeqFeature should have methods hasChildren() and FeatureSet getChildren() - HASA not ISA essentially.
• FlexibleFeatureTierManager: A FeatureTierManager which arranges its tiers in the expanded way (no overlapping featuresets). It may seem odd that this class extends CollapsedFeatureTierManager, but the tiers are in basically the same arrangement (tiers ordered by type), it is just that in the expanded view overlaps are not allowed whereas in the collapsed view they are. CollapsedFeatureTierManager actually does the sorting of the DrawableSeqFeatures within the tiers.
• SimpleDASAdapterGUI: I implement a AbstractDataAdapterUI , allowing Apollo to get information from DAS datasources, using 'simple' implementions of DASServerI , DASDsn etc. My whole reason-for-being is to have a das-reading adapter which doesn't rely on a big external codebase (e.g. omnigene or biojava): I create implementations of DASServerI, DASSegment etc which are 'simple' - SimpleDASServerI etc.
• ReadWriteField: Field that is a JLabel if ReadOnly, if not ReadOnly is an editable component. Convenience class to deal with the 2 cases of ReadOnly and editable. Editable component is either a JComboBox or a JTextField. This was an inner class of FeatureEditorDialog, but it turns out TranscriptEditPanel needs to use it as well. Maybe it should go in util? There should probably be a a separate package apollo.gui.dialog or something like that
• NamedFeatureSelectionEvent: I am fired when the system needs to select a feature by name (e.g. gene stable id) instead of by SeqFeature. The notion is that the name is all you have - the actual object will be found when the even is handled. I was created to ease transmission of selection events (which in the end select genes and exons) between the SyntenyLinkPanel and the two Apollo panels which the link panel knows about.
• SelectionItem: A holder for a selected object, which also records the objects source. At the moment all selection is of SeqFeatureI's, so making the data variable an an Object seems unnecasarily generic. Ive changed it to SeqFeatureI. In the future if we need to select more than just SeqFeatureI's we can change this to Object, or some interface that encompasses selection objects. But for now its nice to have it as a SeqFeatureI

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