org::gel::mauve::gui::sequence::FeaturePanel Class Reference

Inheritance diagram for org::gel::mauve::gui::sequence::FeaturePanel:

[legend]Collaboration diagram for org::gel::mauve::gui::sequence::FeaturePanel:

[legend]List of all members.

Public Member Functions
	FeaturePanel (Genome genome, BaseViewerModel model)
void	genomesReordered (ModelEvent event)
DbXrefMenuItemBuilder	getDbXrefMenuItemBuilder ()
FeaturePopupMenuBuilder	getFeaturePopupMenuBuilder ()
GenbankMenuItemBuilder	getGenbankMenuItemBuilder ()
void	resizeForMoreFeatures ()
void	setBounds (int arg0, int arg1, int arg2, int arg3)
void	viewableRangeChanged (ModelEvent event)
Static Public Attributes
final int	DEFAULT_HEIGHT = 40
final int	DEFAULT_WIDTH = 10000
final int	MAX_FEATURE_DISPLAY_RANGE = 500000
Static Protected Member Functions
void	makeRenderer (BaseViewerModel model, MultiLineRenderer multi, FilterCacheSpec spec) throws ChangeVetoException
	makes renderers for displaying a type of feature
Private Member Functions
void	adjustScaleAndTranslation ()
SequenceRenderer	barRenderer (String type, Color innerColor, double depth, StrandedFeature.Strand strand) throws ChangeVetoException
void	clearTransPanel ()
void	init ()
void	setNewSize (Dimension my_size)
Private Attributes
final DbXrefMenuItemBuilder	dmib = new DbXrefMenuItemBuilder()
final FeaturePopupMenuBuilder	fpmb = new FeaturePopupMenuBuilder()
final GenbankMenuItemBuilder	gmib = new GenbankMenuItemBuilder()
Sequence	seq
TranslatedSequencePanel	trans

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Detailed Description

Author:

Paul Infield-Harm, Aaron Darling (derived from FastBeadDemo by Keith James)

A panel that shows features, duh!

Definition at line 61 of file FeaturePanel.java.

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Constructor & Destructor Documentation

org::gel::mauve::gui::sequence::FeaturePanel::FeaturePanel (  Genome  genome, BaseViewerModel  model )  [inline]

Definition at line 72 of file FeaturePanel.java. References init().

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Member Function Documentation

void org::gel::mauve::gui::sequence::FeaturePanel::adjustScaleAndTranslation (   )  [inline, private]

Definition at line 216 of file FeaturePanel.java. References org::gel::mauve::gui::sequence::AbstractSequencePanel::getGenome(), org::gel::mauve::Genome::getViewLength(), org::gel::mauve::Genome::getViewStart(), MAX_FEATURE_DISPLAY_RANGE, and trans. Referenced by setBounds(), and viewableRangeChanged().

SequenceRenderer org::gel::mauve::gui::sequence::FeaturePanel::barRenderer (  String  type, Color  innerColor, double  depth, StrandedFeature.Strand  strand )  throws ChangeVetoException [inline, private]

Definition at line 202 of file FeaturePanel.java.

void org::gel::mauve::gui::sequence::FeaturePanel::clearTransPanel (   )  [inline, private]

Definition at line 89 of file FeaturePanel.java. References trans. Referenced by init().

void org::gel::mauve::gui::sequence::FeaturePanel::genomesReordered (  ModelEvent  event  )  [inline]

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel. Definition at line 479 of file FeaturePanel.java.

DbXrefMenuItemBuilder org::gel::mauve::gui::sequence::FeaturePanel::getDbXrefMenuItemBuilder (   )  [inline]

Definition at line 198 of file FeaturePanel.java. References dmib.

FeaturePopupMenuBuilder org::gel::mauve::gui::sequence::FeaturePanel::getFeaturePopupMenuBuilder (   )  [inline]

Definition at line 197 of file FeaturePanel.java. References fpmb.

GenbankMenuItemBuilder org::gel::mauve::gui::sequence::FeaturePanel::getGenbankMenuItemBuilder (   )  [inline]

Definition at line 199 of file FeaturePanel.java. References gmib.

void org::gel::mauve::gui::sequence::FeaturePanel::init (   )  [inline, private]

Definition at line 98 of file FeaturePanel.java. References org::gel::mauve::gui::sequence::FeaturePanel::FeaturePopupMenuBuilder::addMenuItemBuilder(), org::gel::mauve::gui::sequence::FeatureFilterer::addMultiRenderer(), clearTransPanel(), DEFAULT_HEIGHT, DEFAULT_WIDTH, dmib, fpmb, org::gel::mauve::Genome::getAnnotationFormat(), org::gel::mauve::Genome::getAnnotationSequence(), org::gel::mauve::FilterCacheSpec::getFeatureRenderer(), org::gel::mauve::SupportedFormat::getFilterCacheSpecs(), org::gel::mauve::gui::sequence::AbstractSequencePanel::getGenome(), gmib, makeRenderer(), setNewSize(), and trans. Referenced by FeaturePanel().

void org::gel::mauve::gui::sequence::FeaturePanel::makeRenderer (  BaseViewerModel  model, MultiLineRenderer  multi, FilterCacheSpec  spec )  throws ChangeVetoException [inline, static, protected]

makes renderers for displaying a type of feature Parameters: multi  the MultiLineRenderer that renders features for this panel spec  the FilterCacheSpec that describes the feature type Exceptions: ChangeVetoException  Definition at line 168 of file FeaturePanel.java. Referenced by init().

void org::gel::mauve::gui::sequence::FeaturePanel::resizeForMoreFeatures (   )  [inline]

Definition at line 180 of file FeaturePanel.java. References setNewSize().

void org::gel::mauve::gui::sequence::FeaturePanel::setBounds (  int  arg0, int  arg1, int  arg2, int  arg3 )  [inline]

Definition at line 81 of file FeaturePanel.java. References adjustScaleAndTranslation(), and trans.

void org::gel::mauve::gui::sequence::FeaturePanel::setNewSize (  Dimension  my_size  )  [inline, private]

Definition at line 186 of file FeaturePanel.java. References trans. Referenced by init(), and resizeForMoreFeatures().

void org::gel::mauve::gui::sequence::FeaturePanel::viewableRangeChanged (  ModelEvent  event  )  [inline]

Reimplemented from org::gel::mauve::gui::sequence::AbstractSequencePanel. Definition at line 471 of file FeaturePanel.java. References adjustScaleAndTranslation(), and trans.

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Member Data Documentation

final int org::gel::mauve::gui::sequence::FeaturePanel::DEFAULT_HEIGHT = 40 [static]

Definition at line 64 of file FeaturePanel.java. Referenced by init().

final int org::gel::mauve::gui::sequence::FeaturePanel::DEFAULT_WIDTH = 10000 [static]

Definition at line 63 of file FeaturePanel.java. Referenced by init().

final DbXrefMenuItemBuilder org::gel::mauve::gui::sequence::FeaturePanel::dmib = new DbXrefMenuItemBuilder() [private]

Definition at line 69 of file FeaturePanel.java. Referenced by getDbXrefMenuItemBuilder(), and init().

final FeaturePopupMenuBuilder org::gel::mauve::gui::sequence::FeaturePanel::fpmb = new FeaturePopupMenuBuilder() [private]

Definition at line 70 of file FeaturePanel.java. Referenced by getFeaturePopupMenuBuilder(), and init().

final GenbankMenuItemBuilder org::gel::mauve::gui::sequence::FeaturePanel::gmib = new GenbankMenuItemBuilder() [private]

Definition at line 68 of file FeaturePanel.java. Referenced by getGenbankMenuItemBuilder(), and init().

final int org::gel::mauve::gui::sequence::FeaturePanel::MAX_FEATURE_DISPLAY_RANGE = 500000 [static]

Definition at line 65 of file FeaturePanel.java. Referenced by adjustScaleAndTranslation().

Sequence org::gel::mauve::gui::sequence::FeaturePanel::seq [private]

Definition at line 67 of file FeaturePanel.java.

TranslatedSequencePanel org::gel::mauve::gui::sequence::FeaturePanel::trans [private]

Definition at line 66 of file FeaturePanel.java. Referenced by adjustScaleAndTranslation(), clearTransPanel(), init(), setBounds(), setNewSize(), and viewableRangeChanged().

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The documentation for this class was generated from the following file:

• src/org/gel/mauve/gui/sequence/FeaturePanel.java

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