org::gel::mauve::gui::SequenceNavigator Class Reference

A gui that allows a user to search genome features by annotation. More...

Inheritance diagram for org::gel::mauve::gui::SequenceNavigator:

[legend]Collaboration diagram for org::gel::mauve::gui::SequenceNavigator:

[legend]List of all members.

Public Member Functions
void	actionPerformed (final ActionEvent e)
	action listener for buttons on this panel
void	addNavigationPanel (NavigationPanel pane)
	adds a newly constructed navigation panel to the gui
void	adjustZoom (Feature feat)
	Adjust zoom so desired feature is a decent size and is all viewable.
void	displayFeature (Feature feat, Genome genome)
	Centers the view on a specific feature of a genome.
void	dispose ()
Vector	getGenomeKeys ()
	Gets all the feature keys present in any of the sequences.
int	getValidCount ()
	Finds out if the data entered into the input panels is valid, and how many valid constraints are possible.
void	goToFeatureByName ()
	A wizard style simplified feature searcher that allows the user to find a feature by name and highlights the first feature in the mauve gui that matches the desired name.
void	goToPosition (long position, Genome chosen)
	Centers view on a specific sequence position.
void	keyPressed (KeyEvent e)
	dummy method - implemented as part of key listener interface
void	keyReleased (KeyEvent e)
	dummy method - implemented as part of key listener interface
void	keyTyped (KeyEvent e)
	converts enters typed into the input panels to action events representing a user desire to perform search
void	loadGenomeList ()
	loads list of genomes user is viewing and should be able to search
void	makeConstraintVisible (NavigationPanel panel)
	scrolls the gui to a specific part of the list of constraints
void	reloadGUI ()
	necessary to call for some reason whenever adding or removing NavigationPanels-- automatically called from addNavigationPanel and removeNavigationPanel
void	removeNavigationPanel (NavigationPanel pane)
	removes unwanted navigation panel from gui
void	reset ()
	resets search so only one navigation panel is present
	SequenceNavigator (Component parent, RearrangementPanel rrpanel, BaseViewerModel dataModel)
	SequenceNavigator (MauveFrame frame)
	Creates new GenomeNavigator.
boolean	shouldClear ()
	determines whether current results should be cleared
void	showNavigator ()
	Shows the navigator so a user may select a genome and a position to go to within the genome.
void	showResultTree (final Genome[] nomes, final String[][] data)
	Performs the final narrowing down of features to those that match the given constraints, and displays a tree of matching features.
Static Public Member Functions
void	expandIfNecessary (JScrollPane pane, Dimension size)
	Expands the frame holding the gui as much as necessary without allowing it to increase over the maximum programmatically allowable size.
void	goToPosition (long position, Genome chosen, RearrangementPanel rrpanel)
	Centers view on a specific sequence position.
void	goToSeqPos (Component parentComponent, BaseViewerModel dataModel, RearrangementPanel rrpanel)
	A simple wizard style routine that allows a user to choose a numeric sequence position from a specific sequence to navigate to, and performs navigation.
Static Public Attributes
int	MAX_HEIGHT = 400
	sets maximum height programmatically given to the frame
int	MAX_WIDTH = 850
	sets maximum height and width programmatically given to the frame.
Protected Member Functions
void	doNavigation ()
	converts user input to features to display and centers view on first matching feature
void	moveFromBehind ()
	finds the best place on screen to place the frame- takes into account size of mauve frame
Protected Attributes
WindowAdapter	adapt
JButton	add
AncestorListener	ancestListener
	if there is no frame containing the alignment, so when it is removed, this SequenceNavigator can be closed
JButton	cancel
JCheckBox	clear
	if checked, previous search results are cleared when a new search is performed
BaseViewerModel	data_model
	The data model being displayed and navigated.
JFrame	frame
	parent frame containing this panel
Vector	genome_choices
	availabe genome sequences to search
JComboBox	genomes
	list of genomes with searchable features
JPanel	nav_panel_holder
	panel that contains all NavPanels
LinkedList	nav_panels
	each NavPanel in the list represents a constraint on the current search
JScrollPane	nav_scroll
	allows constraints to be scrolled through
Component	parent_component
	The parent component of the panel, if it disappears, so will the panel.
JButton	reset
	when pressed, resets search to one constraint with no values entered
SearchResultPanel	result_pane
	panel that shows results
JScrollPane	result_scroller
	allows results to be scrolled through
RearrangementPanel	rrpanel
	The panel displaying data under navigation.
JButton	search
	when pressed, a search is performed
LinkedList	window_listeners
Static Package Functions
	[static initializer]
	initializes hashtable and hashset inherited from NavigationConstants
Private Member Functions
void	initGUI ()
	Does initial gui initialization.
void	makeBottomPanel (JPanel holder)
	initializes bottom part of left side of gui
void	makeFrame ()
	sets up the frame that contains this SequenceNavigation panel and its subcomponents
Private Attributes
Boolean	current_search = Boolean.FALSE
	mechanism for only doing one gui operation at a time/locking

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Detailed Description

A gui that allows a user to search genome features by annotation.

Allows multiple constraints. Results are shown in a tree, and selecting the feature in the tree scrolls to that position in the genome. Results can be added to previous search results, or previous results can be cleared.

Author:

rissman

Definition at line 45 of file SequenceNavigator.java.

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Constructor & Destructor Documentation

org::gel::mauve::gui::SequenceNavigator::SequenceNavigator (  MauveFrame  frame  )  [inline]

Creates new GenomeNavigator. Parameters: frame  the MauveFrame this navigator should be associated with Definition at line 169 of file SequenceNavigator.java. References data_model, org::gel::mauve::gui::MauveFrame::getModel(), org::gel::mauve::gui::MauveFrame::getRearrangementPanel(), initGUI(), nav_panels, and parent_component.

org::gel::mauve::gui::SequenceNavigator::SequenceNavigator (  Component  parent, RearrangementPanel  rrpanel, BaseViewerModel  dataModel )  [inline]

Definition at line 177 of file SequenceNavigator.java. References data_model, initGUI(), nav_panels, and parent_component.

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Member Function Documentation

org::gel::mauve::gui::SequenceNavigator::[static initializer] (   )  [inline, static, package]

initializes hashtable and hashset inherited from NavigationConstants

void org::gel::mauve::gui::SequenceNavigator::actionPerformed (  final ActionEvent  e  )  [inline]

action listener for buttons on this panel Parameters: e  If the source of the action is the search button, checks for valid input and performs search If the source is the cancel button, hides the Navigator If the source is the add button, adds a panel for the use to enter a new constraint in If the source is reset, removes all the input panel except the first Definition at line 398 of file SequenceNavigator.java. References add, current_search, doNavigation(), reset(), and search. Referenced by keyTyped().

void org::gel::mauve::gui::SequenceNavigator::addNavigationPanel (  NavigationPanel  pane  )  [inline]

adds a newly constructed navigation panel to the gui Definition at line 350 of file SequenceNavigator.java. References nav_panel_holder, nav_panels, and reloadGUI(). Referenced by org::gel::mauve::gui::navigation::NavigationPanel::initGUI().

void org::gel::mauve::gui::SequenceNavigator::adjustZoom (  Feature  feat  )  [inline]

Adjust zoom so desired feature is a decent size and is all viewable. Parameters: feat  Definition at line 662 of file SequenceNavigator.java.

void org::gel::mauve::gui::SequenceNavigator::displayFeature (  Feature  feat, Genome  genome )  [inline]

Centers the view on a specific feature of a genome. Parameters: feat  The feature to center on genome  The genome containing the feature Definition at line 647 of file SequenceNavigator.java. Referenced by goToFeatureByName().

void org::gel::mauve::gui::SequenceNavigator::dispose (   )  [inline]

Definition at line 737 of file SequenceNavigator.java. Referenced by org::gel::mauve::gui::MauveFrame::thisWindowClosing().

void org::gel::mauve::gui::SequenceNavigator::doNavigation (   )  [inline, protected]

converts user input to features to display and centers view on first matching feature Definition at line 610 of file SequenceNavigator.java. References getValidCount(), nav_panels, result_pane, showResultTree(), and org::gel::mauve::gui::navigation::SearchResultPanel::waitForResults(). Referenced by actionPerformed().

void org::gel::mauve::gui::SequenceNavigator::expandIfNecessary (  JScrollPane  pane, Dimension  size )  [inline, static]

Expands the frame holding the gui as much as necessary without allowing it to increase over the maximum programmatically allowable size. Parameters: pane  Holds the component that might need more size size  The size of the frame before the resize Definition at line 456 of file SequenceNavigator.java. Referenced by reloadGUI().

Vector org::gel::mauve::gui::SequenceNavigator::getGenomeKeys (   )  [inline]

Gets all the feature keys present in any of the sequences. Returns: A vector of strings representing all the fields in all the currently viewed sequences Definition at line 728 of file SequenceNavigator.java. Referenced by org::gel::mauve::gui::navigation::NavigationPanel::setNavigationChoices().

int org::gel::mauve::gui::SequenceNavigator::getValidCount (   )  [inline]

Finds out if the data entered into the input panels is valid, and how many valid constraints are possible. Input is considered valid if there are no breaks in input; if all fields are filled in. Will allow empty constraints at the bottom Returns: The number of valid constraints Definition at line 506 of file SequenceNavigator.java. References org::gel::mauve::gui::navigation::NavigationPanel::dataValid(), and nav_panels. Referenced by doNavigation().

void org::gel::mauve::gui::SequenceNavigator::goToFeatureByName (   )  [inline]

A wizard style simplified feature searcher that allows the user to find a feature by name and highlights the first feature in the mauve gui that matches the desired name. Definition at line 567 of file SequenceNavigator.java. References data_model, displayFeature(), org::gel::mauve::gui::navigation::SearchResultPanel::displayFeatures(), org::gel::mauve::Genome::length, parent_component, and result_pane. Referenced by org::gel::mauve::gui::MauveFrame::actionPerformed().

void org::gel::mauve::gui::SequenceNavigator::goToPosition (  long  position, Genome  chosen )  [inline]

Centers view on a specific sequence position. Parameters: position  the position to center on chosen  the genome to find the position in Definition at line 718 of file SequenceNavigator.java.

void org::gel::mauve::gui::SequenceNavigator::goToPosition (  long  position, Genome  chosen, RearrangementPanel  rrpanel )  [inline, static]

Centers view on a specific sequence position. Parameters: position  the position to center on chosen  the genome to find the position in mf  the mauve frame containing the p Definition at line 700 of file SequenceNavigator.java. References org::gel::mauve::gui::sequence::RRSequencePanel::goTo(), org::gel::mauve::gui::sequence::RRSequencePanel::isForGenome(), and org::gel::mauve::gui::RearrangementPanel::newPanels. Referenced by goToSeqPos().

void org::gel::mauve::gui::SequenceNavigator::goToSeqPos (  Component  parentComponent, BaseViewerModel  dataModel, RearrangementPanel  rrpanel )  [inline, static]

A simple wizard style routine that allows a user to choose a numeric sequence position from a specific sequence to navigate to, and performs navigation. Parameters: parentComponent  The parent in the GUI heirarchy dataModel  A viewer data model containing sequence data of interest rrpanel  The rearrangement panel to adjust when the user selects a seq coordinate Definition at line 537 of file SequenceNavigator.java. References goToPosition().

void org::gel::mauve::gui::SequenceNavigator::initGUI (   )  [inline, private]

Does initial gui initialization. Definition at line 191 of file SequenceNavigator.java. References org::gel::mauve::gui::navigation::SearchResultPanel::getScrollPane(), loadGenomeList(), makeBottomPanel(), makeFrame(), moveFromBehind(), nav_panel_holder, nav_scroll, reloadGUI(), result_pane, and result_scroller. Referenced by SequenceNavigator().

void org::gel::mauve::gui::SequenceNavigator::keyPressed (  KeyEvent  e  )  [inline]

dummy method - implemented as part of key listener interface Definition at line 469 of file SequenceNavigator.java.

void org::gel::mauve::gui::SequenceNavigator::keyReleased (  KeyEvent  e  )  [inline]

dummy method - implemented as part of key listener interface Definition at line 475 of file SequenceNavigator.java.

void org::gel::mauve::gui::SequenceNavigator::keyTyped (  KeyEvent  e  )  [inline]

converts enters typed into the input panels to action events representing a user desire to perform search Definition at line 482 of file SequenceNavigator.java. References actionPerformed(), and search.

void org::gel::mauve::gui::SequenceNavigator::loadGenomeList (   )  [inline]

loads list of genomes user is viewing and should be able to search Definition at line 330 of file SequenceNavigator.java. References data_model, and result_pane. Referenced by initGUI().

void org::gel::mauve::gui::SequenceNavigator::makeBottomPanel (  JPanel  holder  )  [inline, private]

initializes bottom part of left side of gui Parameters: holder  The panel in which to put the bottom component Definition at line 271 of file SequenceNavigator.java. References add, clear, reset, and search. Referenced by initGUI().

void org::gel::mauve::gui::SequenceNavigator::makeConstraintVisible (  NavigationPanel  panel  )  [inline]

scrolls the gui to a specific part of the list of constraints Parameters: panel  The NavigationPanel that should be visible on screen Definition at line 494 of file SequenceNavigator.java. References nav_scroll. Referenced by org::gel::mauve::gui::navigation::NavigationPanel::dataValid().

void org::gel::mauve::gui::SequenceNavigator::makeFrame (   )  [inline, private]

sets up the frame that contains this SequenceNavigation panel and its subcomponents Definition at line 237 of file SequenceNavigator.java. References adapt, ancestListener, parent_component, and window_listeners. Referenced by initGUI().

void org::gel::mauve::gui::SequenceNavigator::moveFromBehind (   )  [inline, protected]

finds the best place on screen to place the frame- takes into account size of mauve frame Definition at line 303 of file SequenceNavigator.java. References parent_component. Referenced by initGUI().

void org::gel::mauve::gui::SequenceNavigator::reloadGUI (   )  [inline]

necessary to call for some reason whenever adding or removing NavigationPanels-- automatically called from addNavigationPanel and removeNavigationPanel Definition at line 436 of file SequenceNavigator.java. References expandIfNecessary(), MAX_HEIGHT, MAX_WIDTH, nav_scroll, and result_scroller. Referenced by addNavigationPanel(), org::gel::mauve::gui::navigation::SearchResultPanel::displayFeatures(), initGUI(), and removeNavigationPanel().

void org::gel::mauve::gui::SequenceNavigator::removeNavigationPanel (  NavigationPanel  pane  )  [inline]

removes unwanted navigation panel from gui Definition at line 361 of file SequenceNavigator.java. References nav_panel_holder, nav_panels, and reloadGUI(). Referenced by org::gel::mauve::gui::navigation::NavigationPanel::actionPerformed(), and reset().

void org::gel::mauve::gui::SequenceNavigator::reset (   )  [inline]

resets search so only one navigation panel is present Definition at line 372 of file SequenceNavigator.java. References nav_panels, and removeNavigationPanel(). Referenced by actionPerformed().

boolean org::gel::mauve::gui::SequenceNavigator::shouldClear (   )  [inline]

determines whether current results should be cleared Returns: True if they should, false otherwise Definition at line 343 of file SequenceNavigator.java. References clear.

void org::gel::mauve::gui::SequenceNavigator::showNavigator (   )  [inline]

Shows the navigator so a user may select a genome and a position to go to within the genome. Definition at line 383 of file SequenceNavigator.java. Referenced by org::gel::mauve::gui::MauveFrame::actionPerformed().

void org::gel::mauve::gui::SequenceNavigator::showResultTree (  final Genome[]  nomes, final  Stringdata[][] )  [inline]

Performs the final narrowing down of features to those that match the given constraints, and displays a tree of matching features. Parameters: nomes  The genomes the data is from data  A two dimensional array; contains the constraints to search by Definition at line 633 of file SequenceNavigator.java. References org::gel::mauve::gui::navigation::SearchResultPanel::displayFeatures(), and result_pane. Referenced by doNavigation().

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Member Data Documentation

WindowAdapter org::gel::mauve::gui::SequenceNavigator::adapt [protected]

Definition at line 106 of file SequenceNavigator.java. Referenced by makeFrame().

JButton org::gel::mauve::gui::SequenceNavigator::add [protected]

Definition at line 74 of file SequenceNavigator.java. Referenced by actionPerformed(), and makeBottomPanel().

AncestorListener org::gel::mauve::gui::SequenceNavigator::ancestListener [protected]

if there is no frame containing the alignment, so when it is removed, this SequenceNavigator can be closed Definition at line 112 of file SequenceNavigator.java. Referenced by makeFrame().

JButton org::gel::mauve::gui::SequenceNavigator::cancel [protected]

Definition at line 73 of file SequenceNavigator.java.

JCheckBox org::gel::mauve::gui::SequenceNavigator::clear [protected]

if checked, previous search results are cleared when a new search is performed Definition at line 94 of file SequenceNavigator.java. Referenced by makeBottomPanel(), and shouldClear().

Boolean org::gel::mauve::gui::SequenceNavigator::current_search = Boolean.FALSE [private]

mechanism for only doing one gui operation at a time/locking Definition at line 161 of file SequenceNavigator.java. Referenced by actionPerformed().

BaseViewerModel org::gel::mauve::gui::SequenceNavigator::data_model [protected]

The data model being displayed and navigated. Definition at line 53 of file SequenceNavigator.java. Referenced by goToFeatureByName(), loadGenomeList(), and SequenceNavigator().

JFrame org::gel::mauve::gui::SequenceNavigator::frame [protected]

parent frame containing this panel Definition at line 57 of file SequenceNavigator.java.

Vector org::gel::mauve::gui::SequenceNavigator::genome_choices [protected]

availabe genome sequences to search Definition at line 117 of file SequenceNavigator.java.

JComboBox org::gel::mauve::gui::SequenceNavigator::genomes [protected]

list of genomes with searchable features Definition at line 62 of file SequenceNavigator.java.

int org::gel::mauve::gui::SequenceNavigator::MAX_HEIGHT = 400 [static]

sets maximum height programmatically given to the frame Definition at line 122 of file SequenceNavigator.java. Referenced by reloadGUI().

int org::gel::mauve::gui::SequenceNavigator::MAX_WIDTH = 850 [static]

sets maximum height and width programmatically given to the frame. Definition at line 127 of file SequenceNavigator.java. Referenced by reloadGUI().

JPanel org::gel::mauve::gui::SequenceNavigator::nav_panel_holder [protected]

panel that contains all NavPanels Definition at line 84 of file SequenceNavigator.java. Referenced by addNavigationPanel(), initGUI(), and removeNavigationPanel().

LinkedList org::gel::mauve::gui::SequenceNavigator::nav_panels [protected]

each NavPanel in the list represents a constraint on the current search Definition at line 67 of file SequenceNavigator.java. Referenced by addNavigationPanel(), doNavigation(), getValidCount(), removeNavigationPanel(), reset(), and SequenceNavigator().

JScrollPane org::gel::mauve::gui::SequenceNavigator::nav_scroll [protected]

allows constraints to be scrolled through Definition at line 104 of file SequenceNavigator.java. Referenced by initGUI(), makeConstraintVisible(), and reloadGUI().

Component org::gel::mauve::gui::SequenceNavigator::parent_component [protected]

The parent component of the panel, if it disappears, so will the panel. Definition at line 51 of file SequenceNavigator.java. Referenced by goToFeatureByName(), makeFrame(), moveFromBehind(), and SequenceNavigator().

JButton org::gel::mauve::gui::SequenceNavigator::reset [protected]

when pressed, resets search to one constraint with no values entered Definition at line 79 of file SequenceNavigator.java. Referenced by makeBottomPanel().

SearchResultPanel org::gel::mauve::gui::SequenceNavigator::result_pane [protected]

panel that shows results Definition at line 89 of file SequenceNavigator.java. Referenced by doNavigation(), goToFeatureByName(), initGUI(), loadGenomeList(), and showResultTree().

JScrollPane org::gel::mauve::gui::SequenceNavigator::result_scroller [protected]

allows results to be scrolled through Definition at line 99 of file SequenceNavigator.java. Referenced by initGUI(), and reloadGUI().

RearrangementPanel org::gel::mauve::gui::SequenceNavigator::rrpanel [protected]

The panel displaying data under navigation. Definition at line 52 of file SequenceNavigator.java.

JButton org::gel::mauve::gui::SequenceNavigator::search [protected]

when pressed, a search is performed Definition at line 72 of file SequenceNavigator.java. Referenced by actionPerformed(), keyTyped(), and makeBottomPanel().

LinkedList org::gel::mauve::gui::SequenceNavigator::window_listeners [protected]

Definition at line 105 of file SequenceNavigator.java. Referenced by makeFrame().

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

• src/org/gel/mauve/gui/SequenceNavigator.java

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