org::gel::mauve::gui::navigation::SearchResultPanel Class Reference

A Gui component that shows the results of a given query separated by genome. More...

Inheritance diagram for org::gel::mauve::gui::navigation::SearchResultPanel:

[legend]Collaboration diagram for org::gel::mauve::gui::navigation::SearchResultPanel:


Public Member Functions
void	addTreeModelListener (TreeModelListener listen)
	passes on listeners to real tree model
void	displayFeatures (Object[] data)
	displays the data passed into the method
Object	getChild (Object parent, int index)
	Finds the child of the given object.
int	getChildCount (Object parent)
	Returns the number of children the object has.
int	getIndexOfChild (Object parent, Object child)
	Returns the index of the child.
Object	getRoot ()
	returns undisplayed root of the tree
JScrollPane	getScrollPane ()
	returns a reference to the ScrollPane that contains this result_panel
Component	getTreeCellRendererComponent (JTree tree, Object val, boolean selected, boolean expanded, boolean leaf, int row, boolean focus)
	facilitates painting of tree- converts feature to its name
boolean	isLeaf (Object node)
	Returns true if the object is a leaf.
void	removeTreeModelListener (TreeModelListener list)
	passes on listener removes to real tree model
	SearchResultPanel (Vector genomes, SequenceNavigator nav)
	Constructs new SearchResultPanel.
void	valueChanged (TreeSelectionEvent event)
	When the selection in the tree changes, recenters mauve frame gui on selected feature.
void	valueForPathChanged (TreePath path, Object val)
	Passes on events to real tree model.
void	waitForResults ()
	sets display to reflect a search is being performed
Static Public Member Functions
String	getDisplayText (Feature feat)
	returns a string including the feature's name and location
Static Public Attributes
final String	MATCHLESS = "No features found. . ."
	represents genome with no found features
final Icon	MINUS_ICON = SignedIcon.getSignedIcon (false)
	icon shown if a genome did not contain results
final String	NO_RESULTS = "No results to display. . ."
	String representing no results.
final Icon	PLUS_ICON = SignedIcon.getSignedIcon (true)
	icon shown if a genome contained results
Protected Member Functions
void	initGUI ()
	initializes gui components
void	resetData (Object[] data)
	Resets the display to include the new data.
Protected Attributes
Hashtable	genome_data
	contains all the data the tree should display
Object[]	genome_indexes
	contains genomes mapped to their index
DefaultTreeModel	model
	model that represents the data to be displayed
SequenceNavigator	navigator
	reference to SequenceNavigator this panel is associated with
DefaultTreeCellRenderer	renderer
	renders each value in the tree
int	result_state
	represents display state - if there are no results, value is 0, 1 if there is 1 result, any number higher than 1 means multiple results
DefaultMutableTreeNode	root
	reference to root node of tree
JScrollPane	scroller
	allows results to be scrolled through
boolean	searching
	true when a search is in progress, false otherwise
JTree	tree
	Tree that contains search results (features).
Static Protected Attributes
final String	ROOT = "Root"
	represents "dummy" root node of tree
final String	SEARCHING = "Searching. . ."
	represents tree while searching

Detailed Description

A Gui component that shows the results of a given query separated by genome.

Each result represents a feature that matched the search constraints. If a result is selected, the Genome sequence is scrolled to that feature

Author:: rissman

Definition at line 51 of file SearchResultPanel.java.

Constructor & Destructor Documentation

org::gel::mauve::gui::navigation::SearchResultPanel::SearchResultPanel ( Vector genomes,

SequenceNavigator nav

) [inline]

Constructs new SearchResultPanel.

Parameters:

genomes The genomes that the mauve frame displays

nav The SequenceNavigator it belongs to

Definition at line 143 of file SearchResultPanel.java.
References genome_data, genome_indexes, and initGUI().

Member Function Documentation

void org::gel::mauve::gui::navigation::SearchResultPanel::addTreeModelListener ( TreeModelListener listen ) [inline]

passes on listeners to real tree model

Definition at line 329 of file SearchResultPanel.java.

void org::gel::mauve::gui::navigation::SearchResultPanel::displayFeatures ( Object[] data ) [inline]

displays the data passed into the method

Parameters:

data An array of linked lists. Each list should start with a genome object, followed by all the Features to display in that genome

Definition at line 200 of file SearchResultPanel.java.
References genome_data, genome_indexes, getChild(), getChildCount(), org::gel::mauve::gui::SequenceNavigator::reloadGUI(), resetData(), result_state, root, ROOT, searching, and tree.
Referenced by org::gel::mauve::gui::SequenceNavigator::goToFeatureByName(), and org::gel::mauve::gui::SequenceNavigator::showResultTree().

Object org::gel::mauve::gui::navigation::SearchResultPanel::getChild ( Object parent,

int index

) [inline]

Finds the child of the given object.

Parameters:

parent The object whose child should be found

index The index of the desired child

Returns:
An object representing the child node

Definition at line 342 of file SearchResultPanel.java.
Referenced by displayFeatures().

int org::gel::mauve::gui::navigation::SearchResultPanel::getChildCount ( Object parent ) [inline]

Returns the number of children the object has.

Parameters:

parent The object representing the parent

Returns:
The number of children associated with the parent

Definition at line 370 of file SearchResultPanel.java.
Referenced by displayFeatures().

String org::gel::mauve::gui::navigation::SearchResultPanel::getDisplayText ( Feature feat ) [inline, static]

returns a string including the feature's name and location

Parameters:

feat The feature whose information should be displayed

Returns:
The display string for this feature

Definition at line 286 of file SearchResultPanel.java.

int org::gel::mauve::gui::navigation::SearchResultPanel::getIndexOfChild ( Object parent,

Object child

) [inline]

Returns the index of the child.

Parameters:

parent The parent of the child in question

child The child whose index is desired

Returns:
The index of the child

Definition at line 397 of file SearchResultPanel.java.

Object org::gel::mauve::gui::navigation::SearchResultPanel::getRoot ( ) [inline]

returns undisplayed root of the tree

Returns:
An object representing the tree root

Definition at line 430 of file SearchResultPanel.java.

JScrollPane org::gel::mauve::gui::navigation::SearchResultPanel::getScrollPane ( ) [inline]

returns a reference to the ScrollPane that contains this result_panel

Returns:

Definition at line 189 of file SearchResultPanel.java.
References scroller.
Referenced by org::gel::mauve::gui::SequenceNavigator::initGUI().

Component org::gel::mauve::gui::navigation::SearchResultPanel::getTreeCellRendererComponent ( JTree tree,

Object val,

boolean selected,

boolean expanded,

boolean leaf,

int row,

boolean focus

) [inline]

facilitates painting of tree- converts feature to its name

Definition at line 316 of file SearchResultPanel.java.

void org::gel::mauve::gui::navigation::SearchResultPanel::initGUI ( ) [inline, protected]

initializes gui components

Definition at line 159 of file SearchResultPanel.java.
References MINUS_ICON, PLUS_ICON, ROOT, root, scroller, and tree.
Referenced by SearchResultPanel().

boolean org::gel::mauve::gui::navigation::SearchResultPanel::isLeaf ( Object node ) [inline]

Returns true if the object is a leaf.

Parameters:

node The object in question

Returns:
True if the object has no children, false otherwise

Definition at line 441 of file SearchResultPanel.java.

void org::gel::mauve::gui::navigation::SearchResultPanel::removeTreeModelListener ( TreeModelListener list ) [inline]

passes on listener removes to real tree model

Definition at line 451 of file SearchResultPanel.java.

void org::gel::mauve::gui::navigation::SearchResultPanel::resetData ( Object[] data ) [inline, protected]

Resets the display to include the new data.

Parameters:

data The data that should be added. Each array index is a linked list containing first the genome it is for, then all the features to display for that sequence

Definition at line 259 of file SearchResultPanel.java.
Referenced by displayFeatures().

void org::gel::mauve::gui::navigation::SearchResultPanel::valueChanged ( TreeSelectionEvent event ) [inline]

When the selection in the tree changes, recenters mauve frame gui on selected feature.

Definition at line 305 of file SearchResultPanel.java.

void org::gel::mauve::gui::navigation::SearchResultPanel::valueForPathChanged ( TreePath path,

Object val

) [inline]

Passes on events to real tree model.

Definition at line 458 of file SearchResultPanel.java.

void org::gel::mauve::gui::navigation::SearchResultPanel::waitForResults ( ) [inline]

sets display to reflect a search is being performed

Definition at line 242 of file SearchResultPanel.java.
References root, and searching.
Referenced by org::gel::mauve::gui::SequenceNavigator::doNavigation().

Member Data Documentation

Hashtable org::gel::mauve::gui::navigation::SearchResultPanel::genome_data [protected]

contains all the data the tree should display

Definition at line 128 of file SearchResultPanel.java.
Referenced by displayFeatures(), and SearchResultPanel().

Object [] org::gel::mauve::gui::navigation::SearchResultPanel::genome_indexes [protected]

contains genomes mapped to their index

Definition at line 133 of file SearchResultPanel.java.
Referenced by displayFeatures(), and SearchResultPanel().

final String org::gel::mauve::gui::navigation::SearchResultPanel::MATCHLESS = "No features found. . ." [static]

represents genome with no found features

Definition at line 103 of file SearchResultPanel.java.

final Icon org::gel::mauve::gui::navigation::SearchResultPanel::MINUS_ICON = SignedIcon.getSignedIcon (false) [static]

icon shown if a genome did not contain results

Definition at line 123 of file SearchResultPanel.java.
Referenced by initGUI().

DefaultTreeModel org::gel::mauve::gui::navigation::SearchResultPanel::model [protected]

model that represents the data to be displayed

Definition at line 62 of file SearchResultPanel.java.

SequenceNavigator org::gel::mauve::gui::navigation::SearchResultPanel::navigator [protected]

reference to SequenceNavigator this panel is associated with

Definition at line 72 of file SearchResultPanel.java.

final String org::gel::mauve::gui::navigation::SearchResultPanel::NO_RESULTS = "No results to display. . ." [static]

String representing no results.

Definition at line 98 of file SearchResultPanel.java.

final Icon org::gel::mauve::gui::navigation::SearchResultPanel::PLUS_ICON = SignedIcon.getSignedIcon (true) [static]

icon shown if a genome contained results

Definition at line 118 of file SearchResultPanel.java.
Referenced by initGUI().

DefaultTreeCellRenderer org::gel::mauve::gui::navigation::SearchResultPanel::renderer [protected]

renders each value in the tree

Definition at line 67 of file SearchResultPanel.java.

int org::gel::mauve::gui::navigation::SearchResultPanel::result_state [protected]

represents display state - if there are no results, value is 0, 1 if there is 1 result, any number higher than 1 means multiple results

Definition at line 88 of file SearchResultPanel.java.
Referenced by displayFeatures().

final String org::gel::mauve::gui::navigation::SearchResultPanel::ROOT = "Root" [static, protected]

represents "dummy" root node of tree

Definition at line 113 of file SearchResultPanel.java.
Referenced by displayFeatures(), and initGUI().

DefaultMutableTreeNode org::gel::mauve::gui::navigation::SearchResultPanel::root [protected]

reference to root node of tree

Definition at line 77 of file SearchResultPanel.java.
Referenced by displayFeatures(), initGUI(), and waitForResults().

JScrollPane org::gel::mauve::gui::navigation::SearchResultPanel::scroller [protected]

allows results to be scrolled through

Definition at line 82 of file SearchResultPanel.java.
Referenced by getScrollPane(), and initGUI().

final String org::gel::mauve::gui::navigation::SearchResultPanel::SEARCHING = "Searching. . ." [static, protected]

represents tree while searching

Definition at line 108 of file SearchResultPanel.java.

boolean org::gel::mauve::gui::navigation::SearchResultPanel::searching [protected]

true when a search is in progress, false otherwise

Definition at line 93 of file SearchResultPanel.java.
Referenced by displayFeatures(), and waitForResults().

JTree org::gel::mauve::gui::navigation::SearchResultPanel::tree [protected]

Tree that contains search results (features).

Definition at line 57 of file SearchResultPanel.java.
Referenced by displayFeatures(), and initGUI().

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

src/org/gel/mauve/gui/navigation/SearchResultPanel.java

Generated on Mon May 20 06:04:07 2013 for Mauve by

1.3.6

org::gel::mauve::gui::navigation::SearchResultPanel Class Reference

Public Member Functions

Static Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Static Protected Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation