$darkmode
DENOPTIM
denoptim.gui.CompatibilityMatrixForm Class Reference
Inheritance diagram for denoptim.gui.CompatibilityMatrixForm:
[legend]
Collaboration diagram for denoptim.gui.CompatibilityMatrixForm:
[legend]

Classes

class  CompatibilityRuleLine
 Single line in the list of APClass compatibility rules. More...
 
class  CompatRulesHeader
 
class  TargetAPClassToken
 
class  TrgRemovalListener
 Listens for clicks that require removal of a compatible APClass (i.e., the target APClass) from the existing rule of a source APClass. More...
 

Public Member Functions

 CompatibilityMatrixForm ()
 
void writeCopatibilityMatrixFile (JComponent parent, File outFile)
 Writes all the compatibility matrix data to the given file. More...
 
void importAllAPClassesFromCappingGroupLibs (Set< File > fragLibs, boolean cleanup)
 Reads all the APClasses found in a list of files. More...
 
void importAllAPClassesFromFragmentLibs (Set< File > fragLibs, boolean cleanup)
 Reads all the APClasses found in a list of files. More...
 

Protected Member Functions

void clearSearchMatches ()
 
void searchAPClass (String query)
 
void importCPMapFromFile (JComponent parent, File inFile)
 

Static Protected Attributes

static final String REMOVETRGAPC = "REMOVETRGAPC"
 Property used to trigger removal of a target APClass. More...
 

Private Member Functions

void updateAPClassCompatibilitiesList ()
 
void updateCappingRulesTable ()
 
void updateForbiddenEndsTable ()
 
void importAllAPClassesFromCPMatrix (boolean cleanup)
 Reads all the APClasses found in the currently loaded compatibility matrix. More...
 
void importAllCappingGroupsAPClassesFromCPMatrix (boolean cleanup)
 Reads all the APClasses of capping groups as found in the currently loaded capping rules. More...
 

Private Attributes

SortedSet< APClassallAPClasses = new TreeSet<APClass>()
 List of all APClasses. More...
 
SortedSet< String > allAPRules = new TreeSet<String>()
 List of all APRules. More...
 
SortedSet< APClassallCapAPClasses = new TreeSet<APClass>()
 List of APClasses of capping groups. More...
 
SortedSet< APClassallAPClsInCPMap = new TreeSet<APClass>()
 Sorted list of APClasses in the map of compatibility rules. More...
 
HashMap< APClass, ArrayList< APClass > > compatMap
 Data structure that stored the true entries of the attachment point classes compatibility matrix. More...
 
HashMap< APClass, APClasscappingMap
 Data structure that stores the AP-classes to be used to cap unused APS on the growing molecule. More...
 
HashSet< APClassforbiddenEndList = new HashSet<APClass>()
 Data structure that stores AP classes that cannot be held unused. More...
 
JTabbedPane tabbedPane
 
JPanel panelCPMap
 
JButton btnAddCompRul
 
JButton btnDelCompRul
 
JButton btnCopyCompRul
 
JButton btnClearMatch
 
JButton btnHelpCPMap
 
JPanel panelCPRules
 
JScrollPane scrollPanelCPMap
 
JTextField txtSearch
 
JLabel matchCounter
 
JPanel panelCapping
 
DefaultTableModel tabModCapping
 
JTable tableCapping
 
JButton btnAddCapping
 
JButton btnDelCapping
 
JButton btnSortCapping
 
JButton btnHelpCapping
 
JPanel panelFrbEnd
 
DefaultTableModel tabModFrbEnd
 
JTable tableFrbEnd
 
JButton btnAddFrbEnd
 
JButton btnDelFrbEnd
 
JButton btnSortFrbEnd
 
JButton btnHelpFrbEnd
 

Static Private Attributes

static final long serialVersionUID = -8042143358823563589L
 Version UID. More...
 

Detailed Description

Definition at line 70 of file CompatibilityMatrixForm.java.

Constructor & Destructor Documentation

◆ CompatibilityMatrixForm()

denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm ( )

Definition at line 158 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.allAPClasses, denoptim.gui.CompatibilityMatrixForm.allAPClsInCPMap, denoptim.gui.CompatibilityMatrixForm.allAPRules, denoptim.gui.CompatibilityMatrixForm.allCapAPClasses, denoptim.gui.CompatibilityMatrixForm.btnAddCapping, denoptim.gui.CompatibilityMatrixForm.btnAddCompRul, denoptim.gui.CompatibilityMatrixForm.btnAddFrbEnd, denoptim.gui.CompatibilityMatrixForm.btnClearMatch, denoptim.gui.CompatibilityMatrixForm.btnCopyCompRul, denoptim.gui.CompatibilityMatrixForm.btnDelCapping, denoptim.gui.CompatibilityMatrixForm.btnDelCompRul, denoptim.gui.CompatibilityMatrixForm.btnDelFrbEnd, denoptim.gui.CompatibilityMatrixForm.btnHelpCapping, denoptim.gui.CompatibilityMatrixForm.btnHelpCPMap, denoptim.gui.CompatibilityMatrixForm.btnHelpFrbEnd, denoptim.gui.CompatibilityMatrixForm.btnSortCapping, denoptim.gui.CompatibilityMatrixForm.btnSortFrbEnd, denoptim.gui.CompatibilityMatrixForm.cappingMap, denoptim.gui.CompatibilityMatrixForm.clearSearchMatches(), denoptim.gui.CompatibilityMatrixForm.compatMap, denoptim.gui.CompatibilityMatrixForm.forbiddenEndList, denoptim.graph.APClass.getRule(), denoptim.graph.APClass.make(), denoptim.gui.CompatibilityMatrixForm.matchCounter, denoptim.gui.CompatibilityMatrixForm.panelCapping, denoptim.gui.CompatibilityMatrixForm.panelCPMap, denoptim.gui.CompatibilityMatrixForm.panelCPRules, denoptim.gui.CompatibilityMatrixForm.panelFrbEnd, denoptim.gui.CompatibilityMatrixForm.scrollPanelCPMap, denoptim.gui.CompatibilityMatrixForm.searchAPClass(), denoptim.gui.GUIModalDialog.showDialog(), denoptim.gui.CompatibilityMatrixForm.tabbedPane, denoptim.gui.CompatibilityMatrixForm.tableCapping, denoptim.gui.CompatibilityMatrixForm.tableFrbEnd, denoptim.gui.CompatibilityMatrixForm.tabModCapping, denoptim.gui.CompatibilityMatrixForm.tabModFrbEnd, denoptim.gui.CompatibilityMatrixForm.txtSearch, denoptim.gui.CompatibilityMatrixForm.updateAPClassCompatibilitiesList(), denoptim.gui.CompatibilityMatrixForm.updateCappingRulesTable(), and denoptim.gui.CompatibilityMatrixForm.updateForbiddenEndsTable().

Here is the call graph for this function:

Member Function Documentation

◆ clearSearchMatches()

void denoptim.gui.CompatibilityMatrixForm.clearSearchMatches ( )
protected

Definition at line 1092 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.panelCPRules.

Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.searchAPClass().

Here is the caller graph for this function:

◆ importAllAPClassesFromCappingGroupLibs()

void denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCappingGroupLibs ( Set< File >  fragLibs,
boolean  cleanup 
)

Reads all the APClasses found in a list of files.

Parameters
fragLibsthe list of file to inspect.
cleanupset true to cleanup previous listing of APclasses.

Definition at line 1330 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.allAPRules, denoptim.gui.CompatibilityMatrixForm.allCapAPClasses, and denoptim.io.DenoptimIO.readAllAPClasses().

Referenced by denoptim.gui.GUICompatibilityMatrixTab.initialize().

Here is the call graph for this function:
Here is the caller graph for this function:

◆ importAllAPClassesFromCPMatrix()

void denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCPMatrix ( boolean  cleanup)
private

Reads all the APClasses found in the currently loaded compatibility matrix.

Parameters
cleanupset true to cleanup previous listing of APclasses.

Definition at line 1278 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.allAPClasses, denoptim.gui.CompatibilityMatrixForm.allAPRules, and denoptim.gui.CompatibilityMatrixForm.compatMap.

Referenced by denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile().

Here is the caller graph for this function:

◆ importAllAPClassesFromFragmentLibs()

void denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromFragmentLibs ( Set< File >  fragLibs,
boolean  cleanup 
)

Reads all the APClasses found in a list of files.

Parameters
fragLibsthe list of file to inspect.
cleanupset true to cleanup previous listing of APclasses.

Definition at line 1363 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.allAPClasses, denoptim.gui.CompatibilityMatrixForm.allAPRules, and denoptim.io.DenoptimIO.readAllAPClasses().

Referenced by denoptim.gui.GUICompatibilityMatrixTab.initialize().

Here is the call graph for this function:
Here is the caller graph for this function:

◆ importAllCappingGroupsAPClassesFromCPMatrix()

void denoptim.gui.CompatibilityMatrixForm.importAllCappingGroupsAPClassesFromCPMatrix ( boolean  cleanup)
private

Reads all the APClasses of capping groups as found in the currently loaded capping rules.

Parameters
cleanupset true to cleanup previous listing of APclasses.

Definition at line 1307 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.allAPClasses, denoptim.gui.CompatibilityMatrixForm.allAPRules, denoptim.gui.CompatibilityMatrixForm.allCapAPClasses, and denoptim.gui.CompatibilityMatrixForm.cappingMap.

Referenced by denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile().

Here is the caller graph for this function:

◆ importCPMapFromFile()

◆ searchAPClass()

void denoptim.gui.CompatibilityMatrixForm.searchAPClass ( String  query)
protected

Definition at line 1105 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.btnClearMatch, denoptim.gui.CompatibilityMatrixForm.clearSearchMatches(), denoptim.gui.CompatibilityMatrixForm.matchCounter, denoptim.gui.CompatibilityMatrixForm.panelCPRules, and denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.renderIfMatches().

Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().

Here is the call graph for this function:
Here is the caller graph for this function:

◆ updateAPClassCompatibilitiesList()

void denoptim.gui.CompatibilityMatrixForm.updateAPClassCompatibilitiesList ( )
private

◆ updateCappingRulesTable()

void denoptim.gui.CompatibilityMatrixForm.updateCappingRulesTable ( )
private

Definition at line 1222 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.cappingMap, and denoptim.gui.CompatibilityMatrixForm.tabModCapping.

Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile().

Here is the caller graph for this function:

◆ updateForbiddenEndsTable()

void denoptim.gui.CompatibilityMatrixForm.updateForbiddenEndsTable ( )
private

Definition at line 1247 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.forbiddenEndList, and denoptim.gui.CompatibilityMatrixForm.tabModFrbEnd.

Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile().

Here is the caller graph for this function:

◆ writeCopatibilityMatrixFile()

void denoptim.gui.CompatibilityMatrixForm.writeCopatibilityMatrixFile ( JComponent  parent,
File  outFile 
)

Writes all the compatibility matrix data to the given file.

this methods writes all data, that is, compatibility rules, APClass-to- bond type, capping rules, and definition of forbidden ends.

Parameters
parentthe component to which the dialog should be bound.
outFilewhere to write

Definition at line 1183 of file CompatibilityMatrixForm.java.

References denoptim.gui.CompatibilityMatrixForm.cappingMap, denoptim.gui.CompatibilityMatrixForm.compatMap, denoptim.gui.CompatibilityMatrixForm.forbiddenEndList, and denoptim.io.DenoptimIO.writeCompatibilityMatrix().

Referenced by denoptim.gui.GUICompatibilityMatrixTab.initialize().

Here is the call graph for this function:
Here is the caller graph for this function:

Member Data Documentation

◆ allAPClasses

◆ allAPClsInCPMap

SortedSet<APClass> denoptim.gui.CompatibilityMatrixForm.allAPClsInCPMap = new TreeSet<APClass>()
private

◆ allAPRules

◆ allCapAPClasses

SortedSet<APClass> denoptim.gui.CompatibilityMatrixForm.allCapAPClasses = new TreeSet<APClass>()
private

List of APClasses of capping groups.

These can be found in a fragment space or collected from the capping group library

Definition at line 100 of file CompatibilityMatrixForm.java.

Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCappingGroupLibs(), and denoptim.gui.CompatibilityMatrixForm.importAllCappingGroupsAPClassesFromCPMatrix().

◆ btnAddCapping

JButton denoptim.gui.CompatibilityMatrixForm.btnAddCapping
private

◆ btnAddCompRul

JButton denoptim.gui.CompatibilityMatrixForm.btnAddCompRul
private

◆ btnAddFrbEnd

JButton denoptim.gui.CompatibilityMatrixForm.btnAddFrbEnd
private

◆ btnClearMatch

JButton denoptim.gui.CompatibilityMatrixForm.btnClearMatch
private

◆ btnCopyCompRul

JButton denoptim.gui.CompatibilityMatrixForm.btnCopyCompRul
private

◆ btnDelCapping

JButton denoptim.gui.CompatibilityMatrixForm.btnDelCapping
private

◆ btnDelCompRul

JButton denoptim.gui.CompatibilityMatrixForm.btnDelCompRul
private

◆ btnDelFrbEnd

JButton denoptim.gui.CompatibilityMatrixForm.btnDelFrbEnd
private

◆ btnHelpCapping

JButton denoptim.gui.CompatibilityMatrixForm.btnHelpCapping
private

◆ btnHelpCPMap

JButton denoptim.gui.CompatibilityMatrixForm.btnHelpCPMap
private

◆ btnHelpFrbEnd

JButton denoptim.gui.CompatibilityMatrixForm.btnHelpFrbEnd
private

◆ btnSortCapping

JButton denoptim.gui.CompatibilityMatrixForm.btnSortCapping
private

◆ btnSortFrbEnd

JButton denoptim.gui.CompatibilityMatrixForm.btnSortFrbEnd
private

◆ cappingMap

HashMap<APClass, APClass> denoptim.gui.CompatibilityMatrixForm.cappingMap
private

◆ compatMap

◆ forbiddenEndList

HashSet<APClass> denoptim.gui.CompatibilityMatrixForm.forbiddenEndList = new HashSet<APClass>()
private

◆ matchCounter

JLabel denoptim.gui.CompatibilityMatrixForm.matchCounter
private

◆ panelCapping

JPanel denoptim.gui.CompatibilityMatrixForm.panelCapping
private

◆ panelCPMap

JPanel denoptim.gui.CompatibilityMatrixForm.panelCPMap
private

◆ panelCPRules

◆ panelFrbEnd

JPanel denoptim.gui.CompatibilityMatrixForm.panelFrbEnd
private

◆ REMOVETRGAPC

final String denoptim.gui.CompatibilityMatrixForm.REMOVETRGAPC = "REMOVETRGAPC"
staticprotected

◆ scrollPanelCPMap

JScrollPane denoptim.gui.CompatibilityMatrixForm.scrollPanelCPMap
private

◆ serialVersionUID

final long denoptim.gui.CompatibilityMatrixForm.serialVersionUID = -8042143358823563589L
staticprivate

Version UID.

Definition at line 75 of file CompatibilityMatrixForm.java.

◆ tabbedPane

JTabbedPane denoptim.gui.CompatibilityMatrixForm.tabbedPane
private

◆ tableCapping

JTable denoptim.gui.CompatibilityMatrixForm.tableCapping
private

◆ tableFrbEnd

JTable denoptim.gui.CompatibilityMatrixForm.tableFrbEnd
private

◆ tabModCapping

DefaultTableModel denoptim.gui.CompatibilityMatrixForm.tabModCapping
private

◆ tabModFrbEnd

DefaultTableModel denoptim.gui.CompatibilityMatrixForm.tabModFrbEnd
private

◆ txtSearch

JTextField denoptim.gui.CompatibilityMatrixForm.txtSearch
private

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