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DENOPTIM
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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< APClass > | allAPClasses = new TreeSet<APClass>() |
List of all APClasses. More... | |
SortedSet< String > | allAPRules = new TreeSet<String>() |
List of all APRules. More... | |
SortedSet< APClass > | allCapAPClasses = new TreeSet<APClass>() |
List of APClasses of capping groups. More... | |
SortedSet< APClass > | allAPClsInCPMap = 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, APClass > | cappingMap |
Data structure that stores the AP-classes to be used to cap unused APS on the growing molecule. More... | |
HashSet< APClass > | forbiddenEndList = 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... | |
Definition at line 70 of file CompatibilityMatrixForm.java.
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().
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Definition at line 1092 of file CompatibilityMatrixForm.java.
References denoptim.gui.CompatibilityMatrixForm.panelCPRules.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.searchAPClass().
void denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCappingGroupLibs | ( | Set< File > | fragLibs, |
boolean | cleanup | ||
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Reads all the APClasses found in a list of files.
fragLibs | the list of file to inspect. |
cleanup | set 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().
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Reads all the APClasses found in the currently loaded compatibility matrix.
cleanup | set 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().
void denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromFragmentLibs | ( | Set< File > | fragLibs, |
boolean | cleanup | ||
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Reads all the APClasses found in a list of files.
fragLibs | the list of file to inspect. |
cleanup | set 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().
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Reads all the APClasses of capping groups as found in the currently loaded capping rules.
cleanup | set 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().
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Definition at line 1139 of file CompatibilityMatrixForm.java.
References denoptim.gui.CompatibilityMatrixForm.allAPClsInCPMap, denoptim.gui.CompatibilityMatrixForm.cappingMap, denoptim.gui.CompatibilityMatrixForm.compatMap, denoptim.gui.CompatibilityMatrixForm.forbiddenEndList, denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCPMatrix(), denoptim.gui.CompatibilityMatrixForm.importAllCappingGroupsAPClassesFromCPMatrix(), denoptim.io.DenoptimIO.readCompatibilityMatrix(), denoptim.gui.CompatibilityMatrixForm.updateAPClassCompatibilitiesList(), denoptim.gui.CompatibilityMatrixForm.updateCappingRulesTable(), and denoptim.gui.CompatibilityMatrixForm.updateForbiddenEndsTable().
Referenced by denoptim.gui.GUICompatibilityMatrixTab.importCPMapFromFile(), and denoptim.gui.GUICompatibilityMatrixTab.initialize().
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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().
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Definition at line 1201 of file CompatibilityMatrixForm.java.
References denoptim.gui.CompatibilityMatrixForm.allAPClsInCPMap, and denoptim.gui.CompatibilityMatrixForm.panelCPRules.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile(), and denoptim.gui.CompatibilityMatrixForm.TrgRemovalListener.propertyChange().
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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().
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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().
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.
parent | the component to which the dialog should be bound. |
outFile | where 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().
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List of all APClasses.
These can be found in a fragment space or collected from fragment libraries
Definition at line 87 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCPMatrix(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromFragmentLibs(), and denoptim.gui.CompatibilityMatrixForm.importAllCappingGroupsAPClassesFromCPMatrix().
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Sorted list of APClasses in the map of compatibility rules.
Definition at line 105 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile(), and denoptim.gui.CompatibilityMatrixForm.updateAPClassCompatibilitiesList().
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List of all APRules.
This list can be edited by creating/removing an APRule or by creating/removing an APClass.
Definition at line 93 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCappingGroupLibs(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCPMatrix(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromFragmentLibs(), and denoptim.gui.CompatibilityMatrixForm.importAllCappingGroupsAPClassesFromCPMatrix().
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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().
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Definition at line 142 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 129 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 150 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 132 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.searchAPClass().
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Definition at line 131 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 143 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 130 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 151 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 145 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 133 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 153 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 144 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 152 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
Data structure that stores the AP-classes to be used to cap unused APS on the growing molecule.
Definition at line 118 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.importAllCappingGroupsAPClassesFromCPMatrix(), denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile(), denoptim.gui.CompatibilityMatrixForm.updateCappingRulesTable(), and denoptim.gui.CompatibilityMatrixForm.writeCopatibilityMatrixFile().
Data structure that stored the true entries of the attachment point classes compatibility matrix.
Definition at line 111 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), denoptim.gui.CompatibilityMatrixForm.importAllAPClassesFromCPMatrix(), denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile(), denoptim.gui.CompatibilityMatrixForm.TrgRemovalListener.propertyChange(), and denoptim.gui.CompatibilityMatrixForm.writeCopatibilityMatrixFile().
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Data structure that stores AP classes that cannot be held unused.
Definition at line 124 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.importCPMapFromFile(), denoptim.gui.CompatibilityMatrixForm.updateForbiddenEndsTable(), and denoptim.gui.CompatibilityMatrixForm.writeCopatibilityMatrixFile().
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Definition at line 137 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.searchAPClass().
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Definition at line 139 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 128 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 134 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.clearSearchMatches(), denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), denoptim.gui.CompatibilityMatrixForm.searchAPClass(), and denoptim.gui.CompatibilityMatrixForm.updateAPClassCompatibilitiesList().
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Definition at line 147 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Property used to trigger removal of a target APClass.
Definition at line 80 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityRuleLine.CompatibilityRuleLine(), and denoptim.gui.CompatibilityMatrixForm.TargetAPClassToken.TargetAPClassToken().
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Definition at line 135 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Version UID.
Definition at line 75 of file CompatibilityMatrixForm.java.
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Definition at line 126 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 141 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 149 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().
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Definition at line 140 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.updateCappingRulesTable().
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Definition at line 148 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm(), and denoptim.gui.CompatibilityMatrixForm.updateForbiddenEndsTable().
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Definition at line 136 of file CompatibilityMatrixForm.java.
Referenced by denoptim.gui.CompatibilityMatrixForm.CompatibilityMatrixForm().