public class ModifyCellDesignerNotes
extends java.lang.Object
Modifier and Type | Class and Description |
---|---|
class |
ModifyCellDesignerNotes.AnnotationSection |
Modifier and Type | Field and Description |
---|---|
boolean |
allannotations |
java.lang.String |
comments |
boolean |
formatAnnotation |
boolean |
generateReadableNamesForReactionsAndSpecies |
boolean |
guessIdentifiers |
boolean |
insertMapsTagBeforeModules |
boolean |
markMissingInformation |
java.lang.String |
moduleGMTFileName |
boolean |
moveNonannotatedTextToReferenceSection |
boolean |
overwriteModuleSection |
boolean |
removeEmptySections |
boolean |
removeInvalidTags |
SbmlDocument |
sbmlDoc |
java.lang.String[] |
tags |
boolean |
useHUGOIdsForModuleIdentification |
boolean |
verbose |
Constructor and Description |
---|
ModifyCellDesignerNotes() |
Modifier and Type | Method and Description |
---|---|
void |
addModuleNames(java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> secs,
java.lang.String entityName,
java.lang.String id) |
void |
automaticallyProcessNotes() |
java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> |
divideInSections(java.lang.String annot) |
java.lang.String |
exportCellDesignerNotes() |
void |
fillIdentifiers(ModifyCellDesignerNotes.AnnotationSection identifiers,
java.lang.String entityName) |
static java.util.Vector<java.lang.String> |
findStringInVectorBySubstring(java.util.Vector<java.lang.String> v,
java.lang.String s) |
static ModifyCellDesignerNotes.AnnotationSection |
getSectionByName(java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> v,
java.lang.String name) |
static java.lang.String |
guessPMIDIds(java.lang.String annot) |
void |
insertMapsTagBeforeModuleTag(java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> secs) |
static void |
main(java.lang.String[] args) |
void |
ModifyCellDesignerNotes() |
java.lang.String |
processAnnotations(java.lang.String annot,
java.lang.String entityName,
java.lang.String id,
java.lang.String[] reqsections,
boolean _guessIdentifiers) |
java.lang.String |
processAnnotations(java.lang.String annot,
java.lang.String entityName,
java.lang.String id,
java.lang.String[] reqsections,
boolean _guessIdentifiers,
java.lang.StringBuffer _newnonannotated,
java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> _secs) |
void |
synchronizeAnnotations(ModifyCellDesignerNotes global) |
void |
synchronizeSections(java.lang.String id,
java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> secs) |
public SbmlDocument sbmlDoc
public java.lang.String comments
public java.lang.String moduleGMTFileName
public boolean useHUGOIdsForModuleIdentification
public boolean overwriteModuleSection
public boolean allannotations
public boolean formatAnnotation
public boolean guessIdentifiers
public boolean removeEmptySections
public boolean removeInvalidTags
public boolean moveNonannotatedTextToReferenceSection
public boolean insertMapsTagBeforeModules
public boolean markMissingInformation
public boolean verbose
public boolean generateReadableNamesForReactionsAndSpecies
public java.lang.String[] tags
public static ModifyCellDesignerNotes.AnnotationSection getSectionByName(java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> v, java.lang.String name)
public static void main(java.lang.String[] args)
public void automaticallyProcessNotes()
public void ModifyCellDesignerNotes() throws java.lang.Exception
java.lang.Exception
public java.lang.String exportCellDesignerNotes() throws java.lang.Exception
java.lang.Exception
public java.lang.String processAnnotations(java.lang.String annot, java.lang.String entityName, java.lang.String id, java.lang.String[] reqsections, boolean _guessIdentifiers)
public java.lang.String processAnnotations(java.lang.String annot, java.lang.String entityName, java.lang.String id, java.lang.String[] reqsections, boolean _guessIdentifiers, java.lang.StringBuffer _newnonannotated, java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> _secs)
public void fillIdentifiers(ModifyCellDesignerNotes.AnnotationSection identifiers, java.lang.String entityName)
public static java.util.Vector<java.lang.String> findStringInVectorBySubstring(java.util.Vector<java.lang.String> v, java.lang.String s)
public java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> divideInSections(java.lang.String annot)
public static java.lang.String guessPMIDIds(java.lang.String annot)
public void addModuleNames(java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> secs, java.lang.String entityName, java.lang.String id)
public void insertMapsTagBeforeModuleTag(java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> secs)
public void synchronizeAnnotations(ModifyCellDesignerNotes global) throws java.lang.Exception
java.lang.Exception
public void synchronizeSections(java.lang.String id, java.util.Vector<ModifyCellDesignerNotes.AnnotationSection> secs)