java.lang.Object
AbstractDataAdapter
org.bdgp.apps.dagedit.dataadapter.GOFlatFileAdapter
- All Implemented Interfaces:
- DEDataAdapterI
- public class GOFlatFileAdapter
- extends AbstractDataAdapter
- implements DEDataAdapterI
|
Method Summary |
protected void |
addPath(java.lang.String path)
|
void |
checkParentage(java.util.Hashtable allterms,
java.util.Vector parentageList,
java.net.URL filename)
|
protected static boolean |
contains(org.bdgp.apps.dagedit.datamodel.Term a,
org.bdgp.apps.dagedit.datamodel.Term b)
|
private static boolean |
contains(org.bdgp.apps.dagedit.datamodel.Term a,
org.bdgp.apps.dagedit.datamodel.Term b,
java.util.Hashtable lookedAt)
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protected int |
countLeadingSpaces(java.lang.String line)
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void |
delegateToIDAdapter(DEDataAdapterI idAdapter)
|
protected void |
discardParentageTokens(GOToken typeToken,
java.lang.String id,
Queue tokens)
|
protected java.lang.String |
escape(java.lang.String text)
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protected static java.lang.String |
escapeDefText(java.lang.String def)
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void |
exportTerms(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Vector relationshipTypes,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType,
boolean showPathToRoot)
|
private int |
findStartOfDefFieldData(java.lang.String in)
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org.bdgp.apps.dagedit.datamodel.Term |
findTermInHash(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Hashtable hash)
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protected java.lang.String |
formatSynonym(org.bdgp.apps.dagedit.datamodel.Synonym syn)
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protected java.lang.String |
formatSynonymForID(org.bdgp.apps.dagedit.datamodel.Synonym syn)
|
boolean |
getAllowCycles()
|
boolean |
getAllowDangling()
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protected java.lang.String |
getCharForRelationship(org.bdgp.apps.dagedit.datamodel.TermRelationship tr)
|
protected java.lang.String |
getCharForRelationship(org.bdgp.apps.dagedit.datamodel.TermRelationshipType type)
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protected java.lang.String |
getDbxrefString(org.bdgp.apps.dagedit.datamodel.Term term)
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protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType |
getDefaultTermRelationship()
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org.bdgp.apps.dagedit.datamodel.TermRelationshipType |
getDefaultType()
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protected static java.util.Hashtable |
getDefaultTypeBindings()
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java.util.Vector |
getHistories()
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java.lang.String[] |
getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int length,
int count)
|
java.lang.String[] |
getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int min,
int max,
int length,
int count)
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protected int |
getLinesInFile(java.net.URL filename)
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java.lang.String |
getName()
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protected java.lang.String |
getNChars(int n,
char c)
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protected java.lang.String |
getParentString(org.bdgp.apps.dagedit.datamodel.Term term,
org.bdgp.apps.dagedit.datamodel.Term parent)
|
protected Queue |
getQueueForLine(java.net.URL filename,
java.lang.String in,
int lineNum)
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java.util.Vector |
getRelationshipTypes()
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org.bdgp.apps.dagedit.datamodel.DEEditHistory |
getRoot()
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org.bdgp.apps.dagedit.datamodel.Term |
getRoot(java.util.Hashtable allterms)
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java.util.Properties |
getStateInformation()
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IOOperation[] |
getSupportedOperations()
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protected java.lang.String |
getSynonymString(org.bdgp.apps.dagedit.datamodel.Term term,
boolean id)
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java.util.Vector |
getTermCategories()
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protected org.bdgp.apps.dagedit.datamodel.Term |
getTermFromTokens(Queue tokens,
java.net.URL filename,
java.lang.String line,
int lineNum)
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org.bdgp.apps.dagedit.datamodel.Term |
getTerms(java.util.Hashtable allterms,
java.net.URL filename)
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protected java.lang.String |
getTermString(org.bdgp.apps.dagedit.datamodel.DanglingRelationship dr)
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protected java.lang.String |
getTermString(org.bdgp.apps.dagedit.datamodel.Term term)
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java.util.Vector |
getTRsForParentWithID(org.bdgp.apps.dagedit.datamodel.Term child,
java.lang.String id)
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java.lang.String |
getType()
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DataAdapterUI |
getUI(IOOperation op)
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protected java.net.URL |
getURLForPath(java.lang.String path)
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org.bdgp.apps.dagedit.datamodel.Term |
importTerms(org.bdgp.apps.dagedit.datamodel.Term root,
boolean stripIds)
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void |
init()
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void |
init(java.lang.Object params)
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protected boolean |
isComment(java.lang.String in)
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protected boolean |
isNextItemID(Queue tokens)
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static boolean |
isReservedCharacter(char c)
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static void |
main(java.lang.String[] args)
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protected org.bdgp.apps.dagedit.datamodel.Term |
parseLine(java.net.URL filename,
java.lang.String line,
int lineNum)
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void |
populateDefinitions(java.util.Hashtable allterms,
java.net.URL filename)
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protected static void |
println(java.io.PrintStream stream)
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protected static void |
println(java.io.PrintStream stream,
java.lang.String string)
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protected GOFlatFileAdapter.IDWrapper |
pullOffID(Queue tokens,
CompoundGOFlatFileParseException exList)
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protected java.util.Vector |
pullOffIDList(Queue tokens)
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protected java.lang.String |
pullOffTerm(Queue tokens)
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protected java.lang.String |
pullOffType(Queue tokens)
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protected java.lang.String |
pullOffValues(Queue tokens)
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void |
putTermInHash(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Hashtable hash)
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void |
setAllowCycles(boolean allowCycles)
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void |
setAllowDangling(boolean allowDangling)
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void |
setCharTypeMappings(java.util.Hashtable charToType,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType)
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void |
setComment(java.lang.String comment)
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protected void |
setDefinition(GOFlatFileAdapter.IDWrapper id,
java.util.Hashtable terms,
java.lang.String definition,
java.lang.String comment,
java.util.Vector refs,
CompoundGOFlatFileParseException defExceptions,
java.net.URL filename,
java.lang.String startline,
int startlineNumber)
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void |
setDefinitionPath(java.lang.String defFilename)
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void |
setHideDownstream(boolean hide)
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void |
setPath(java.lang.String filename)
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void |
setPath(java.util.Vector filenames)
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void |
setReduceSize(boolean reduceSize)
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void |
setStateInformation(java.util.Properties props)
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void |
setStrictDefinition(boolean strict)
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void |
setStrictParentage(boolean strict)
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void |
setUseLegacyTypes(boolean useLegacyTypes)
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protected static java.lang.String |
unescapeDefText(java.lang.String def)
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boolean |
useLegacyTypes()
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private void |
wipeOutIDs(org.bdgp.apps.dagedit.datamodel.Term term)
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org.bdgp.apps.dagedit.datamodel.DEEditHistory |
write(org.bdgp.apps.dagedit.datamodel.DEEditHistory history)
|
void |
write(java.lang.String filename,
java.lang.String defFilename,
org.bdgp.apps.dagedit.datamodel.Term root,
java.util.Vector relationshipTypes,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType)
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protected void |
writeDef(java.io.PrintStream stream,
org.bdgp.apps.dagedit.datamodel.Term term)
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void |
writeDefinitions(org.bdgp.apps.dagedit.datamodel.Term root)
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protected void |
writeDefs(java.lang.String filename,
java.io.PrintStream stream,
org.bdgp.apps.dagedit.datamodel.Term root)
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protected void |
writeHeader(org.bdgp.apps.dagedit.datamodel.Term root,
java.util.Vector relationshipTypes,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType,
java.io.PrintStream stream)
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protected void |
writeLineForTerm(java.io.PrintStream stream,
int spaceDepth,
java.lang.String leaderChar,
org.bdgp.apps.dagedit.datamodel.Term term,
org.bdgp.apps.dagedit.datamodel.Term currentParent,
boolean treatAsRoot)
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protected void |
writeTerm(java.lang.String filename,
java.io.PrintStream stream,
int spaceDepth,
java.lang.String leaderChar,
org.bdgp.apps.dagedit.datamodel.Term term,
org.bdgp.apps.dagedit.datamodel.Term currentParent,
boolean treatAsRoot,
java.util.Hashtable lookedAt,
int termCount)
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void |
writeTypeLine(org.bdgp.apps.dagedit.datamodel.TermRelationshipType trt,
java.io.PrintStream stream)
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| Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
termStack
java.util.Stack termStack
root
org.bdgp.apps.dagedit.datamodel.Term root
writeRoot
org.bdgp.apps.dagedit.datamodel.Term writeRoot
currentType
java.lang.String currentType
filenames
java.util.Vector filenames
defFilename
java.net.URL defFilename
parentageList
java.util.Vector parentageList
exceptionHolder
CompoundGOFlatFileParseException exceptionHolder
strictParentage
protected boolean strictParentage
strictDefinition
protected boolean strictDefinition
hideDownstream
protected boolean hideDownstream
allowCycles
protected boolean allowCycles
allowDangling
protected boolean allowDangling
idAdapter
private DEDataAdapterI idAdapter
FAILED_TYPE
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType FAILED_TYPE
UNKNOWN_TYPE
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType UNKNOWN_TYPE
defaultType
protected org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType
RESERVED_SYMBOLS
protected static final java.util.Hashtable RESERVED_SYMBOLS
categories
protected java.util.Vector categories
relationshipTypes
protected java.util.Vector relationshipTypes
comment
protected java.lang.String comment
reduceSize
protected boolean reduceSize
useLegacyTypes
protected boolean useLegacyTypes
BOUNDARY_CHAR
public static final char BOUNDARY_CHAR
- See Also:
- Constant Field Values
charToType
java.util.Hashtable charToType
typeToChar
java.util.Hashtable typeToChar
danglingSorter
protected static GOFlatFileAdapter.DanglingSorter danglingSorter
GOFlatFileAdapter
public GOFlatFileAdapter()
isReservedCharacter
public static boolean isReservedCharacter(char c)
setReduceSize
public void setReduceSize(boolean reduceSize)
setComment
public void setComment(java.lang.String comment)
getDefaultTypeBindings
protected static java.util.Hashtable getDefaultTypeBindings()
getDefaultTermRelationship
protected static org.bdgp.apps.dagedit.datamodel.TermRelationshipType getDefaultTermRelationship()
getRelationshipTypes
public java.util.Vector getRelationshipTypes()
- Specified by:
getRelationshipTypes in interface DEDataAdapterI
setAllowCycles
public void setAllowCycles(boolean allowCycles)
getAllowCycles
public boolean getAllowCycles()
setAllowDangling
public void setAllowDangling(boolean allowDangling)
getAllowDangling
public boolean getAllowDangling()
getTermCategories
public java.util.Vector getTermCategories()
throws DataAdapterException
- Specified by:
getTermCategories in interface DEDataAdapterI
setCharTypeMappings
public void setCharTypeMappings(java.util.Hashtable charToType,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType)
setHideDownstream
public void setHideDownstream(boolean hide)
getIDs
public java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int length,
int count)
throws DataAdapterException
- Specified by:
getIDs in interface DEDataAdapterI
getIDs
public java.lang.String[] getIDs(org.bdgp.apps.dagedit.datamodel.Term root,
org.bdgp.apps.dagedit.datamodel.Term term,
java.lang.String prefix,
int min,
int max,
int length,
int count)
throws DataAdapterException
- Specified by:
getIDs in interface DEDataAdapterI
getHistories
public java.util.Vector getHistories()
throws DataAdapterException
- Specified by:
getHistories in interface DEDataAdapterI
setStrictParentage
public void setStrictParentage(boolean strict)
setStrictDefinition
public void setStrictDefinition(boolean strict)
getUI
public DataAdapterUI getUI(IOOperation op)
main
public static void main(java.lang.String[] args)
throws java.lang.Exception
setDefinition
protected void setDefinition(GOFlatFileAdapter.IDWrapper id,
java.util.Hashtable terms,
java.lang.String definition,
java.lang.String comment,
java.util.Vector refs,
CompoundGOFlatFileParseException defExceptions,
java.net.URL filename,
java.lang.String startline,
int startlineNumber)
throws DataAdapterException
populateDefinitions
public void populateDefinitions(java.util.Hashtable allterms,
java.net.URL filename)
throws DataAdapterException
findStartOfDefFieldData
private int findStartOfDefFieldData(java.lang.String in)
init
public void init()
setPath
public void setPath(java.lang.String filename)
setPath
public void setPath(java.util.Vector filenames)
addPath
protected void addPath(java.lang.String path)
getURLForPath
protected java.net.URL getURLForPath(java.lang.String path)
setDefinitionPath
public void setDefinitionPath(java.lang.String defFilename)
getLinesInFile
protected int getLinesInFile(java.net.URL filename)
throws java.io.IOException
importTerms
public org.bdgp.apps.dagedit.datamodel.Term importTerms(org.bdgp.apps.dagedit.datamodel.Term root,
boolean stripIds)
throws DataAdapterException
wipeOutIDs
private void wipeOutIDs(org.bdgp.apps.dagedit.datamodel.Term term)
getRoot
public org.bdgp.apps.dagedit.datamodel.DEEditHistory getRoot()
throws DataAdapterException
- Specified by:
getRoot in interface DEDataAdapterI
getRoot
public org.bdgp.apps.dagedit.datamodel.Term getRoot(java.util.Hashtable allterms)
throws DataAdapterException
println
protected static void println(java.io.PrintStream stream)
println
protected static void println(java.io.PrintStream stream,
java.lang.String string)
checkParentage
public void checkParentage(java.util.Hashtable allterms,
java.util.Vector parentageList,
java.net.URL filename)
throws DataAdapterException
contains
protected static boolean contains(org.bdgp.apps.dagedit.datamodel.Term a,
org.bdgp.apps.dagedit.datamodel.Term b)
contains
private static boolean contains(org.bdgp.apps.dagedit.datamodel.Term a,
org.bdgp.apps.dagedit.datamodel.Term b,
java.util.Hashtable lookedAt)
getTRsForParentWithID
public java.util.Vector getTRsForParentWithID(org.bdgp.apps.dagedit.datamodel.Term child,
java.lang.String id)
findTermInHash
public org.bdgp.apps.dagedit.datamodel.Term findTermInHash(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Hashtable hash)
putTermInHash
public void putTermInHash(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Hashtable hash)
getTerms
public org.bdgp.apps.dagedit.datamodel.Term getTerms(java.util.Hashtable allterms,
java.net.URL filename)
throws DataAdapterException
isComment
protected boolean isComment(java.lang.String in)
parseLine
protected org.bdgp.apps.dagedit.datamodel.Term parseLine(java.net.URL filename,
java.lang.String line,
int lineNum)
throws GOFlatFileParseException
getTermFromTokens
protected org.bdgp.apps.dagedit.datamodel.Term getTermFromTokens(Queue tokens,
java.net.URL filename,
java.lang.String line,
int lineNum)
throws GOFlatFileParseException
pullOffValues
protected java.lang.String pullOffValues(Queue tokens)
discardParentageTokens
protected void discardParentageTokens(GOToken typeToken,
java.lang.String id,
Queue tokens)
throws GOFlatFileParseException
pullOffIDList
protected java.util.Vector pullOffIDList(Queue tokens)
throws GOFlatFileParseException
pullOffType
protected java.lang.String pullOffType(Queue tokens)
throws GOFlatFileParseException
pullOffTerm
protected java.lang.String pullOffTerm(Queue tokens)
isNextItemID
protected boolean isNextItemID(Queue tokens)
pullOffID
protected GOFlatFileAdapter.IDWrapper pullOffID(Queue tokens,
CompoundGOFlatFileParseException exList)
throws GOFlatFileParseException
getQueueForLine
protected Queue getQueueForLine(java.net.URL filename,
java.lang.String in,
int lineNum)
throws GOFlatFileParseException
countLeadingSpaces
protected int countLeadingSpaces(java.lang.String line)
getName
public java.lang.String getName()
getType
public java.lang.String getType()
getSupportedOperations
public IOOperation[] getSupportedOperations()
init
public void init(java.lang.Object params)
throws DataAdapterException
write
public org.bdgp.apps.dagedit.datamodel.DEEditHistory write(org.bdgp.apps.dagedit.datamodel.DEEditHistory history)
throws DataAdapterException
- Specified by:
write in interface DEDataAdapterI
exportTerms
public void exportTerms(org.bdgp.apps.dagedit.datamodel.Term term,
java.util.Vector relationshipTypes,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType,
boolean showPathToRoot)
throws DataAdapterException
getDefaultType
public org.bdgp.apps.dagedit.datamodel.TermRelationshipType getDefaultType()
write
public void write(java.lang.String filename,
java.lang.String defFilename,
org.bdgp.apps.dagedit.datamodel.Term root,
java.util.Vector relationshipTypes,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType)
throws DataAdapterException
writeDefinitions
public void writeDefinitions(org.bdgp.apps.dagedit.datamodel.Term root)
throws DataAdapterException
writeDefs
protected void writeDefs(java.lang.String filename,
java.io.PrintStream stream,
org.bdgp.apps.dagedit.datamodel.Term root)
unescapeDefText
protected static java.lang.String unescapeDefText(java.lang.String def)
escapeDefText
protected static java.lang.String escapeDefText(java.lang.String def)
writeDef
protected void writeDef(java.io.PrintStream stream,
org.bdgp.apps.dagedit.datamodel.Term term)
writeHeader
protected void writeHeader(org.bdgp.apps.dagedit.datamodel.Term root,
java.util.Vector relationshipTypes,
org.bdgp.apps.dagedit.datamodel.TermRelationshipType defaultType,
java.io.PrintStream stream)
throws DataAdapterException
writeTypeLine
public void writeTypeLine(org.bdgp.apps.dagedit.datamodel.TermRelationshipType trt,
java.io.PrintStream stream)
throws DataAdapterException
setUseLegacyTypes
public void setUseLegacyTypes(boolean useLegacyTypes)
useLegacyTypes
public boolean useLegacyTypes()
writeTerm
protected void writeTerm(java.lang.String filename,
java.io.PrintStream stream,
int spaceDepth,
java.lang.String leaderChar,
org.bdgp.apps.dagedit.datamodel.Term term,
org.bdgp.apps.dagedit.datamodel.Term currentParent,
boolean treatAsRoot,
java.util.Hashtable lookedAt,
int termCount)
throws DataAdapterException
writeLineForTerm
protected void writeLineForTerm(java.io.PrintStream stream,
int spaceDepth,
java.lang.String leaderChar,
org.bdgp.apps.dagedit.datamodel.Term term,
org.bdgp.apps.dagedit.datamodel.Term currentParent,
boolean treatAsRoot)
getDbxrefString
protected java.lang.String getDbxrefString(org.bdgp.apps.dagedit.datamodel.Term term)
getSynonymString
protected java.lang.String getSynonymString(org.bdgp.apps.dagedit.datamodel.Term term,
boolean id)
formatSynonymForID
protected java.lang.String formatSynonymForID(org.bdgp.apps.dagedit.datamodel.Synonym syn)
formatSynonym
protected java.lang.String formatSynonym(org.bdgp.apps.dagedit.datamodel.Synonym syn)
getParentString
protected java.lang.String getParentString(org.bdgp.apps.dagedit.datamodel.Term term,
org.bdgp.apps.dagedit.datamodel.Term parent)
getCharForRelationship
protected java.lang.String getCharForRelationship(org.bdgp.apps.dagedit.datamodel.TermRelationshipType type)
getCharForRelationship
protected java.lang.String getCharForRelationship(org.bdgp.apps.dagedit.datamodel.TermRelationship tr)
escape
protected java.lang.String escape(java.lang.String text)
delegateToIDAdapter
public void delegateToIDAdapter(DEDataAdapterI idAdapter)
- Specified by:
delegateToIDAdapter in interface DEDataAdapterI
getTermString
protected java.lang.String getTermString(org.bdgp.apps.dagedit.datamodel.Term term)
getTermString
protected java.lang.String getTermString(org.bdgp.apps.dagedit.datamodel.DanglingRelationship dr)
getNChars
protected java.lang.String getNChars(int n,
char c)
getStateInformation
public java.util.Properties getStateInformation()
- Specified by:
getStateInformation in interface DEDataAdapterI
setStateInformation
public void setStateInformation(java.util.Properties props)
- Specified by:
setStateInformation in interface DEDataAdapterI