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SUMMARY: JavaDoc of joelib.io.types.cml.CMLCoreModule JAVADOC | Sourc code of joelib.io.types.cml.CMLCoreModule SOURCE | Download joelib.io.types.cml.CMLCoreModule DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD

joelib.io.types.cml
Class CMLCoreModule  view CMLCoreModule download CMLCoreModule.java

java.lang.Object
  extended byjoelib.io.types.cml.CMLCoreModule
All Implemented Interfaces:
ModuleInterface
Direct Known Subclasses:
CDKConvention, CMLReactionModule
public class CMLCoreModule
extends java.lang.Object
implements ModuleInterface

Core CML 1.x and 2.0 elements are parsed by this class.

Please file a bug report if this parser fails to parse a certain element or attribute value in a valid CML document.

Field Summary
static int ANGLE
           
protected  joelib.io.types.cml.elements.ArrayCML array
           
static int ARRAY
           
protected  java.util.Vector arrays
           
protected  java.lang.String arrayTitle
           
static int ATOM
           
static int ATOMARRAY
           
 java.util.Hashtable atomElements
           
protected  java.util.Vector atomParities
           
static int BOND
           
static int BOND_STEREO
           
protected  java.util.Vector bondARef1
           
protected  java.util.Vector bondARef2
           
static int BONDARRAY
           
protected  java.util.Vector bondid
           
protected  java.util.Vector bondStereo
           
protected  java.lang.String BUILTIN
           
protected  CDOInterface cdo
           
static int COORDINATE2
           
static int COORDINATE3
           
static int CRYSTAL
           
protected  int curRef
           
protected  java.lang.String currentChars
           
protected  int currentElement
           
protected  java.lang.String delimiter
           
static int ELECTRON
           
 java.util.Hashtable elements
           
protected  java.lang.String elementTitle
           
protected  java.util.Vector elid
           
protected  java.util.Vector elsym
           
static int FEATURE
           
static int FLOAT
           
static int FLOATARRAY
           
static int FLOATMATRIX
           
protected  java.util.Vector formalCharges
           
protected  java.util.Vector hCounts
           
static int INTEGER
           
static int INTEGERARRAY
           
protected  java.util.Vector isotopes
           
static int LINK
           
static int LIST
           
private static org.apache.log4j.Category logger
           
protected  java.util.Vector matrices
           
protected  joelib.io.types.cml.elements.MatrixCML matrix
           
static int MATRIX
           
protected  java.lang.String matrixColumns
           
protected  java.lang.String matrixDelimiter
           
protected  java.lang.String matrixRows
           
protected  java.lang.String matrixTitle
           
static int MOLECULE
           
protected  java.lang.String moleculeName
           
static int NAME
           
protected  java.util.Vector order
           
protected  java.util.Vector partialCharges
           
static int REACTION
           
protected  joelib.io.types.cml.elements.ScalarCML scalar
           
static int SCALAR
           
protected  java.util.Vector scalars
           
static int SEQUENCE
           
protected  boolean stereoGiven
           
static int STRING
           
static int STRINGARRAY
           
protected  java.util.Vector strings
           
protected  java.lang.String SYSTEMID
           
static int TORSION
           
static int UNKNOWN
           
protected  java.util.Vector x2
           
protected  java.util.Vector x3
           
protected  java.util.Vector y2
           
protected  java.util.Vector y3
           
protected  java.util.Vector z3
           
 
Constructor Summary
CMLCoreModule(CDOInterface cdo)
           
CMLCoreModule(ModuleInterface conv)
           
 
Method Summary
 void characterData(char[] ch, int start, int length)
           
 void endDocument()
           
 void endElement(java.lang.String uri, java.lang.String name, java.lang.String raw)
           
 void inherit(ModuleInterface convention)
           
private  void initialize()
           
protected  void newMolecule()
           
protected  void notify(java.lang.String message, java.lang.String systemId, int line, int column)
           
 CDOInterface returnCDO()
           
protected  void setCurrentElement(java.lang.String name)
           
 void startDocument()
           
 void startElement(java.lang.String uri, java.lang.String local, java.lang.String raw, org.xml.sax.Attributes atts)
           
protected  void storeData()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

logger

private static org.apache.log4j.Category logger

UNKNOWN

public static final int UNKNOWN
See Also:
Constant Field Values

STRING

public static final int STRING
See Also:
Constant Field Values

LINK

public static final int LINK
See Also:
Constant Field Values

FLOAT

public static final int FLOAT
See Also:
Constant Field Values

INTEGER

public static final int INTEGER
See Also:
Constant Field Values

STRINGARRAY

public static final int STRINGARRAY
See Also:
Constant Field Values

FLOATARRAY

public static final int FLOATARRAY
See Also:
Constant Field Values

INTEGERARRAY

public static final int INTEGERARRAY
See Also:
Constant Field Values

FLOATMATRIX

public static final int FLOATMATRIX
See Also:
Constant Field Values

COORDINATE2

public static final int COORDINATE2
See Also:
Constant Field Values

COORDINATE3

public static final int COORDINATE3
See Also:
Constant Field Values

ANGLE

public static final int ANGLE
See Also:
Constant Field Values

TORSION

public static final int TORSION
See Also:
Constant Field Values

LIST

public static final int LIST
See Also:
Constant Field Values

MOLECULE

public static final int MOLECULE
See Also:
Constant Field Values

ATOM

public static final int ATOM
See Also:
Constant Field Values

ATOMARRAY

public static final int ATOMARRAY
See Also:
Constant Field Values

BOND

public static final int BOND
See Also:
Constant Field Values

BONDARRAY

public static final int BONDARRAY
See Also:
Constant Field Values

ELECTRON

public static final int ELECTRON
See Also:
Constant Field Values

REACTION

public static final int REACTION
See Also:
Constant Field Values

CRYSTAL

public static final int CRYSTAL
See Also:
Constant Field Values

SEQUENCE

public static final int SEQUENCE
See Also:
Constant Field Values

FEATURE

public static final int FEATURE
See Also:
Constant Field Values

MATRIX

public static final int MATRIX
See Also:
Constant Field Values

ARRAY

public static final int ARRAY
See Also:
Constant Field Values

SCALAR

public static final int SCALAR
See Also:
Constant Field Values

BOND_STEREO

public static final int BOND_STEREO
See Also:
Constant Field Values

NAME

public static final int NAME
See Also:
Constant Field Values

atomElements

public java.util.Hashtable atomElements

elements

public java.util.Hashtable elements

SYSTEMID

protected final java.lang.String SYSTEMID
See Also:
Constant Field Values

array

protected joelib.io.types.cml.elements.ArrayCML array

cdo

protected CDOInterface cdo

matrix

protected joelib.io.types.cml.elements.MatrixCML matrix

scalar

protected joelib.io.types.cml.elements.ScalarCML scalar

BUILTIN

protected java.lang.String BUILTIN

arrayTitle

protected java.lang.String arrayTitle

currentChars

protected java.lang.String currentChars

delimiter

protected java.lang.String delimiter

elementTitle

protected java.lang.String elementTitle

matrixColumns

protected java.lang.String matrixColumns

matrixDelimiter

protected java.lang.String matrixDelimiter

matrixRows

protected java.lang.String matrixRows

matrixTitle

protected java.lang.String matrixTitle

moleculeName

protected java.lang.String moleculeName

arrays

protected java.util.Vector arrays

atomParities

protected java.util.Vector atomParities

bondARef1

protected java.util.Vector bondARef1

bondARef2

protected java.util.Vector bondARef2

bondStereo

protected java.util.Vector bondStereo

bondid

protected java.util.Vector bondid

elid

protected java.util.Vector elid

elsym

protected java.util.Vector elsym

formalCharges

protected java.util.Vector formalCharges

hCounts

protected java.util.Vector hCounts

isotopes

protected java.util.Vector isotopes

matrices

protected java.util.Vector matrices

order

protected java.util.Vector order

partialCharges

protected java.util.Vector partialCharges

scalars

protected java.util.Vector scalars

strings

protected java.util.Vector strings

x2

protected java.util.Vector x2

x3

protected java.util.Vector x3

y2

protected java.util.Vector y2

y3

protected java.util.Vector y3

z3

protected java.util.Vector z3

stereoGiven

protected boolean stereoGiven

curRef

protected int curRef

currentElement

protected int currentElement
Constructor Detail

CMLCoreModule

public CMLCoreModule(CDOInterface cdo)

CMLCoreModule

public CMLCoreModule(ModuleInterface conv)
Method Detail

characterData

public void characterData(char[] ch,
                          int start,
                          int length)
Specified by:
characterData in interface ModuleInterface

endDocument

public void endDocument()
Specified by:
endDocument in interface ModuleInterface

endElement

public void endElement(java.lang.String uri,
                       java.lang.String name,
                       java.lang.String raw)
Specified by:
endElement in interface ModuleInterface

inherit

public void inherit(ModuleInterface convention)
Specified by:
inherit in interface ModuleInterface

returnCDO

public CDOInterface returnCDO()
Specified by:
returnCDO in interface ModuleInterface

startDocument

public void startDocument()
Specified by:
startDocument in interface ModuleInterface

startElement

public void startElement(java.lang.String uri,
                         java.lang.String local,
                         java.lang.String raw,
                         org.xml.sax.Attributes atts)
Specified by:
startElement in interface ModuleInterface

setCurrentElement

protected void setCurrentElement(java.lang.String name)

newMolecule

protected void newMolecule()

notify

protected void notify(java.lang.String message,
                      java.lang.String systemId,
                      int line,
                      int column)

storeData

protected void storeData()

initialize

private void initialize()
Overview  Package   Class  Use  Deprecated  Index 
Home >> All >> joelib >> io >> types >> [ cml overview ]  PREV CLASS  NEXT CLASS
SUMMARY: JavaDoc of joelib.io.types.cml.CMLCoreModule JAVADOC | Sourc code of joelib.io.types.cml.CMLCoreModule SOURCE | Download joelib.io.types.cml.CMLCoreModule DOWNLOAD | NESTED | FIELD | CONSTR | METHOD DETAIL: FIELD | CONSTR | METHOD