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org.xmlcml.noncml
Class NonCMLDocumentImpl  

java.lang.Object
  PMRDocumentImpl
      org.xmlcml.cmlimpl.CMLDocumentImpl
          org.xmlcml.noncml.NonCMLDocumentImpl

All Implemented Interfaces:

org.xmlcml.cml.CMLDocument, org.w3c.dom.Document, org.xmlcml.cml.mvc.HasController, org.w3c.dom.Node, NonCMLDocument

Direct Known Subclasses:

CASTEPImpl, CIFImpl, DummyImpl, FormatImpl, G94Impl, GAMESSImpl, JCAMPImpl, JMEImpl, MDLMolImpl, MOL2Impl, MOPACImpl, MOPACInImpl, PDBConectImpl, PDBImpl, PreStyleImpl, SDFImpl, SMILESImpl, VAMPImpl, XYZImpl

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public abstract class NonCMLDocumentImpl

extends org.xmlcml.cmlimpl.CMLDocumentImpl

implements NonCMLDocument

base class for all nonCML molecules

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Field Summary
static org.xmlcml.cml.CMLAtomFactory	ATOM_FACTORY           creates Atoms of the appropriate subclass
protected  org.xmlcml.cml.AbstractBase	atomParent
protected  java.util.Vector	atomVector           general tools for input and output
static org.xmlcml.cml.CMLBondFactory	BOND_FACTORY           creates Bonds of the appropriate subclass
protected  org.xmlcml.cml.AbstractBase	bondParent
protected  java.util.Vector	bondVector
protected  java.io.BufferedReader	bReader           most input requires a BufferedReader
protected  java.lang.String	convention
protected  java.lang.String	currentLine           and uses a line as the container
static org.xmlcml.cml.CMLDocumentFactory	DOCUMENT_FACTORY           creates Documents of the appropriate subclass
protected  org.xmlcml.cml.CML	inputCML           the CML object created from the input legacy
protected  org.xmlcml.cml.CMLMolecule	inputCMLMolecule           the molecule created from the input legacy
static java.util.Hashtable	inputDescription2TypeTable
protected static org.xmlcml.cml.metadata.CMLDictionary	localDictionary
(package private)  int	markLine
static org.xmlcml.cml.CMLMoleculeFactory	MOLECULE_FACTORY           creates Molecules of the appropriate subclass
protected  int	natoms
protected  int	nbonds
(package private)  java.lang.String	nextLine
protected  int	nLine
protected  org.xmlcml.cml.CMLDocument	nonCmlDoc           result of a parse
protected  org.xmlcml.cml.CML	outputCML           a CML object to be output as legacy
protected  org.xmlcml.cml.CMLMolecule	outputCMLMolecule           a CML CMLMolecule to be output as legacy
static java.util.Hashtable	outputDescription2TypeTable
(package private) static java.lang.String	parseFile           the current parse script (messy) - not thread-safe! Set this immediately before oarsing legacy file.
protected  Selector	selector
static java.lang.String	SPACE40           crude hacks for traling blanks in fortran
static java.lang.String	SPACE80

 

Fields inherited from class org.xmlcml.cmlimpl.CMLDocumentImpl

CML_DICTIONARY, controller, moleculeVector

 

Fields inherited from interface org.xmlcml.noncml.NonCMLDocument

CASTEP, CIF, CML, CMLARRAY, FORMAT, G94, GAMESS, INPUT_DESCRIPTIONS, INPUT_SUFFIXES, INPUT_TYPES, JCAMP, JME, MDLMOL, MIF, MMCIF, MOL2, MOPAC, MOPACIn, OUTPUT_DESCRIPTIONS, OUTPUT_SUFFIXES, OUTPUT_TYPES, PDB, PDBConect, SDF, SMILES, SWISS, TEST, VAMP, XML, XYZ

 

Fields inherited from interface org.xmlcml.cml.CMLDocument

CML_DICTIONARY_FILENAME, CML_DICTIONARY_NAME, CML_DICTIONARY_NAMESPACE_URI, CML_DICTIONARY_PREFIX, PACKAGE_NAME

 

Fields inherited from interface org.w3c.dom.Node

ATTRIBUTE_NODE, CDATA_SECTION_NODE, COMMENT_NODE, DOCUMENT_FRAGMENT_NODE, DOCUMENT_NODE, DOCUMENT_POSITION_CONTAINED_BY, DOCUMENT_POSITION_CONTAINS, DOCUMENT_POSITION_DISCONNECTED, DOCUMENT_POSITION_FOLLOWING, DOCUMENT_POSITION_IMPLEMENTATION_SPECIFIC, DOCUMENT_POSITION_PRECEDING, DOCUMENT_TYPE_NODE, ELEMENT_NODE, ENTITY_NODE, ENTITY_REFERENCE_NODE, NOTATION_NODE, PROCESSING_INSTRUCTION_NODE, TEXT_NODE

 

Constructor Summary
protected	NonCMLDocumentImpl()

 

Method Summary
void	addDataItem(org.w3c.dom.Element parent, java.lang.String id, java.lang.Object obj)           creates an object of type determined by a dictionary id
static void	convertFile(java.lang.String inFile, java.lang.String inType, java.io.FileWriter fw, java.lang.String outType)
static void	convertList(java.lang.String inList, java.lang.String inType, java.lang.String outDir, java.lang.String outFile, java.lang.String outType)
protected  void	createAndAddCMLElement(java.lang.String convention, java.lang.String id)
void	createAndAddMoleculeElement(java.lang.String convention, java.lang.String id)           create molecule (inputCMLMolecule) *and add as document Element*
static org.xmlcml.cml.CMLDocument	createCMLDocument(java.lang.String type)           create from file and subclass using SAX; the default CMLDOMSAXBuilder determines the subclassing
static org.xmlcml.cml.CMLDocument	createCMLDocument(java.net.URL url)           Convenience method - uses defaults to create a CMLDocument from the input URL.
static org.xmlcml.cml.CMLDocument	createCMLDocument(java.net.URL urlx, java.lang.String type)           Convenience method - uses defaults to create a CMLDocument from the input URL.
protected  void	createCMLElement(java.lang.String convention, java.lang.String id)
void	createMoleculeElement(java.lang.String convention, java.lang.String id)           Create a molecule of given convention and id; convention is e.g.
protected  void	getAndCheckVectors()
(package private)  java.lang.String	getCurrentLine()
static org.xmlcml.cml.metadata.CMLDictionary	getDictionary(org.xmlcml.cmlimpl.CMLDocumentImpl doc)
static java.lang.String[]	getInputDescriptions()           get allowed file suffixes
static java.lang.String[][]	getInputSuffixes()           get allowed file suffixes
static java.lang.String[]	getInputTypes()           get allowed file types
static java.util.Vector	getMoleculeVector(java.lang.String inputFile, java.lang.String type)           creates a nonCMLDocument from the input URL.
static java.lang.String[]	getOutputDescriptions()           get allowed file suffixes
static java.lang.String[]	getOutputSuffixes()           get allowed file suffixes
static java.lang.String[]	getOutputTypes()           get allowed file types
Selector	getSelector()
static java.lang.String	getSuffixFromType(java.lang.String type)           hardcoded suffixes - probably will be phased out in favout of getTypesFromFile
static java.lang.String	getTypeFromFile(java.lang.String fileName)           hardcoded types - probably will be phased out in favout of getTypesFromFile
static java.lang.String[]	getTypesFromFile(java.lang.String fileName)           gives all possible types which have the suffix on fileName.
static void	main(java.lang.String[] args)
org.xmlcml.cml.AbstractBase	makeDataItem(org.xmlcml.cml.metadata.CMLDictionaryEntry entry, java.lang.String value)           creates an object of type determined by a dictionary entry
(package private) static java.lang.String	makeFileStem(java.lang.String file)
static java.lang.String	outform(double v, int f, int d)
abstract  java.lang.String	output(java.io.Writer w)           The main output routine.
abstract  void	parse(java.io.BufferedReader reader)           The main parsing routine.
void	parse(java.net.URL url)           convenience method - routes to bufferedReader
(package private)  java.lang.String	peekLine()
static void	processLinks(org.xmlcml.cml.CMLDocument cmlDoc)
static double	readFortranReal(java.lang.String f)
(package private)  java.lang.String	readNextLine()
(package private)  void	resetMark()
(package private)  void	setMark()
void	setOutputCML(org.xmlcml.cml.CML outputCML)           to output a CML in legacy form - still under development
void	setOutputCMLMolecule(org.xmlcml.cml.CMLMolecule outputCMLMolecule)           to output a CML-CMLMolecule in legacy form the molecule must be added to the NonCMLDocument and then the output() method called
static void	setParseFile(java.lang.String f)           set the parse file - use null to reset it
void	setSelector(Selector selector)

 

Methods inherited from class org.xmlcml.cmlimpl.CMLDocumentImpl

addTracer, arrayify, createCMLDocument, deArrayify, debug, debug, dereferenceDescendantLinks, dereferenceLinks, getController, getDictionaryFileName, getDictionaryName, getDictionaryNamespaceURI, getDictionaryPrefix, getMolecule, getMoleculeFactory, getMoleculeList, getMoleculeVector, hasLinkElements, isTrace, readXMLTest, removeTracer, setController, setMoleculeFactory, setTrace, test1, trace

 

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

 

Methods inherited from interface org.xmlcml.cml.CMLDocument

arrayify, deArrayify, debug, debug, dereferenceLinks, getMolecule, getMoleculeFactory, getMoleculeList, getMoleculeVector, hasLinkElements, readXMLTest, setMoleculeFactory

 

Methods inherited from interface org.w3c.dom.Document

adoptNode, createAttribute, createAttributeNS, createCDATASection, createComment, createDocumentFragment, createElement, createElementNS, createEntityReference, createProcessingInstruction, createTextNode, getDoctype, getDocumentElement, getDocumentURI, getDomConfig, getElementById, getElementsByTagName, getElementsByTagNameNS, getImplementation, getInputEncoding, getStrictErrorChecking, getXmlEncoding, getXmlStandalone, getXmlVersion, importNode, normalizeDocument, renameNode, setDocumentURI, setStrictErrorChecking, setXmlStandalone, setXmlVersion

 

Methods inherited from interface org.w3c.dom.Node

appendChild, cloneNode, compareDocumentPosition, getAttributes, getBaseURI, getChildNodes, getFeature, getFirstChild, getLastChild, getLocalName, getNamespaceURI, getNextSibling, getNodeName, getNodeType, getNodeValue, getOwnerDocument, getParentNode, getPrefix, getPreviousSibling, getTextContent, getUserData, hasAttributes, hasChildNodes, insertBefore, isDefaultNamespace, isEqualNode, isSameNode, isSupported, lookupNamespaceURI, lookupPrefix, normalize, removeChild, replaceChild, setNodeValue, setPrefix, setTextContent, setUserData

 

Field Detail

SPACE40

public static final java.lang.String SPACE40

crude hacks for traling blanks in fortran

See Also:

Constant Field Values

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SPACE80

public static final java.lang.String SPACE80

See Also:

Constant Field Values

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localDictionary

protected static org.xmlcml.cml.metadata.CMLDictionary localDictionary

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ATOM_FACTORY

public static final org.xmlcml.cml.CMLAtomFactory ATOM_FACTORY

creates Atoms of the appropriate subclass

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BOND_FACTORY

public static final org.xmlcml.cml.CMLBondFactory BOND_FACTORY

creates Bonds of the appropriate subclass

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DOCUMENT_FACTORY

public static final org.xmlcml.cml.CMLDocumentFactory DOCUMENT_FACTORY

creates Documents of the appropriate subclass

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MOLECULE_FACTORY

public static final org.xmlcml.cml.CMLMoleculeFactory MOLECULE_FACTORY

creates Molecules of the appropriate subclass

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parseFile

static java.lang.String parseFile

the current parse script (messy) - not thread-safe! Set this immediately before oarsing legacy file. Set to null to disable script-based parsing

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inputCML

protected org.xmlcml.cml.CML inputCML

the CML object created from the input legacy

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outputCML

protected org.xmlcml.cml.CML outputCML

a CML object to be output as legacy

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inputCMLMolecule

protected org.xmlcml.cml.CMLMolecule inputCMLMolecule

the molecule created from the input legacy

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outputCMLMolecule

protected org.xmlcml.cml.CMLMolecule outputCMLMolecule

a CML CMLMolecule to be output as legacy

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nonCmlDoc

protected org.xmlcml.cml.CMLDocument nonCmlDoc

result of a parse

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bReader

protected java.io.BufferedReader bReader

most input requires a BufferedReader

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currentLine

protected java.lang.String currentLine

and uses a line as the container

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nLine

protected int nLine

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atomVector

protected java.util.Vector atomVector

general tools for input and output

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bondVector

protected java.util.Vector bondVector

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natoms

protected int natoms

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nbonds

protected int nbonds

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selector

protected Selector selector

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atomParent

protected org.xmlcml.cml.AbstractBase atomParent

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bondParent

protected org.xmlcml.cml.AbstractBase bondParent

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convention

protected java.lang.String convention

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inputDescription2TypeTable

public static java.util.Hashtable inputDescription2TypeTable

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outputDescription2TypeTable

public static java.util.Hashtable outputDescription2TypeTable

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nextLine

java.lang.String nextLine

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markLine

int markLine

Constructor Detail

NonCMLDocumentImpl

protected NonCMLDocumentImpl()

Method Detail

parse

public abstract void parse(java.io.BufferedReader reader)
                    throws java.lang.Exception

The main parsing routine. must be overridden

Specified by:

parse in interface NonCMLDocument

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output

public abstract java.lang.String output(java.io.Writer w)
                                 throws java.io.IOException,
                                        org.xmlcml.cml.CMLException

The main output routine. Must be overridden

Specified by:

output in interface NonCMLDocument

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setOutputCMLMolecule

public void setOutputCMLMolecule(org.xmlcml.cml.CMLMolecule outputCMLMolecule)

Description copied from interface: NonCMLDocument

to output a CML-CMLMolecule in legacy form the molecule must be added to the NonCMLDocument and then the output() method called

Specified by:

setOutputCMLMolecule in interface NonCMLDocument

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setOutputCML

public void setOutputCML(org.xmlcml.cml.CML outputCML)

Description copied from interface: NonCMLDocument

to output a CML in legacy form - still under development

Specified by:

setOutputCML in interface NonCMLDocument

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getAndCheckVectors

protected void getAndCheckVectors()
                           throws org.xmlcml.cml.CMLException

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createAndAddMoleculeElement

public void createAndAddMoleculeElement(java.lang.String convention,
                                        java.lang.String id)

create molecule (inputCMLMolecule) *and add as document Element*

Specified by:

createAndAddMoleculeElement in interface NonCMLDocument

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createMoleculeElement

public void createMoleculeElement(java.lang.String convention,
                                  java.lang.String id)

Description copied from interface: NonCMLDocument

Create a molecule of given convention and id; convention is e.g. XYZ

Specified by:

createMoleculeElement in interface NonCMLDocument

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createCMLElement

protected void createCMLElement(java.lang.String convention,
                                java.lang.String id)

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createAndAddCMLElement

protected void createAndAddCMLElement(java.lang.String convention,
                                      java.lang.String id)

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getMoleculeVector

public static java.util.Vector getMoleculeVector(java.lang.String inputFile,
                                                 java.lang.String type)
                                          throws java.lang.Exception

creates a nonCMLDocument from the input URL. Many formats only return one molecule but some (e.g. SDF) may return many Perhaps obsolete

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parse

public void parse(java.net.URL url)
           throws java.lang.Exception

convenience method - routes to bufferedReader

Specified by:

parse in interface org.xmlcml.cml.CMLDocument

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getInputTypes

public static java.lang.String[] getInputTypes()

get allowed file types

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getInputSuffixes

public static java.lang.String[][] getInputSuffixes()

get allowed file suffixes

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getInputDescriptions

public static java.lang.String[] getInputDescriptions()

get allowed file suffixes

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getOutputTypes

public static java.lang.String[] getOutputTypes()

get allowed file types

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getOutputSuffixes

public static java.lang.String[] getOutputSuffixes()

get allowed file suffixes

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getOutputDescriptions

public static java.lang.String[] getOutputDescriptions()

get allowed file suffixes

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createCMLDocument

public static org.xmlcml.cml.CMLDocument createCMLDocument(java.lang.String type)
                                                    throws org.xmlcml.cml.CMLException

Description copied from class: org.xmlcml.cmlimpl.CMLDocumentImpl

create from file and subclass using SAX; the default CMLDOMSAXBuilder determines the subclassing

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makeFileStem

static java.lang.String makeFileStem(java.lang.String file)

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processLinks

public static void processLinks(org.xmlcml.cml.CMLDocument cmlDoc)
                         throws java.lang.Exception

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setParseFile

public static void setParseFile(java.lang.String f)

set the parse file - use null to reset it

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createCMLDocument

public static org.xmlcml.cml.CMLDocument createCMLDocument(java.net.URL urlx,
                                                           java.lang.String type)
                                                    throws java.lang.Exception

Convenience method - uses defaults to create a CMLDocument from the input URL. Very variable returns according to type. Many formats only return one molecule but some (e.g. SDF) may return many

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getTypesFromFile

public static final java.lang.String[] getTypesFromFile(java.lang.String fileName)

gives all possible types which have the suffix on fileName. Thus "foo.mol" could return MDLMol and MOL2

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getTypeFromFile

public static final java.lang.String getTypeFromFile(java.lang.String fileName)

hardcoded types - probably will be phased out in favout of getTypesFromFile

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getSuffixFromType

public static final java.lang.String getSuffixFromType(java.lang.String type)

hardcoded suffixes - probably will be phased out in favout of getTypesFromFile

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convertList

public static void convertList(java.lang.String inList,
                               java.lang.String inType,
                               java.lang.String outDir,
                               java.lang.String outFile,
                               java.lang.String outType)
                        throws java.lang.Exception

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convertFile

public static void convertFile(java.lang.String inFile,
                               java.lang.String inType,
                               java.io.FileWriter fw,
                               java.lang.String outType)
                        throws java.lang.Exception

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createCMLDocument

public static org.xmlcml.cml.CMLDocument createCMLDocument(java.net.URL url)
                                                    throws java.lang.Exception

Convenience method - uses defaults to create a CMLDocument from the input URL. and its suffix. Very variable returns according to type. Many formats only return one molecule but some (e.g. SDF) may return many

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makeDataItem

public org.xmlcml.cml.AbstractBase makeDataItem(org.xmlcml.cml.metadata.CMLDictionaryEntry entry,
                                                java.lang.String value)
                                         throws org.xmlcml.cml.CMLException

creates an object of type determined by a dictionary entry

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addDataItem

public void addDataItem(org.w3c.dom.Element parent,
                        java.lang.String id,
                        java.lang.Object obj)
                 throws org.xmlcml.cml.CMLException

creates an object of type determined by a dictionary id

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getDictionary

public static org.xmlcml.cml.metadata.CMLDictionary getDictionary(org.xmlcml.cmlimpl.CMLDocumentImpl doc)

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setSelector

public void setSelector(Selector selector)

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getSelector

public Selector getSelector()

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getCurrentLine

java.lang.String getCurrentLine()
                          throws java.io.IOException

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peekLine

java.lang.String peekLine()
                    throws java.io.IOException

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readNextLine

java.lang.String readNextLine()
                        throws java.io.IOException

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setMark

void setMark()
       throws java.io.IOException

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resetMark

void resetMark()
         throws java.io.IOException

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outform

public static java.lang.String outform(double v,
                                       int f,
                                       int d)

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readFortranReal

public static double readFortranReal(java.lang.String f)
                              throws java.lang.NumberFormatException

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main

public static void main(java.lang.String[] args)

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Overview  Package   Class  Use  Deprecated  Index
Home >> All >> org >> xmlcml >> [ noncml overview ]	PREV CLASS  NEXT CLASS
SUMMARY:  JAVADOC |  SOURCE |  DOWNLOAD | NESTED | FIELD | CONSTR | METHOD	DETAIL: FIELD | CONSTR | METHOD

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