java.lang.Object
PMRDocumentImpl
org.xmlcml.cmlimpl.CMLDocumentImpl
org.xmlcml.noncml.NonCMLDocumentImpl
org.xmlcml.noncml.G94Impl
- All Implemented Interfaces:
- org.xmlcml.cml.CMLDocument, org.w3c.dom.Document, G94, org.xmlcml.cml.mvc.HasController, org.w3c.dom.Node, NonCMLDocument
- public class G94Impl
- extends NonCMLDocumentImpl
- implements G94
class to read (? and write?) G94 files
NOT COMPLETE
| Fields inherited from class org.xmlcml.noncml.NonCMLDocumentImpl |
ATOM_FACTORY, atomParent, atomVector, BOND_FACTORY, bondParent, bondVector, bReader, convention, currentLine, DOCUMENT_FACTORY, inputCML, inputCMLMolecule, inputDescription2TypeTable, localDictionary, markLine, MOLECULE_FACTORY, natoms, nbonds, nextLine, nLine, nonCmlDoc, outputCML, outputCMLMolecule, outputDescription2TypeTable, parseFile, selector, SPACE40, SPACE80 |
| 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.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 |
| Methods inherited from class org.xmlcml.noncml.NonCMLDocumentImpl |
addDataItem, convertFile, convertList, createAndAddCMLElement, createAndAddMoleculeElement, createCMLDocument, createCMLDocument, createCMLDocument, createCMLElement, createMoleculeElement, getAndCheckVectors, getCurrentLine, getDictionary, getInputDescriptions, getInputSuffixes, getInputTypes, getMoleculeVector, getOutputDescriptions, getOutputSuffixes, getOutputTypes, getSelector, getSuffixFromType, getTypeFromFile, getTypesFromFile, makeDataItem, makeFileStem, outform, parse, peekLine, processLinks, readFortranReal, readNextLine, resetMark, setMark, setOutputCML, setOutputCMLMolecule, setParseFile, setSelector |
| 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, parse, 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 |
nline
int nline
title
java.lang.String title
omitTable
java.util.Hashtable omitTable
G94Impl
public G94Impl()
- form a G94 object from a local file
G94Impl
public G94Impl(java.io.BufferedReader bReader,
java.lang.String id)
throws java.lang.Exception
- form an G94 object from a local file
G94Impl
public G94Impl(org.xmlcml.cml.CMLMolecule outputCMLMolecule)
- form a G94 object from a CML file
G94Selector
private void G94Selector()
parse
public void parse(java.io.BufferedReader bReader)
throws java.io.IOException,
org.xmlcml.cml.CMLException
- Description copied from interface:
NonCMLDocument
- input from a Reader. If the String value is to be input, use a StringReader.
This could be used after a default constructor either immediately
or with some additional customisation and may be used in
the class constructors. Note that parse(URL) is inherited from CMLDocument
- Specified by:
parse in interface NonCMLDocument- Specified by:
parse in class NonCMLDocumentImpl
processHistory
void processHistory()
readl1
public void readl1(boolean ignore)
throws java.io.IOException
readl101
public void readl101(boolean ignore)
throws java.io.IOException
readl103
public void readl103(boolean ignore)
throws java.io.IOException
readl202
public void readl202(boolean ignore)
throws org.xmlcml.cml.CMLException,
java.io.IOException
readl301
public void readl301(boolean ignore)
throws java.io.IOException
readl302
public void readl302(boolean ignore)
throws java.io.IOException
readl311
public void readl311(boolean ignore)
throws java.io.IOException
readl314
public void readl314(boolean ignore)
throws java.io.IOException
readl303
public void readl303(boolean ignore)
throws java.io.IOException
readl401
public void readl401(boolean ignore)
throws java.io.IOException
readl502
public void readl502(boolean ignore)
throws java.io.IOException
readl601
public void readl601(boolean ignore)
throws java.io.IOException
readl602
public void readl602(boolean ignore)
throws java.io.IOException
readl701
public void readl701(boolean ignore)
throws java.io.IOException
readl702
public void readl702(boolean ignore)
throws java.io.IOException
readl703
public void readl703(boolean ignore)
throws java.io.IOException
readl716
public void readl716(boolean ignore)
throws java.io.IOException
readl801
public void readl801(boolean ignore)
throws java.io.IOException
readl1002
public void readl1002(boolean ignore)
throws java.io.IOException
readl1101
public void readl1101(boolean ignore)
throws java.io.IOException
readl1102
public void readl1102(boolean ignore)
throws java.io.IOException
readl1110
public void readl1110(boolean ignore)
throws java.io.IOException
readl9999
public void readl9999(boolean ignore)
throws java.io.IOException
output
public java.lang.String output(java.io.Writer writer)
throws org.xmlcml.cml.CMLException,
java.io.IOException
- outputs CMLMolecule as G94 if possible. G94.
- Specified by:
output in interface NonCMLDocument- Specified by:
output in class NonCMLDocumentImpl
writeHeader
public void writeHeader(java.io.Writer w)
throws java.io.IOException
main
public static void main(java.lang.String[] args)
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