org.jmol.adapter.smarter

Class Resolver

public class Resolver extends Object

Field Summary
static String[]adfRecords
static String[]cifRecords
static StringclassBase
static String[][]containsRecords
static String[]csfRecords
static String[]cubeRecords
static StringCML_NAMESPACE_URI
static String[][]fileStartsWithRecords
static String[]gamessUKRecords
static String[]gamessUSRecords
static String[]gaussianRecords
static String[]ghemicalMMRecords
static String[]hinRecords
static String[]jaguarRecords
static String[][]lineStartsWithRecords
static intLEADER_CHAR_MAX
static String[]mdlRecords
static String[]mol2Records
static String[]moldenRecords
static String[]mopacRecords
static String[]nwchemRecords
static String[]pdbRecords
static String[]pqrRecords
static String[]psiRecords
static String[]qchemRecords
static String[]readerSets
static String[]shelxRecords
static String[]spartanBinaryRecords
static String[]spartanRecords
static String[]spartanSmolRecords
static String[][]specialTags
static intSPECIAL_ARGUS_DOM
static intSPECIAL_ARGUS_XML
static intSPECIAL_CHEM3D_DOM
static intSPECIAL_CHEM3D_XML
static intSPECIAL_CML_DOM
static intSPECIAL_CML_XML
static intSPECIAL_CUBE
static intSPECIAL_FOLDINGXYZ
static intSPECIAL_JME
static intSPECIAL_MOL
static intSPECIAL_MOLPRO_DOM
static intSPECIAL_MOLPRO_XML
static intSPECIAL_MOPACGRAPHF
static intSPECIAL_ODYSSEY
static intSPECIAL_ODYSSEY_DOM
static intSPECIAL_ODYSSEY_XML
static intSPECIAL_V3000
static intSPECIAL_XYZ
static String[]webmoRecords
static String[]xmlRecords
Method Summary
static booleancheckCube(String[] lines)
static booleancheckFoldingXyz(String[] lines)
static booleancheckMol(String[] lines)
static booleancheckMopacGraphf(String[] lines)
static booleancheckOdyssey(String[] lines)
static StringcheckSpecial(int nLines, String[] lines)
static StringcheckType(String[][] typeTags, String type)
static booleancheckV3000(String[] lines)
static booleancheckXyz(String[] lines)
static StringdetermineAtomSetCollectionReader(BufferedReader bufferedReader, boolean returnLines)
static ObjectDOMResolve(Object DOMNode)
static Objectfinalize(AtomSetCollection atomSetCollection, String filename)
static StringgetFileType(BufferedReader br)
static StringgetReaderClassBase(String type)
static StringgetReaderFromType(String type)
static StringgetXmlType(JSObject DOMNode)
static StringgetXmlType(String header)
static Objectresolve(String name, String type, BufferedReader bufferedReader)
static Objectresolve(String fullName, String type, BufferedReader bufferedReader, Hashtable htParams)
static String[]specialLoad(String name, String type)
In the case of spt files, no need to load them; here we are just checking for type In the case of .spardir directories, we need to provide a list of the critical files that need loading and concatenation for the SpartanSmolReader we return an array for which: [0] file type (class prefix) or null for SPT file [1] header to add for each BEGIN/END block [2...] files to load and concatenate

Field Detail

adfRecords

static final String[] adfRecords

cifRecords

static final String[] cifRecords

classBase

private static final String classBase

containsRecords

static final String[][] containsRecords

csfRecords

static final String[] csfRecords

cubeRecords

static final String[] cubeRecords

CML_NAMESPACE_URI

private static final String CML_NAMESPACE_URI

fileStartsWithRecords

static final String[][] fileStartsWithRecords

gamessUKRecords

static final String[] gamessUKRecords

gamessUSRecords

static final String[] gamessUSRecords

gaussianRecords

static final String[] gaussianRecords

ghemicalMMRecords

static final String[] ghemicalMMRecords

hinRecords

static final String[] hinRecords

jaguarRecords

static final String[] jaguarRecords

lineStartsWithRecords

static final String[][] lineStartsWithRecords

LEADER_CHAR_MAX

static final int LEADER_CHAR_MAX

mdlRecords

static final String[] mdlRecords

mol2Records

static final String[] mol2Records

moldenRecords

static final String[] moldenRecords

mopacRecords

static final String[] mopacRecords

nwchemRecords

static final String[] nwchemRecords

pdbRecords

static final String[] pdbRecords

pqrRecords

static final String[] pqrRecords

psiRecords

static final String[] psiRecords

qchemRecords

static final String[] qchemRecords

readerSets

private static final String[] readerSets

shelxRecords

static final String[] shelxRecords

spartanBinaryRecords

static final String[] spartanBinaryRecords

spartanRecords

static final String[] spartanRecords

spartanSmolRecords

static final String[] spartanSmolRecords

specialTags

public static final String[][] specialTags

SPECIAL_ARGUS_DOM

public static final int SPECIAL_ARGUS_DOM

SPECIAL_ARGUS_XML

public static final int SPECIAL_ARGUS_XML

SPECIAL_CHEM3D_DOM

public static final int SPECIAL_CHEM3D_DOM

SPECIAL_CHEM3D_XML

public static final int SPECIAL_CHEM3D_XML

SPECIAL_CML_DOM

public static final int SPECIAL_CML_DOM

SPECIAL_CML_XML

public static final int SPECIAL_CML_XML

SPECIAL_CUBE

static final int SPECIAL_CUBE

SPECIAL_FOLDINGXYZ

static final int SPECIAL_FOLDINGXYZ

SPECIAL_JME

static final int SPECIAL_JME

SPECIAL_MOL

static final int SPECIAL_MOL

SPECIAL_MOLPRO_DOM

public static final int SPECIAL_MOLPRO_DOM

SPECIAL_MOLPRO_XML

public static final int SPECIAL_MOLPRO_XML

SPECIAL_MOPACGRAPHF

static final int SPECIAL_MOPACGRAPHF

SPECIAL_ODYSSEY

static final int SPECIAL_ODYSSEY

SPECIAL_ODYSSEY_DOM

public static final int SPECIAL_ODYSSEY_DOM

SPECIAL_ODYSSEY_XML

public static final int SPECIAL_ODYSSEY_XML

SPECIAL_V3000

static final int SPECIAL_V3000

SPECIAL_XYZ

static final int SPECIAL_XYZ

webmoRecords

static final String[] webmoRecords

xmlRecords

static final String[] xmlRecords

Method Detail

checkCube

private static boolean checkCube(String[] lines)

checkFoldingXyz

private static boolean checkFoldingXyz(String[] lines)

Parameters: lines First lines of the files.

Returns: Indicates if the file may be a Folding@Home file.

checkMol

private static boolean checkMol(String[] lines)

checkMopacGraphf

private static boolean checkMopacGraphf(String[] lines)

Parameters: lines First lines of the files.

Returns: Indicates if the file is a Mopac GRAPHF output file.

checkOdyssey

private static boolean checkOdyssey(String[] lines)

checkSpecial

static final String checkSpecial(int nLines, String[] lines)

checkType

private static final String checkType(String[][] typeTags, String type)

checkV3000

private static boolean checkV3000(String[] lines)

checkXyz

private static boolean checkXyz(String[] lines)

determineAtomSetCollectionReader

static String determineAtomSetCollectionReader(BufferedReader bufferedReader, boolean returnLines)

DOMResolve

static Object DOMResolve(Object DOMNode)

finalize

static Object finalize(AtomSetCollection atomSetCollection, String filename)

getFileType

static String getFileType(BufferedReader br)

getReaderClassBase

private static final String getReaderClassBase(String type)

getReaderFromType

public static final String getReaderFromType(String type)

getXmlType

private static String getXmlType(JSObject DOMNode)

getXmlType

private static String getXmlType(String header)

resolve

static Object resolve(String name, String type, BufferedReader bufferedReader)

resolve

static Object resolve(String fullName, String type, BufferedReader bufferedReader, Hashtable htParams)

specialLoad

public static String[] specialLoad(String name, String type)
In the case of spt files, no need to load them; here we are just checking for type In the case of .spardir directories, we need to provide a list of the critical files that need loading and concatenation for the SpartanSmolReader we return an array for which: [0] file type (class prefix) or null for SPT file [1] header to add for each BEGIN/END block [2...] files to load and concatenate

Parameters: name type

Returns: array detailing action for this set of files