Package org.jmol.adapter.smarter
Class Resolver
java.lang.Object
org.jmol.adapter.smarter.Resolver
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Field Summary
FieldsModifier and TypeFieldDescriptionprivate static final String[]
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private static byte[]
private static final String[]
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private static final String
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private static final int
private static final String[][]
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private static int[]
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate static boolean
bytesMatch
(byte[] a, byte[] b) private static boolean
private static boolean
checkAlchemy
(String line) private static String
checkCastepVaspSiesta
(String[] lines) private static boolean
checkCrystal
(String[] lines) private static boolean
private static boolean
private static String
checkFileStart
(String leader) private static boolean
checkFoldingXyz
(String[] lines) private static boolean
checkGenNBO
(String[] lines, String leader) private static boolean
checkGromacs
(String[] lines) private static String
checkHeaderContains
(String header) private static String
checkHeaderRecords
(String header, String[] recordTags) private static String
checkJSONContains
(String header) private static String
checkLineStarts
(String[] lines) private static int
private static boolean
checkMopacGraphf
(String[] lines) private static boolean
checkOdyssey
(String[] lines) private static final String
checkSpecial1
(int nLines, String[] lines, String leader) private static final String
checkSpecial2
(String[] lines) private static boolean
checkWien2k
(String[] lines) private static boolean
private static int
private static String
determineAtomSetCollectionReader
(Object readerOrDocument, Map<String, Object> htParams) the main resolver method.static Object
DOMResolve
(Map<String, Object> htParams) a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page.(package private) static Object
getAtomCollectionReader
(String fullName, String type, Object readerOrDocument, Map<String, Object> htParams, int ptFile) the main method for reading files.static String
getBinaryType
(InputStream inputStream) static String
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issuesstatic Object
Get a reader based on its name.static final String
getReaderClassBase
(String type) private static final String
getReaderFromType
(String type) private static String
getXmlType
(String header) private static boolean
private static boolean
private static String
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Field Details
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classBase
- See Also:
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readerSets
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CML_NAMESPACE_URI
- See Also:
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cdxMagic
private static byte[] cdxMagic -
LEADER_CHAR_MAX
private static final int LEADER_CHAR_MAX- See Also:
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sptRecords
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m3dStartRecords
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cubeFileStartRecords
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mol2Records
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webmoFileStartRecords
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moldenFileStartRecords
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dcdFileStartRecords
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tlsDataOnlyFileStartRecords
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inputFileStartRecords
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magresFileStartRecords
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pymolStartRecords
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janaStartRecords
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jsonStartRecords
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jcampdxStartRecords
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jmoldataStartRecords
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pqrStartRecords
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p2nStartRecords
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cif2StartRecords
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xmlStartRecords
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cfiStartRecords
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fileStartsWithRecords
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n
private static int[] n -
mmcifLineStartRecords
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cifLineStartRecords
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pdbLineStartRecords
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cgdLineStartRecords
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shelxLineStartRecords
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ghemicalMMLineStartRecords
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jaguarLineStartRecords
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mdlLineStartRecords
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spartanSmolLineStartRecords
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csfLineStartRecords
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mdTopLineStartRecords
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hyperChemLineStartRecords
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vaspOutcarLineStartRecords
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orcaInputLineStartRecords
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lineStartsWithRecords
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bilbaoContainsRecords
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xmlContainsRecords
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gaussianContainsRecords
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ampacContainsRecords
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mopacContainsRecords
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qchemContainsRecords
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gamessUKContainsRecords
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gamessUSContainsRecords
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spartanBinaryContainsRecords
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spartanContainsRecords
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adfContainsRecords
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psiContainsRecords
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nwchemContainsRecords
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uicrcifContainsRecords
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dgridContainsRecords
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crystalContainsRecords
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dmolContainsRecords
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gulpContainsRecords
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espressoContainsRecords
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siestaContainsRecords
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xcrysDenContainsRecords
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mopacArchiveContainsRecords
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abinitContainsRecords
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qcJsonContainsRecords
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optimadeContainsRecords
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jsonArrayContainsRecords
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orcaContainsRecords
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gaussianFchkContainsRecords
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inputContainsRecords
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aflowContainsRecords
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magCifContainsRecords
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headerContainsRecords
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jsonContainsRecords
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Constructor Details
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Resolver
public Resolver()
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Method Details
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getReaderClassBase
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getFileType
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues- Parameters:
br
-- Returns:
- String file type
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getAtomCollectionReader
static Object getAtomCollectionReader(String fullName, String type, Object readerOrDocument, Map<String, Object> htParams, int ptFile) throws Exceptionthe main method for reading files. Called from SmarterJmolAdapter when reading a file, reading a set of files, or reading a ZIP file- Parameters:
fullName
-type
-readerOrDocument
-htParams
-ptFile
-- Returns:
- an AtomSetCollection or a String error
- Throws:
Exception
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getReader
Get a reader based on its name.- Parameters:
readerName
-htParams
-- Returns:
- AtomSetCollectionReader or error message
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getReaderFromType
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split
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DOMResolve
a largely untested reader of the DOM - where in a browser there is model actually in XML format already present on the page. -- Egon Willighagen- Parameters:
htParams
-- Returns:
- an AtomSetCollection or a String error
- Throws:
Exception
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determineAtomSetCollectionReader
private static String determineAtomSetCollectionReader(Object readerOrDocument, Map<String, Object> htParams) throws Exceptionthe main resolver method. One of the great advantages of Jmol is that it can smartly determine a file type from its contents. In cases where this is not possible, one can force a file type using a prefix to a filename. For example: load mol2::xxxx.whatever This is only necessary for a few file types, where only numbers are involved -- molecular dynamics coordinate files, for instance (mdcrd).- Parameters:
readerOrDocument
-htParams
-- Returns:
- readerName or a few lines, if requested, or null
- Throws:
Exception
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getBinaryType
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bytesMatch
private static boolean bytesMatch(byte[] a, byte[] b) -
checkFileStart
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checkSpecial1
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checkXSF
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checkAims
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checkAlchemy
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isInt
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isFloat
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checkCube
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checkFoldingXyz
- Parameters:
lines
- First lines of the files.- Returns:
- Indicates if the file may be a Folding@Home file.
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checkGenNBO
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checkMol
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checkMopacGraphf
- Parameters:
lines
- First lines of the files.- Returns:
- Indicates if the file is a Mopac GRAPHF output file.
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checkOdyssey
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checkWien2k
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checkXyz
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checkLineStarts
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checkHeaderContains
- Throws:
Exception
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checkJSONContains
- Throws:
Exception
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checkHeaderRecords
- Throws:
Exception
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getXmlType
- Throws:
Exception
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checkSpecial2
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checkFAH
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checkCrystal
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checkGromacs
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checkCastepVaspSiesta
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