Package org.jmol.adapter.smarter
Class Resolver
- java.lang.Object
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- org.jmol.adapter.smarter.Resolver
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public class Resolver extends Object
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Field Summary
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Constructor Summary
Constructors Constructor Description Resolver()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description private static boolean
checkAims(String[] lines)
private static boolean
checkAlchemy(String line)
private static String
checkCastepVaspSiesta(String[] lines)
private static boolean
checkCrystal(String[] lines)
private static boolean
checkCube(String[] lines)
private static boolean
checkFAH(String[] lines)
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
checkLineStarts(String[] lines)
private static int
checkMol(String[] lines)
private static boolean
checkMopacGraphf(String[] lines)
private static boolean
checkOdyssey(String[] lines)
private static String
checkSpecial1(int nLines, String[] lines, String leader)
private static String
checkSpecial2(String[] lines)
private static boolean
checkWien2k(String[] lines)
private static int
checkXyz(String[] lines)
private static String
determineAtomSetCollectionReader(Object readerOrDocument, boolean returnLines)
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)
(package private) static String
getFileType(BufferedReader br)
From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issuesstatic Object
getReader(String readerName, Map<String,Object> htParams)
Get a reader based on its name.static String
getReaderClassBase(String type)
private static String
getReaderFromType(String type)
private static String
getXmlType(String header)
private static boolean
isFloat(String s)
private static boolean
isInt(String s)
private static String
split(String a, int n)
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Field Detail
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classBase
private static final String classBase
- See Also:
- Constant Field Values
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readerSets
private static final String[] readerSets
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CML_NAMESPACE_URI
private static final String CML_NAMESPACE_URI
- See Also:
- Constant Field Values
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LEADER_CHAR_MAX
private static final int LEADER_CHAR_MAX
- See Also:
- Constant Field Values
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sptRecords
private static final String[] sptRecords
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m3dStartRecords
private static final String[] m3dStartRecords
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cubeFileStartRecords
private static final String[] cubeFileStartRecords
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mol2Records
private static final String[] mol2Records
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webmoFileStartRecords
private static final String[] webmoFileStartRecords
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moldenFileStartRecords
private static final String[] moldenFileStartRecords
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dcdFileStartRecords
private static final String[] dcdFileStartRecords
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tlsDataOnlyFileStartRecords
private static final String[] tlsDataOnlyFileStartRecords
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inputFileStartRecords
private static final String[] inputFileStartRecords
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magresFileStartRecords
private static final String[] magresFileStartRecords
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pymolStartRecords
private static final String[] pymolStartRecords
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janaStartRecords
private static final String[] janaStartRecords
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jsonStartRecords
private static final String[] jsonStartRecords
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jcampdxStartRecords
private static final String[] jcampdxStartRecords
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jmoldataStartRecords
private static final String[] jmoldataStartRecords
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pqrStartRecords
private static final String[] pqrStartRecords
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p2nStartRecords
private static final String[] p2nStartRecords
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cif2StartRecords
private static final String[] cif2StartRecords
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xmlStartRecords
private static final String[] xmlStartRecords
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cfiStartRecords
private static final String[] cfiStartRecords
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fileStartsWithRecords
private static final String[][] fileStartsWithRecords
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n
private static int[] n
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mmcifLineStartRecords
private static final String[] mmcifLineStartRecords
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cifLineStartRecords
private static final String[] cifLineStartRecords
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pdbLineStartRecords
private static final String[] pdbLineStartRecords
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cgdLineStartRecords
private static final String[] cgdLineStartRecords
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shelxLineStartRecords
private static final String[] shelxLineStartRecords
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ghemicalMMLineStartRecords
private static final String[] ghemicalMMLineStartRecords
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jaguarLineStartRecords
private static final String[] jaguarLineStartRecords
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mdlLineStartRecords
private static final String[] mdlLineStartRecords
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spartanSmolLineStartRecords
private static final String[] spartanSmolLineStartRecords
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csfLineStartRecords
private static final String[] csfLineStartRecords
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mdTopLineStartRecords
private static final String[] mdTopLineStartRecords
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hyperChemLineStartRecords
private static final String[] hyperChemLineStartRecords
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vaspOutcarLineStartRecords
private static final String[] vaspOutcarLineStartRecords
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lineStartsWithRecords
private static final String[][] lineStartsWithRecords
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bilbaoContainsRecords
private static final String[] bilbaoContainsRecords
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xmlContainsRecords
private static final String[] xmlContainsRecords
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gaussianContainsRecords
private static final String[] gaussianContainsRecords
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ampacContainsRecords
private static final String[] ampacContainsRecords
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mopacContainsRecords
private static final String[] mopacContainsRecords
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qchemContainsRecords
private static final String[] qchemContainsRecords
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gamessUKContainsRecords
private static final String[] gamessUKContainsRecords
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gamessUSContainsRecords
private static final String[] gamessUSContainsRecords
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spartanBinaryContainsRecords
private static final String[] spartanBinaryContainsRecords
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spartanContainsRecords
private static final String[] spartanContainsRecords
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adfContainsRecords
private static final String[] adfContainsRecords
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psiContainsRecords
private static final String[] psiContainsRecords
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nwchemContainsRecords
private static final String[] nwchemContainsRecords
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uicrcifContainsRecords
private static final String[] uicrcifContainsRecords
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dgridContainsRecords
private static final String[] dgridContainsRecords
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crystalContainsRecords
private static final String[] crystalContainsRecords
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dmolContainsRecords
private static final String[] dmolContainsRecords
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gulpContainsRecords
private static final String[] gulpContainsRecords
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espressoContainsRecords
private static final String[] espressoContainsRecords
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siestaContainsRecords
private static final String[] siestaContainsRecords
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xcrysDenContainsRecords
private static final String[] xcrysDenContainsRecords
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mopacArchiveContainsRecords
private static final String[] mopacArchiveContainsRecords
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abinitContainsRecords
private static final String[] abinitContainsRecords
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qcJsonContainsRecords
private static final String[] qcJsonContainsRecords
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gaussianFchkContainsRecords
private static final String[] gaussianFchkContainsRecords
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inputContainsRecords
private static final String[] inputContainsRecords
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aflowContainsRecords
private static final String[] aflowContainsRecords
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magCifContainsRecords
private static final String[] magCifContainsRecords
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headerContainsRecords
private static final String[][] headerContainsRecords
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Method Detail
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getFileType
static String getFileType(BufferedReader br)
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 Exception
the 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
public static Object getReader(String readerName, Map<String,Object> htParams)
Get a reader based on its name.- Parameters:
readerName
-htParams
-- Returns:
- AtomSetCollectionReader or error message
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DOMResolve
public static Object DOMResolve(Map<String,Object> htParams) throws Exception
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, boolean returnLines) throws Exception
the 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
-returnLines
-- Returns:
- readerName or a few lines, if requested, or null
- Throws:
Exception
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getBinaryType
public static String getBinaryType(InputStream inputStream)
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checkAims
private static boolean checkAims(String[] lines)
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checkAlchemy
private static boolean checkAlchemy(String line)
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isInt
private static boolean isInt(String s)
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isFloat
private static boolean isFloat(String s)
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checkCube
private static boolean checkCube(String[] lines)
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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.
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checkMol
private static int checkMol(String[] lines)
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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.
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checkOdyssey
private static boolean checkOdyssey(String[] lines)
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checkWien2k
private static boolean checkWien2k(String[] lines)
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checkXyz
private static int checkXyz(String[] lines)
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checkHeaderContains
private static String checkHeaderContains(String header) throws Exception
- Throws:
Exception
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checkFAH
private static boolean checkFAH(String[] lines)
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checkCrystal
private static boolean checkCrystal(String[] lines)
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checkGromacs
private static boolean checkGromacs(String[] lines)
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