Class Resolver


  • public class Resolver
    extends java.lang.Object
    • Field Detail

      • readerSets

        private static final java.lang.String[] readerSets
      • CML_NAMESPACE_URI

        private static final java.lang.String CML_NAMESPACE_URI
        See Also:
        Constant Field Values
      • sptRecords

        private static final java.lang.String[] sptRecords
      • m3dStartRecords

        private static final java.lang.String[] m3dStartRecords
      • cubeFileStartRecords

        private static final java.lang.String[] cubeFileStartRecords
      • mol2Records

        private static final java.lang.String[] mol2Records
      • webmoFileStartRecords

        private static final java.lang.String[] webmoFileStartRecords
      • moldenFileStartRecords

        private static final java.lang.String[] moldenFileStartRecords
      • dcdFileStartRecords

        private static final java.lang.String[] dcdFileStartRecords
      • tlsDataOnlyFileStartRecords

        private static final java.lang.String[] tlsDataOnlyFileStartRecords
      • inputFileStartRecords

        private static final java.lang.String[] inputFileStartRecords
      • magresFileStartRecords

        private static final java.lang.String[] magresFileStartRecords
      • pymolStartRecords

        private static final java.lang.String[] pymolStartRecords
      • janaStartRecords

        private static final java.lang.String[] janaStartRecords
      • jsonStartRecords

        private static final java.lang.String[] jsonStartRecords
      • jcampdxStartRecords

        private static final java.lang.String[] jcampdxStartRecords
      • jmoldataStartRecords

        private static final java.lang.String[] jmoldataStartRecords
      • pqrStartRecords

        private static final java.lang.String[] pqrStartRecords
      • p2nStartRecords

        private static final java.lang.String[] p2nStartRecords
      • cif2StartRecords

        private static final java.lang.String[] cif2StartRecords
      • xmlStartRecords

        private static final java.lang.String[] xmlStartRecords
      • cfiStartRecords

        private static final java.lang.String[] cfiStartRecords
      • fileStartsWithRecords

        private static final java.lang.String[][] fileStartsWithRecords
      • n

        private static int[] n
      • mmcifLineStartRecords

        private static final java.lang.String[] mmcifLineStartRecords
      • cifLineStartRecords

        private static final java.lang.String[] cifLineStartRecords
      • pdbLineStartRecords

        private static final java.lang.String[] pdbLineStartRecords
      • cgdLineStartRecords

        private static final java.lang.String[] cgdLineStartRecords
      • shelxLineStartRecords

        private static final java.lang.String[] shelxLineStartRecords
      • ghemicalMMLineStartRecords

        private static final java.lang.String[] ghemicalMMLineStartRecords
      • jaguarLineStartRecords

        private static final java.lang.String[] jaguarLineStartRecords
      • mdlLineStartRecords

        private static final java.lang.String[] mdlLineStartRecords
      • spartanSmolLineStartRecords

        private static final java.lang.String[] spartanSmolLineStartRecords
      • csfLineStartRecords

        private static final java.lang.String[] csfLineStartRecords
      • mdTopLineStartRecords

        private static final java.lang.String[] mdTopLineStartRecords
      • hyperChemLineStartRecords

        private static final java.lang.String[] hyperChemLineStartRecords
      • vaspOutcarLineStartRecords

        private static final java.lang.String[] vaspOutcarLineStartRecords
      • lineStartsWithRecords

        private static final java.lang.String[][] lineStartsWithRecords
      • bilbaoContainsRecords

        private static final java.lang.String[] bilbaoContainsRecords
      • xmlContainsRecords

        private static final java.lang.String[] xmlContainsRecords
      • gaussianContainsRecords

        private static final java.lang.String[] gaussianContainsRecords
      • ampacContainsRecords

        private static final java.lang.String[] ampacContainsRecords
      • mopacContainsRecords

        private static final java.lang.String[] mopacContainsRecords
      • qchemContainsRecords

        private static final java.lang.String[] qchemContainsRecords
      • gamessUKContainsRecords

        private static final java.lang.String[] gamessUKContainsRecords
      • gamessUSContainsRecords

        private static final java.lang.String[] gamessUSContainsRecords
      • spartanBinaryContainsRecords

        private static final java.lang.String[] spartanBinaryContainsRecords
      • spartanContainsRecords

        private static final java.lang.String[] spartanContainsRecords
      • adfContainsRecords

        private static final java.lang.String[] adfContainsRecords
      • psiContainsRecords

        private static final java.lang.String[] psiContainsRecords
      • nwchemContainsRecords

        private static final java.lang.String[] nwchemContainsRecords
      • uicrcifContainsRecords

        private static final java.lang.String[] uicrcifContainsRecords
      • dgridContainsRecords

        private static final java.lang.String[] dgridContainsRecords
      • crystalContainsRecords

        private static final java.lang.String[] crystalContainsRecords
      • dmolContainsRecords

        private static final java.lang.String[] dmolContainsRecords
      • gulpContainsRecords

        private static final java.lang.String[] gulpContainsRecords
      • espressoContainsRecords

        private static final java.lang.String[] espressoContainsRecords
      • siestaContainsRecords

        private static final java.lang.String[] siestaContainsRecords
      • xcrysDenContainsRecords

        private static final java.lang.String[] xcrysDenContainsRecords
      • mopacArchiveContainsRecords

        private static final java.lang.String[] mopacArchiveContainsRecords
      • abinitContainsRecords

        private static final java.lang.String[] abinitContainsRecords
      • qcJsonContainsRecords

        private static final java.lang.String[] qcJsonContainsRecords
      • optimadeContainsRecords

        private static final java.lang.String[] optimadeContainsRecords
      • gaussianFchkContainsRecords

        private static final java.lang.String[] gaussianFchkContainsRecords
      • inputContainsRecords

        private static final java.lang.String[] inputContainsRecords
      • aflowContainsRecords

        private static final java.lang.String[] aflowContainsRecords
      • magCifContainsRecords

        private static final java.lang.String[] magCifContainsRecords
      • headerContainsRecords

        private static final java.lang.String[][] headerContainsRecords
      • jsonContainsRecords

        private static final java.lang.String[][] jsonContainsRecords
    • Constructor Detail

      • Resolver

        public Resolver()
    • Method Detail

      • getReaderClassBase

        public static final java.lang.String getReaderClassBase​(java.lang.String type)
      • getFileType

        public static java.lang.String getFileType​(java.io.BufferedReader br)
        From SmarterJmolAdapter.getFileTypeName(Object ascOrReader) just return the file type with no exception issues
        Parameters:
        br -
        Returns:
        String file type
      • getAtomCollectionReader

        static java.lang.Object getAtomCollectionReader​(java.lang.String fullName,
                                                        java.lang.String type,
                                                        java.lang.Object readerOrDocument,
                                                        java.util.Map<java.lang.String,​java.lang.Object> htParams,
                                                        int ptFile)
                                                 throws java.lang.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:
        java.lang.Exception
      • getReader

        public static java.lang.Object getReader​(java.lang.String readerName,
                                                 java.util.Map<java.lang.String,​java.lang.Object> htParams)
        Get a reader based on its name.
        Parameters:
        readerName -
        htParams -
        Returns:
        AtomSetCollectionReader or error message
      • getReaderFromType

        private static final java.lang.String getReaderFromType​(java.lang.String type)
      • split

        private static java.lang.String split​(java.lang.String a,
                                              int n)
      • DOMResolve

        public static java.lang.Object DOMResolve​(java.util.Map<java.lang.String,​java.lang.Object> htParams)
                                           throws java.lang.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:
        java.lang.Exception
      • determineAtomSetCollectionReader

        private static java.lang.String determineAtomSetCollectionReader​(java.lang.Object readerOrDocument,
                                                                         java.util.Map<java.lang.String,​java.lang.Object> htParams)
                                                                  throws java.lang.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 -
        htParams -
        Returns:
        readerName or a few lines, if requested, or null
        Throws:
        java.lang.Exception
      • getBinaryType

        public static java.lang.String getBinaryType​(java.io.InputStream inputStream)
      • checkFileStart

        private static java.lang.String checkFileStart​(java.lang.String leader)
      • checkSpecial1

        private static final java.lang.String checkSpecial1​(int nLines,
                                                            java.lang.String[] lines,
                                                            java.lang.String leader)
      • checkXSF

        private static boolean checkXSF​(java.lang.String[] lines)
      • checkAims

        private static boolean checkAims​(java.lang.String[] lines)
      • checkAlchemy

        private static boolean checkAlchemy​(java.lang.String line)
      • isInt

        private static boolean isInt​(java.lang.String s)
      • isFloat

        private static boolean isFloat​(java.lang.String s)
      • checkCube

        private static boolean checkCube​(java.lang.String[] lines)
      • checkFoldingXyz

        private static boolean checkFoldingXyz​(java.lang.String[] lines)
        Parameters:
        lines - First lines of the files.
        Returns:
        Indicates if the file may be a Folding@Home file.
      • checkGenNBO

        private static boolean checkGenNBO​(java.lang.String[] lines,
                                           java.lang.String leader)
      • checkMol

        private static int checkMol​(java.lang.String[] lines)
      • checkMopacGraphf

        private static boolean checkMopacGraphf​(java.lang.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​(java.lang.String[] lines)
      • checkWien2k

        private static boolean checkWien2k​(java.lang.String[] lines)
      • checkXyz

        private static int checkXyz​(java.lang.String[] lines)
      • checkLineStarts

        private static java.lang.String checkLineStarts​(java.lang.String[] lines)
      • checkHeaderContains

        private static java.lang.String checkHeaderContains​(java.lang.String header)
                                                     throws java.lang.Exception
        Throws:
        java.lang.Exception
      • checkJSONContains

        private static java.lang.String checkJSONContains​(java.lang.String header)
                                                   throws java.lang.Exception
        Throws:
        java.lang.Exception
      • checkHeaderRecords

        private static java.lang.String checkHeaderRecords​(java.lang.String header,
                                                           java.lang.String[] recordTags)
                                                    throws java.lang.Exception
        Throws:
        java.lang.Exception
      • getXmlType

        private static java.lang.String getXmlType​(java.lang.String header)
                                            throws java.lang.Exception
        Throws:
        java.lang.Exception
      • checkSpecial2

        private static final java.lang.String checkSpecial2​(java.lang.String[] lines)
      • checkFAH

        private static boolean checkFAH​(java.lang.String[] lines)
      • checkCrystal

        private static boolean checkCrystal​(java.lang.String[] lines)
      • checkGromacs

        private static boolean checkGromacs​(java.lang.String[] lines)
      • checkCastepVaspSiesta

        private static java.lang.String checkCastepVaspSiesta​(java.lang.String[] lines)