Class Resolver


  • public class Resolver
    extends Object
    • Field Detail

      • readerSets

        private static final String[] readerSets
      • sptRecords

        private static final String[] sptRecords
      • m3dStartRecords

        private static final String[] m3dStartRecords
      • cubeFileStartRecords

        private static final String[] cubeFileStartRecords
      • mol2Records

        private static final String[] mol2Records
      • webmoFileStartRecords

        private static final String[] webmoFileStartRecords
      • moldenFileStartRecords

        private static final String[] moldenFileStartRecords
      • dcdFileStartRecords

        private static final String[] dcdFileStartRecords
      • tlsDataOnlyFileStartRecords

        private static final String[] tlsDataOnlyFileStartRecords
      • inputFileStartRecords

        private static final String[] inputFileStartRecords
      • magresFileStartRecords

        private static final String[] magresFileStartRecords
      • pymolStartRecords

        private static final String[] pymolStartRecords
      • janaStartRecords

        private static final String[] janaStartRecords
      • jsonStartRecords

        private static final String[] jsonStartRecords
      • jcampdxStartRecords

        private static final String[] jcampdxStartRecords
      • jmoldataStartRecords

        private static final String[] jmoldataStartRecords
      • pqrStartRecords

        private static final String[] pqrStartRecords
      • p2nStartRecords

        private static final String[] p2nStartRecords
      • cif2StartRecords

        private static final String[] cif2StartRecords
      • xmlStartRecords

        private static final String[] xmlStartRecords
      • cfiStartRecords

        private static final String[] cfiStartRecords
      • fileStartsWithRecords

        private static final String[][] fileStartsWithRecords
      • n

        private static int[] n
      • mmcifLineStartRecords

        private static final String[] mmcifLineStartRecords
      • cifLineStartRecords

        private static final String[] cifLineStartRecords
      • pdbLineStartRecords

        private static final String[] pdbLineStartRecords
      • cgdLineStartRecords

        private static final String[] cgdLineStartRecords
      • shelxLineStartRecords

        private static final String[] shelxLineStartRecords
      • ghemicalMMLineStartRecords

        private static final String[] ghemicalMMLineStartRecords
      • jaguarLineStartRecords

        private static final String[] jaguarLineStartRecords
      • mdlLineStartRecords

        private static final String[] mdlLineStartRecords
      • spartanSmolLineStartRecords

        private static final String[] spartanSmolLineStartRecords
      • csfLineStartRecords

        private static final String[] csfLineStartRecords
      • mdTopLineStartRecords

        private static final String[] mdTopLineStartRecords
      • hyperChemLineStartRecords

        private static final String[] hyperChemLineStartRecords
      • vaspOutcarLineStartRecords

        private static final String[] vaspOutcarLineStartRecords
      • lineStartsWithRecords

        private static final String[][] lineStartsWithRecords
      • bilbaoContainsRecords

        private static final String[] bilbaoContainsRecords
      • xmlContainsRecords

        private static final String[] xmlContainsRecords
      • gaussianContainsRecords

        private static final String[] gaussianContainsRecords
      • ampacContainsRecords

        private static final String[] ampacContainsRecords
      • mopacContainsRecords

        private static final String[] mopacContainsRecords
      • qchemContainsRecords

        private static final String[] qchemContainsRecords
      • gamessUKContainsRecords

        private static final String[] gamessUKContainsRecords
      • gamessUSContainsRecords

        private static final String[] gamessUSContainsRecords
      • spartanBinaryContainsRecords

        private static final String[] spartanBinaryContainsRecords
      • spartanContainsRecords

        private static final String[] spartanContainsRecords
      • adfContainsRecords

        private static final String[] adfContainsRecords
      • psiContainsRecords

        private static final String[] psiContainsRecords
      • nwchemContainsRecords

        private static final String[] nwchemContainsRecords
      • uicrcifContainsRecords

        private static final String[] uicrcifContainsRecords
      • dgridContainsRecords

        private static final String[] dgridContainsRecords
      • crystalContainsRecords

        private static final String[] crystalContainsRecords
      • dmolContainsRecords

        private static final String[] dmolContainsRecords
      • gulpContainsRecords

        private static final String[] gulpContainsRecords
      • espressoContainsRecords

        private static final String[] espressoContainsRecords
      • siestaContainsRecords

        private static final String[] siestaContainsRecords
      • xcrysDenContainsRecords

        private static final String[] xcrysDenContainsRecords
      • mopacArchiveContainsRecords

        private static final String[] mopacArchiveContainsRecords
      • abinitContainsRecords

        private static final String[] abinitContainsRecords
      • qcJsonContainsRecords

        private static final String[] qcJsonContainsRecords
      • gaussianFchkContainsRecords

        private static final String[] gaussianFchkContainsRecords
      • inputContainsRecords

        private static final String[] inputContainsRecords
      • aflowContainsRecords

        private static final String[] aflowContainsRecords
      • magCifContainsRecords

        private static final String[] magCifContainsRecords
      • headerContainsRecords

        private static final String[][] headerContainsRecords
    • Constructor Detail

      • Resolver

        public Resolver()
    • Method Detail

      • getReaderClassBase

        public static final String getReaderClassBase​(String type)
      • 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
      • 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
      • 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
      • getReaderFromType

        private static final String getReaderFromType​(String type)
      • 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
      • 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
      • checkFileStart

        private static String checkFileStart​(String leader)
      • checkSpecial1

        private static final String checkSpecial1​(int nLines,
                                                  String[] lines,
                                                  String leader)
      • checkAims

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

        private static boolean checkAlchemy​(String line)
      • isInt

        private static boolean isInt​(String s)
      • isFloat

        private static boolean isFloat​(String s)
      • 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.
      • checkGenNBO

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

        private static int 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)
      • checkWien2k

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

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

        private static String checkLineStarts​(String[] lines)
      • checkSpecial2

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

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

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

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

        private static String checkCastepVaspSiesta​(String[] lines)