public class Resolver
extends java.lang.Object
Modifier and Type | Field and Description |
---|---|
private static java.lang.String[] |
adfContainsRecords |
private static java.lang.String[] |
ampacContainsRecords |
private static java.lang.String[] |
cifLineStartRecords |
private static java.lang.String |
classBase |
private static java.lang.String |
CML_NAMESPACE_URI |
private static java.lang.String[] |
crystalContainsRecords |
private static java.lang.String[] |
csfLineStartRecords |
private static java.lang.String[] |
cubeFileStartRecords |
private static java.lang.String[] |
dcdFileStartRecords |
private static java.lang.String[] |
dgridContainsRecords |
private static java.lang.String[] |
dmolContainsRecords |
private static java.lang.String[] |
espressoContainsRecords |
private static java.lang.String[][] |
fileStartsWithRecords |
private static java.lang.String[] |
gamessUKContainsRecords |
private static java.lang.String[] |
gamessUSContainsRecords |
private static java.lang.String[] |
gaussianContainsRecords |
private static java.lang.String[] |
ghemicalMMLineStartRecords |
private static java.lang.String[] |
gulpContainsRecords |
private static java.lang.String[][] |
headerContainsRecords |
private static java.lang.String[] |
hyperChemLineStartRecords |
private static java.lang.String[] |
jaguarLineStartRecords |
private static int |
LEADER_CHAR_MAX |
private static java.lang.String[][] |
lineStartsWithRecords |
private static java.lang.String[] |
magResFileStartRecords |
private static java.lang.String[] |
mdlLineStartRecords |
private static java.lang.String[] |
mdTopLineStartRecords |
private static java.lang.String[] |
mol2Records |
private static java.lang.String[] |
moldenFileStartRecords |
private static java.lang.String[] |
mopacArchiveContainsRecords |
private static java.lang.String[] |
mopacContainsRecords |
private static java.lang.String[] |
nwchemContainsRecords |
private static java.lang.String[] |
p2nLineStartRecords |
private static java.lang.String[] |
pdbLineStartRecords |
private static java.lang.String[] |
pqrLineStartRecords |
private static java.lang.String[] |
psiContainsRecords |
private static java.lang.String[] |
qchemContainsRecords |
private static java.lang.String[] |
readerSets |
private static java.lang.String[] |
shelxLineStartRecords |
private static java.lang.String[] |
siestaContainsRecords |
private static java.lang.String[] |
spartanBinaryContainsRecords |
private static java.lang.String[] |
spartanContainsRecords |
private static java.lang.String[] |
spartanSmolLineStartRecords |
private static int |
SPECIAL_AIMS |
private static int |
SPECIAL_ALCHEMY |
static int |
SPECIAL_ARGUS_DOM |
static int |
SPECIAL_ARGUS_XML |
private static int |
SPECIAL_CASTEP |
static int |
SPECIAL_CHEM3D_DOM |
static int |
SPECIAL_CHEM3D_XML |
static int |
SPECIAL_CML_DOM |
static int |
SPECIAL_CML_XML |
private static int |
SPECIAL_CRYSTAL |
private static int |
SPECIAL_CUBE |
private static int |
SPECIAL_FOLDINGXYZ |
private static int |
SPECIAL_GENNBO |
private static int |
SPECIAL_GROMACS |
private static int |
SPECIAL_JME |
private static int |
SPECIAL_MOL |
static int |
SPECIAL_MOLPRO_DOM |
static int |
SPECIAL_MOLPRO_XML |
private static int |
SPECIAL_MOPACGRAPHF |
private static int |
SPECIAL_ODYSSEY |
static int |
SPECIAL_ODYSSEY_DOM |
static int |
SPECIAL_ODYSSEY_XML |
static int |
SPECIAL_QE_XML |
static int |
SPECIAL_VASP_DOM |
static int |
SPECIAL_VASP_XML |
private static int |
SPECIAL_WIEN |
static int |
SPECIAL_XSD_DOM |
static int |
SPECIAL_XSD_XML |
private static int |
SPECIAL_XYZ |
static java.lang.String[][] |
specialTags |
private static java.lang.String[] |
sptContainsRecords |
private static java.lang.String[] |
tlsDataOnlyFileStartRecords |
private static java.lang.String[] |
uicrcifContainsRecords |
private static java.lang.String[] |
vaspOutcarLineStartRecords |
private static java.lang.String[] |
webmoFileStartRecords |
private static java.lang.String[] |
xmlContainsRecords |
private static java.lang.String[] |
zMatrixFileStartRecords |
Constructor and Description |
---|
Resolver() |
Modifier and Type | Method and Description |
---|---|
private static boolean |
checkAims(java.lang.String[] lines) |
private static boolean |
checkAlchemy(java.lang.String line) |
private static boolean |
checkCastep(java.lang.String[] lines) |
private static boolean |
checkCrystal(java.lang.String[] lines) |
private static boolean |
checkCube(java.lang.String[] lines) |
private static boolean |
checkFoldingXyz(java.lang.String[] lines) |
private static boolean |
checkGenNBO(java.lang.String[] lines) |
private static boolean |
checkGromacs(java.lang.String[] lines) |
private static java.lang.String |
checkHeaderContains(java.lang.String header) |
private static java.lang.String |
checkLineStarts(java.lang.String[] lines) |
private static boolean |
checkMol(java.lang.String[] lines) |
private static boolean |
checkMopacGraphf(java.lang.String[] lines) |
private static boolean |
checkOdyssey(java.lang.String[] lines) |
private static java.lang.String |
checkSpecial(int nLines,
java.lang.String[] lines,
boolean isEnd) |
(package private) static java.lang.StringBuffer |
checkSpecialData(java.io.InputStream is,
java.lang.String[] zipDirectory)
called by SmarterJmolAdapter to see if we have a Spartan directory and, if so,
open it and get all the data into the correct order.
|
(package private) static java.lang.String[] |
checkSpecialInZip(java.lang.String[] zipDirectory)
called by SmarterJmolAdapter to see if we can automatically assign a file
from the zip file.
|
private static java.lang.String |
checkType(java.lang.String[][] typeTags,
java.lang.String type) |
private static boolean |
checkWien2k(java.lang.String[] lines) |
private static boolean |
checkXyz(java.lang.String[] lines) |
private static java.lang.String |
determineAtomSetCollectionReader(java.io.BufferedReader bufferedReader,
boolean returnLines)
the main resolver method.
|
(package private) static java.lang.Object |
DOMResolve(java.lang.Object DOMNode,
java.util.Map<java.lang.String,java.lang.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 java.lang.Object |
getAtomCollectionReader(java.lang.String fullName,
java.lang.String type,
java.io.BufferedReader bufferedReader,
java.util.Map<java.lang.String,java.lang.Object> htParams,
int ptFile)
the main method for reading files.
|
(package private) static java.lang.String |
getFileType(java.io.BufferedReader br)
From SmarterJmolAdapter.getFileTypeName(Object atomSetCollectionOrReader)
just return the file type with no exception issues
|
static java.lang.String |
getReaderClassBase(java.lang.String type) |
private static java.lang.String |
getReaderFromType(java.lang.String type) |
private static java.lang.String[] |
getSpartanDirs(java.lang.String outputFileData)
read the output file from the Spartan directory and decide from that what
files need to be read and in what order - usually M0001 or a set of Profiles.
|
private static java.lang.String[] |
getSpartanFileList(java.lang.String name,
java.lang.String[] dirNums)
returns the list of files to read for every Spartan spardir.
|
private static java.lang.String |
getXmlType(java.lang.String header) |
(package private) static java.lang.String[] |
specialLoad(java.lang.String name,
java.lang.String type)
Special loading for file directories.
|
private static final java.lang.String classBase
private static final java.lang.String[] readerSets
private static final java.lang.String CML_NAMESPACE_URI
private static final int SPECIAL_JME
private static final int SPECIAL_MOPACGRAPHF
private static final int SPECIAL_ODYSSEY
private static final int SPECIAL_MOL
private static final int SPECIAL_XYZ
private static final int SPECIAL_FOLDINGXYZ
private static final int SPECIAL_CUBE
private static final int SPECIAL_ALCHEMY
private static final int SPECIAL_WIEN
private static final int SPECIAL_CASTEP
private static final int SPECIAL_AIMS
private static final int SPECIAL_CRYSTAL
private static final int SPECIAL_GROMACS
private static final int SPECIAL_GENNBO
public static final int SPECIAL_ARGUS_XML
public static final int SPECIAL_CML_XML
public static final int SPECIAL_CHEM3D_XML
public static final int SPECIAL_MOLPRO_XML
public static final int SPECIAL_ODYSSEY_XML
public static final int SPECIAL_XSD_XML
public static final int SPECIAL_VASP_XML
public static final int SPECIAL_QE_XML
public static final int SPECIAL_ARGUS_DOM
public static final int SPECIAL_CML_DOM
public static final int SPECIAL_CHEM3D_DOM
public static final int SPECIAL_MOLPRO_DOM
public static final int SPECIAL_ODYSSEY_DOM
public static final int SPECIAL_XSD_DOM
public static final int SPECIAL_VASP_DOM
public static final java.lang.String[][] specialTags
private static final int LEADER_CHAR_MAX
private static final java.lang.String[] sptContainsRecords
private static final java.lang.String[] cubeFileStartRecords
private static final java.lang.String[] mol2Records
private static final java.lang.String[] webmoFileStartRecords
private static final java.lang.String[] moldenFileStartRecords
private static final java.lang.String[] dcdFileStartRecords
private static final java.lang.String[] tlsDataOnlyFileStartRecords
private static final java.lang.String[] zMatrixFileStartRecords
private static final java.lang.String[] magResFileStartRecords
private static final java.lang.String[][] fileStartsWithRecords
private static final java.lang.String[] pqrLineStartRecords
private static final java.lang.String[] p2nLineStartRecords
private static final java.lang.String[] pdbLineStartRecords
private static final java.lang.String[] shelxLineStartRecords
private static final java.lang.String[] cifLineStartRecords
private static final java.lang.String[] ghemicalMMLineStartRecords
private static final java.lang.String[] jaguarLineStartRecords
private static final java.lang.String[] mdlLineStartRecords
private static final java.lang.String[] spartanSmolLineStartRecords
private static final java.lang.String[] csfLineStartRecords
private static final java.lang.String[] mdTopLineStartRecords
private static final java.lang.String[] hyperChemLineStartRecords
private static final java.lang.String[] vaspOutcarLineStartRecords
private static final java.lang.String[][] lineStartsWithRecords
private static final java.lang.String[] xmlContainsRecords
private static final java.lang.String[] gaussianContainsRecords
private static final java.lang.String[] ampacContainsRecords
private static final java.lang.String[] mopacContainsRecords
private static final java.lang.String[] qchemContainsRecords
private static final java.lang.String[] gamessUKContainsRecords
private static final java.lang.String[] gamessUSContainsRecords
private static final java.lang.String[] spartanBinaryContainsRecords
private static final java.lang.String[] spartanContainsRecords
private static final java.lang.String[] adfContainsRecords
private static final java.lang.String[] dgridContainsRecords
private static final java.lang.String[] dmolContainsRecords
private static final java.lang.String[] gulpContainsRecords
private static final java.lang.String[] psiContainsRecords
private static final java.lang.String[] nwchemContainsRecords
private static final java.lang.String[] uicrcifContainsRecords
private static final java.lang.String[] crystalContainsRecords
private static final java.lang.String[] espressoContainsRecords
private static final java.lang.String[] siestaContainsRecords
private static final java.lang.String[] mopacArchiveContainsRecords
private static final java.lang.String[][] headerContainsRecords
public static final java.lang.String getReaderClassBase(java.lang.String type)
static java.lang.String getFileType(java.io.BufferedReader br)
br
- static java.lang.String[] specialLoad(java.lang.String name, java.lang.String type)
name
- type
- static java.lang.String[] checkSpecialInZip(java.lang.String[] zipDirectory)
zipDirectory
- static java.lang.StringBuffer checkSpecialData(java.io.InputStream is, java.lang.String[] zipDirectory)
is
- zipDirectory
- static java.lang.Object getAtomCollectionReader(java.lang.String fullName, java.lang.String type, java.io.BufferedReader bufferedReader, java.util.Map<java.lang.String,java.lang.Object> htParams, int ptFile) throws java.lang.Exception
fullName
- type
- bufferedReader
- htParams
- ptFile
- java.lang.Exception
static java.lang.Object DOMResolve(java.lang.Object DOMNode, java.util.Map<java.lang.String,java.lang.Object> htParams) throws java.lang.Exception
DOMNode
- htParams
- java.lang.Exception
private static java.lang.String[] getSpartanFileList(java.lang.String name, java.lang.String[] dirNums)
name
- dirNums
- private static java.lang.String[] getSpartanDirs(java.lang.String outputFileData)
outputFileData
- private static java.lang.String determineAtomSetCollectionReader(java.io.BufferedReader bufferedReader, boolean returnLines) throws java.lang.Exception
bufferedReader
- returnLines
- java.lang.Exception
private static java.lang.String checkHeaderContains(java.lang.String header) throws java.lang.Exception
java.lang.Exception
private static java.lang.String checkLineStarts(java.lang.String[] lines)
private static java.lang.String getXmlType(java.lang.String header) throws java.lang.Exception
java.lang.Exception
private static final java.lang.String getReaderFromType(java.lang.String type)
private static final java.lang.String checkType(java.lang.String[][] typeTags, java.lang.String type)
private static final java.lang.String checkSpecial(int nLines, java.lang.String[] lines, boolean isEnd)
private static boolean checkAims(java.lang.String[] lines)
private static boolean checkAlchemy(java.lang.String line)
private static boolean checkCastep(java.lang.String[] lines)
private static boolean checkCrystal(java.lang.String[] lines)
private static boolean checkCube(java.lang.String[] lines)
private static boolean checkFoldingXyz(java.lang.String[] lines)
lines
- First lines of the files.private static boolean checkGenNBO(java.lang.String[] lines)
private static boolean checkGromacs(java.lang.String[] lines)
private static boolean checkMol(java.lang.String[] lines)
private static boolean checkMopacGraphf(java.lang.String[] lines)
lines
- First lines of the files.private static boolean checkOdyssey(java.lang.String[] lines)
private static boolean checkWien2k(java.lang.String[] lines)
private static boolean checkXyz(java.lang.String[] lines)