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java.lang.Objectorg.jmol.adapter.smarter.Resolver
public class Resolver
Field Summary | |
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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[][] |
containsRecords
|
private static java.lang.String[] |
crystalContainsRecords
|
private static java.lang.String[] |
csfLineStartRecords
|
private static java.lang.String[] |
cubeFileStartRecords
|
private static java.lang.String[] |
dgridContainsRecords
|
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[] |
hyperChemLineStartRecords
|
private static java.lang.String[] |
jaguarLineStartRecords
|
private static int |
LEADER_CHAR_MAX
|
private static java.lang.String[][] |
lineStartsWithRecords
|
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[] |
mopacContainsRecords
|
private static java.lang.String[] |
nwchemContainsRecords
|
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[] |
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_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[] |
uicrcifContainsRecords
|
private static java.lang.String[] |
webmoFileStartRecords
|
private static java.lang.String[] |
xmlContainsRecords
|
Constructor Summary | |
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Resolver()
|
Method Summary | |
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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 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.Hashtable 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.Hashtable 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(netscape.javascript.JSObject DOMNode)
|
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. |
Methods inherited from class java.lang.Object |
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clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Field Detail |
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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_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[] 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[][] fileStartsWithRecords
private static final java.lang.String[] pqrLineStartRecords
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[][] 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[] 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[][] containsRecords
Constructor Detail |
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public Resolver()
Method Detail |
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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.Hashtable 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.Hashtable 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 getXmlType(netscape.javascript.JSObject DOMNode)
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 getXmlType(java.lang.String header) throws java.lang.Exception
java.lang.Exception
private static final java.lang.String checkSpecial(int nLines, java.lang.String[] lines, boolean isEnd)
private static boolean checkGenNBO(java.lang.String[] lines)
private static boolean checkGromacs(java.lang.String[] lines)
private static boolean checkCrystal(java.lang.String[] lines)
private static boolean checkWien2k(java.lang.String[] lines)
private static boolean checkCastep(java.lang.String[] lines)
private static boolean checkAims(java.lang.String[] lines)
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 boolean checkOdyssey(java.lang.String[] lines)
private static boolean checkMol(java.lang.String[] lines)
private static boolean checkAlchemy(java.lang.String line)
private static boolean checkXyz(java.lang.String[] lines)
private static boolean checkFoldingXyz(java.lang.String[] lines)
lines
- First lines of the files.
private static boolean checkMopacGraphf(java.lang.String[] lines)
lines
- First lines of the files.
private static boolean checkCube(java.lang.String[] lines)
|
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |