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java.lang.Objectorg.jmol.api.JmolAdapter
org.jmol.adapter.smarter.SmarterJmolAdapter
public class SmarterJmolAdapter
Nested Class Summary | |
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(package private) class |
SmarterJmolAdapter.AtomIterator
|
(package private) class |
SmarterJmolAdapter.BondIterator
|
class |
SmarterJmolAdapter.StructureIterator
|
Field Summary | |
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static java.lang.String |
PATH_KEY
|
static java.lang.String |
PATH_SEPARATOR
|
Constructor Summary | |
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SmarterJmolAdapter()
|
Method Summary | |
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boolean |
coordinatesAreFractional(java.lang.Object atomSetCollection)
Get the boolean whether coordinates are fractional. |
void |
finish(java.lang.Object atomSetCollection)
|
JmolAdapter.AtomIterator |
getAtomIterator(java.lang.Object atomSetCollection)
Get an AtomIterator for retrieval of all atoms in the file. |
java.util.Hashtable |
getAtomSetAuxiliaryInfo(java.lang.Object atomSetCollection,
int atomSetIndex)
Get the auxiliary information for a particular atomSet. |
java.util.Hashtable |
getAtomSetCollectionAuxiliaryInfo(java.lang.Object atomSetCollection)
Get the auxiliary information for this atomSetCollection. |
java.lang.Object |
getAtomSetCollectionFromDOM(java.lang.Object DOMNode)
|
java.lang.Object |
getAtomSetCollectionFromReader(java.lang.String name,
java.lang.String type,
java.io.BufferedReader bufferedReader,
java.util.Hashtable htParams)
Read an atomSetCollection object from a bufferedReader and close the reader. |
java.lang.Object |
getAtomSetCollectionFromReaders(JmolFileReaderInterface fileReader,
java.lang.String[] names,
java.lang.String[] types,
java.util.Hashtable[] htparamsSet)
Associate a atomSetCollection object with an array of BufferedReader. |
java.lang.String |
getAtomSetCollectionName(java.lang.Object atomSetCollection)
Get the name of the atom set collection, if known. |
java.lang.Object |
getAtomSetCollectionOrBufferedReaderFromZip(java.io.InputStream is,
java.lang.String fileName,
java.lang.String[] zipDirectory,
java.util.Hashtable htParams,
boolean asBufferedReader)
|
java.util.Properties |
getAtomSetCollectionProperties(java.lang.Object atomSetCollection)
Get the properties for this atomSetCollection. |
int |
getAtomSetCount(java.lang.Object atomSetCollection)
Get number of atomSets in the file. |
java.lang.String |
getAtomSetName(java.lang.Object atomSetCollection,
int atomSetIndex)
Get the name of an atomSet. |
int |
getAtomSetNumber(java.lang.Object atomSetCollection,
int atomSetIndex)
Get the number identifying each atomSet. |
java.util.Properties |
getAtomSetProperties(java.lang.Object atomSetCollection,
int atomSetIndex)
Get the properties for an atomSet. |
JmolAdapter.BondIterator |
getBondIterator(java.lang.Object atomSetCollection)
Get a BondIterator for retrieval of all bonds in the file. |
java.lang.String |
getClientAtomStringProperty(java.lang.Object clientAtom,
java.lang.String propertyName)
Get a property from a clientAtom. |
int |
getEstimatedAtomCount(java.lang.Object atomSetCollection)
Get the estimated number of atoms contained in the file. |
java.lang.String |
getFileTypeName(java.lang.Object atomSetCollectionOrReader)
Get the type of this file or molecular model, if known. |
float[] |
getNotionalUnitcell(java.lang.Object atomSetCollection)
Get the notional unit cell. |
float[] |
getPdbScaleMatrix(java.lang.Object atomSetCollection)
Get the PDB scale matrix. |
float[] |
getPdbScaleTranslate(java.lang.Object atomSetCollection)
Get the PDB scale translation vector. |
JmolAdapter.StructureIterator |
getStructureIterator(java.lang.Object atomSetCollection)
Get a StructureIterator. |
java.lang.String[] |
specialLoad(java.lang.String name,
java.lang.String type)
|
private static java.lang.Object |
staticGetAtomSetCollectionFromDOM(java.lang.Object DOMNode)
|
private static java.lang.Object |
staticGetAtomSetCollectionFromReader(java.lang.String name,
java.lang.String type,
java.io.BufferedReader bufferedReader,
java.util.Hashtable htParams)
|
private static java.lang.Object |
staticGetAtomSetCollectionFromReaders(JmolFileReaderInterface fileReader,
java.lang.String[] names,
java.lang.String[] types,
java.util.Hashtable[] htparamsSet)
|
private static java.lang.Object |
staticGetAtomSetCollectionOrBufferedReaderFromZip(java.io.InputStream is,
java.lang.String fileName,
java.lang.String[] zipDirectory,
java.util.Hashtable htParams,
int subFilePtr,
boolean asBufferedReader)
|
private static java.lang.String |
staticGetFileTypeName(java.lang.Object atomSetCollectionOrReader)
|
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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public static final java.lang.String PATH_KEY
public static final java.lang.String PATH_SEPARATOR
Constructor Detail |
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public SmarterJmolAdapter()
Method Detail |
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public void finish(java.lang.Object atomSetCollection)
finish
in class JmolAdapter
public java.lang.String[] specialLoad(java.lang.String name, java.lang.String type)
specialLoad
in class JmolAdapter
public java.lang.Object getAtomSetCollectionFromReader(java.lang.String name, java.lang.String type, java.io.BufferedReader bufferedReader, java.util.Hashtable htParams)
JmolAdapter
Given the BufferedReader, return an object which represents the file
contents. The parameter name
is assumed to be the
file name or URL which is the source of reader. Note that this 'file'
may have been automatically decompressed. Also note that the name
may be 'String', representing a string constant. Therefore, few
assumptions should be made about the name
parameter.
The return value is an object which represents a atomSetCollection
.
This atomSetCollection
will be passed back in to other methods.
If the return value is instanceof String
then it is
considered an error condition and the returned String is the error
message.
getAtomSetCollectionFromReader
in class JmolAdapter
name
- File name, String or URL acting as the source of the readertype
- File type, if known, or nullbufferedReader
- The BufferedReaderhtParams
- a hash table containing parameter information
private static java.lang.Object staticGetAtomSetCollectionFromReader(java.lang.String name, java.lang.String type, java.io.BufferedReader bufferedReader, java.util.Hashtable htParams)
public java.lang.Object getAtomSetCollectionFromReaders(JmolFileReaderInterface fileReader, java.lang.String[] names, java.lang.String[] types, java.util.Hashtable[] htparamsSet)
JmolAdapter
Given the array of BufferedReader, return an object which represents
the concatenation of every file contents. The parameter name
is assumed to be the file names or URL which are the source of each
reader. Note that each of this 'file' may have been automatically
decompressed. Also note that the name may be 'String',
representing a string constant. Therefore, few
assumptions should be made about the name
parameter.
The return value is an object which represents a atomSetCollection
.
This atomSetCollection
will be passed back in to other methods.
If the return value is instanceof String
then it is
considered an error condition and the returned String is the error
message.
getAtomSetCollectionFromReaders
in class JmolAdapter
fileReader
- the thread requesting a set of files if bufferedReaders is nullnames
- File names, String or URL acting as the source of each readertypes
- File types, if known, or nullhtparamsSet
- The input parameters for each file to load
private static java.lang.Object staticGetAtomSetCollectionFromReaders(JmolFileReaderInterface fileReader, java.lang.String[] names, java.lang.String[] types, java.util.Hashtable[] htparamsSet)
public java.lang.Object getAtomSetCollectionOrBufferedReaderFromZip(java.io.InputStream is, java.lang.String fileName, java.lang.String[] zipDirectory, java.util.Hashtable htParams, boolean asBufferedReader)
getAtomSetCollectionOrBufferedReaderFromZip
in class JmolAdapter
private static java.lang.Object staticGetAtomSetCollectionOrBufferedReaderFromZip(java.io.InputStream is, java.lang.String fileName, java.lang.String[] zipDirectory, java.util.Hashtable htParams, int subFilePtr, boolean asBufferedReader)
public java.lang.Object getAtomSetCollectionFromDOM(java.lang.Object DOMNode)
getAtomSetCollectionFromDOM
in class JmolAdapter
private static java.lang.Object staticGetAtomSetCollectionFromDOM(java.lang.Object DOMNode)
public java.lang.String getFileTypeName(java.lang.Object atomSetCollectionOrReader)
JmolAdapter
getFileTypeName
in class JmolAdapter
atomSetCollectionOrReader
- The client file
"unknown"
private static java.lang.String staticGetFileTypeName(java.lang.Object atomSetCollectionOrReader)
public java.lang.String getAtomSetCollectionName(java.lang.Object atomSetCollection)
JmolAdapter
Some file formats contain a formal name of the molecule in the file.
If this method returns null
then the JmolViewer will
automatically supply the file/URL name as a default.
getAtomSetCollectionName
in class JmolAdapter
null
public java.util.Properties getAtomSetCollectionProperties(java.lang.Object atomSetCollection)
JmolAdapter
Not yet implemented everywhere, it is in the smarterJmolAdapter
getAtomSetCollectionProperties
in class JmolAdapter
atomSetCollection
- The client file
null
public java.util.Hashtable getAtomSetCollectionAuxiliaryInfo(java.lang.Object atomSetCollection)
JmolAdapter
Via the smarterJmolAdapter
getAtomSetCollectionAuxiliaryInfo
in class JmolAdapter
atomSetCollection
- The client file
null
public int getAtomSetCount(java.lang.Object atomSetCollection)
JmolAdapter
NOTE WARNING:
Not yet implemented everywhere, it is in the smarterJmolAdapter
getAtomSetCount
in class JmolAdapter
atomSetCollection
- The client file
public int getAtomSetNumber(java.lang.Object atomSetCollection, int atomSetIndex)
JmolAdapter
For a PDB file, this is is the model number. For others it is a 1-based atomSet number.
Note that this is not currently implemented in PdbReader
getAtomSetNumber
in class JmolAdapter
atomSetCollection
- The client fileatomSetIndex
- The atom set's index for which to get
the atom set number
public java.lang.String getAtomSetName(java.lang.Object atomSetCollection, int atomSetIndex)
JmolAdapter
getAtomSetName
in class JmolAdapter
atomSetCollection
- The client fileatomSetIndex
- The atom set index
public java.util.Properties getAtomSetProperties(java.lang.Object atomSetCollection, int atomSetIndex)
JmolAdapter
getAtomSetProperties
in class JmolAdapter
atomSetCollection
- The client fileatomSetIndex
- The atom set index
null
public java.util.Hashtable getAtomSetAuxiliaryInfo(java.lang.Object atomSetCollection, int atomSetIndex)
JmolAdapter
Via the smarterJmolAdapter
getAtomSetAuxiliaryInfo
in class JmolAdapter
atomSetCollection
- The client fileatomSetIndex
- The atom set index
null
public int getEstimatedAtomCount(java.lang.Object atomSetCollection)
JmolAdapter
Just return -1 if you don't know (or don't want to figure it out)
getEstimatedAtomCount
in class JmolAdapter
atomSetCollection
- The client file
public boolean coordinatesAreFractional(java.lang.Object atomSetCollection)
JmolAdapter
coordinatesAreFractional
in class JmolAdapter
atomSetCollection
- The client file
false
public float[] getNotionalUnitcell(java.lang.Object atomSetCollection)
JmolAdapter
This method returns the parameters that define a crystal unitcell
the parameters are returned in a float[] in the following order
a, b, c, alpha, beta, gamma
a, b, c
: angstroms
alpha, beta, gamma
: degrees
if there is no unit cell data then return null
getNotionalUnitcell
in class JmolAdapter
atomSetCollection
- The client file
null
public float[] getPdbScaleMatrix(java.lang.Object atomSetCollection)
JmolAdapter
Does not seem to be overriden by any descendent
getPdbScaleMatrix
in class JmolAdapter
atomSetCollection
- The client file
null
public float[] getPdbScaleTranslate(java.lang.Object atomSetCollection)
JmolAdapter
Does not seem to be overriden by any descendent
getPdbScaleTranslate
in class JmolAdapter
atomSetCollection
- The client file
null
public java.lang.String getClientAtomStringProperty(java.lang.Object clientAtom, java.lang.String propertyName)
JmolAdapter
getClientAtomStringProperty
in class JmolAdapter
clientAtom
- The clientAtompropertyName
- the key of the property
public JmolAdapter.AtomIterator getAtomIterator(java.lang.Object atomSetCollection)
JmolAdapter
This method may not return null
.
getAtomIterator
in class JmolAdapter
atomSetCollection
- The client file
JmolAdapter.AtomIterator
public JmolAdapter.BondIterator getBondIterator(java.lang.Object atomSetCollection)
JmolAdapter
If this method returns null
and no
bonds are defined then the JmolViewer will automatically apply its
rebonding code to build bonds between atoms.
getBondIterator
in class JmolAdapter
atomSetCollection
- The client file
null
JmolAdapter.BondIterator
public JmolAdapter.StructureIterator getStructureIterator(java.lang.Object atomSetCollection)
JmolAdapter
getStructureIterator
in class JmolAdapter
atomSetCollection
- The client file
null
|
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