Package org.jmol.jsv

Class JDXMOLParser

java.lang.Object

org.jmol.jsv.JDXMOLParser

All Implemented Interfaces:

JmolJDXMOLParser

public class JDXMOLParser
extends Object
implements JmolJDXMOLParser

Parses JDX-MOL records ##$MODELS and ##$PEAKS/##$SIGNALS. Used in both Jmol and JSpecView. Also gets info from ACD Labs files JCAMP-DX=5.00 $$ ACD/SpecManager v 12.01

Field Summary

Fields

Modifier and Type	Field	Description
private String	baseModel
private String	lastModel
private String	line
private JmolJDXMOLReader	loader
private String	modelIdList
private String	peakFilePath
private int[]	peakIndex
private String	piUnitsX
private String	piUnitsY
private String	thisModelID
private float	vibScale

Constructor Summary

Constructors

Constructor	Description
JDXMOLParser()

Method Summary

Modifier and Type	Method	Description
private boolean	findRecord(String tag)
private String	fixACDAtomList(String atoms, Map<String,String> zzcMap, int nAtoms)
private float	getACDPeakWidth(String type)
String	getAttribute(String line, String tag)
private void	getModelData(boolean isFirst)
String	getRecord(String key)
private void	getStringInfo(String file, String title, String mytype, String model, String atoms, Map<String,Object[]> htSets, String key, javajs.util.Lst<Object[]> list, String more)
javajs.util.Lst<String[]>	readACDAssignments(int nPoints, boolean isPeakAssignment)
String	readACDMolFile()	MOL file embedded in JDX file
private String	readLine()
boolean	readModels()
int	readPeaks(boolean isSignals, int peakCount)
JmolJDXMOLParser	set(JmolJDXMOLReader loader, String filePath, Map<String,Object> htParams)
int	setACDAssignments(String model, String mytype, int peakCount, javajs.util.Lst<String[]> acdlist, String molFile)
void	setLine(String s)
private int	setPeakData(javajs.util.Lst<Object[]> list, int offset)

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

line

private String line

lastModel

private String lastModel

thisModelID

private String thisModelID

baseModel

private String baseModel

vibScale

private float vibScale

piUnitsX

private String piUnitsX

piUnitsY

private String piUnitsY

loader

private JmolJDXMOLReader loader

modelIdList

private String modelIdList

peakIndex

private int[] peakIndex

peakFilePath

private String peakFilePath

Constructor Detail

JDXMOLParser

public JDXMOLParser()

Method Detail

set

public JmolJDXMOLParser set(JmolJDXMOLReader loader,
                            String filePath,
                            Map<String,Object> htParams)

Specified by:

set in interface JmolJDXMOLParser

getAttribute

public String getAttribute(String line,
                           String tag)

Specified by:

getAttribute in interface JmolJDXMOLParser

getRecord

public String getRecord(String key)
                 throws Exception

Specified by:

getRecord in interface JmolJDXMOLParser

Throws:

Exception

readModels

public boolean readModels()
                   throws Exception

Specified by:

readModels in interface JmolJDXMOLParser

Throws:

Exception

readACDMolFile

public String readACDMolFile()
                      throws Exception

MOL file embedded in JDX file

Specified by:

readACDMolFile in interface JmolJDXMOLParser

Throws:

Exception

readACDAssignments

public javajs.util.Lst<String[]> readACDAssignments(int nPoints,
                                                    boolean isPeakAssignment)
                                             throws Exception

Specified by:

readACDAssignments in interface JmolJDXMOLParser

Throws:

Exception

setACDAssignments

public int setACDAssignments(String model,
                             String mytype,
                             int peakCount,
                             javajs.util.Lst<String[]> acdlist,
                             String molFile)
                      throws Exception

Specified by:

setACDAssignments in interface JmolJDXMOLParser

Throws:

Exception

fixACDAtomList

private String fixACDAtomList(String atoms,
                              Map<String,String> zzcMap,
                              int nAtoms)

getACDPeakWidth

private float getACDPeakWidth(String type)

readPeaks

public int readPeaks(boolean isSignals,
                     int peakCount)
              throws Exception

Specified by:

readPeaks in interface JmolJDXMOLParser

Throws:

Exception

setPeakData

private int setPeakData(javajs.util.Lst<Object[]> list,
                        int offset)

getStringInfo

private void getStringInfo(String file,
                           String title,
                           String mytype,
                           String model,
                           String atoms,
                           Map<String,Object[]> htSets,
                           String key,
                           javajs.util.Lst<Object[]> list,
                           String more)

getModelData

private void getModelData(boolean isFirst)
                   throws Exception

Throws:

Exception

findRecord

private boolean findRecord(String tag)
                    throws Exception

Parameters:

tag -

Returns:

line

Throws:

Exception

readLine

private String readLine()
                 throws Exception

Throws:

Exception

setLine

public void setLine(String s)

Specified by:

setLine in interface JmolJDXMOLParser