jspecview.source.JDXReader

All Implemented Interfaces:: JmolJDXMOLReader

public class JDXReader extends Object implements JmolJDXMOLReader

JDXFileReader reads JDX data, including complex BLOCK files that contain NTUPLE blocks or nested BLOCK data. In addition, this reader allows for simple concatenation -- no LINK record is required. This allows for testing simply by joining files. We also might be able to adapt this to reading a ZIP file collection.

Author:: Debbie-Ann Facey, Khari A. Bryan, Prof. Robert J. Lancashire, Bob Hanson, hansonr@stolaf.edu

Method Summary

Modifier and Type

Method

Description

void

addPeakData(String info)

static JDXSource

createJDXSource(GenericFileInterface file, Object in, String filePath, boolean obscure, boolean loadImaginary, int iSpecFirst, int iSpecLast, float nmrMaxY)

general entrance method

static JDXSource

createJDXSourceFromStream(InputStream in, boolean obscure, boolean loadImaginary, float nmrMaxY)

used only for preferences display and Android

String

discardLinesUntilContains(String containsMatch)

String

discardLinesUntilContains2(String s1, String s2)

String

discardLinesUntilNonBlank()

static Map<String,String>

getHeaderMap(InputStream in, Map<String,String> map)

static Map<String,String>

getHeaderMapS(InputStream in, Map<String,String> map, int index, String suffix)

static String

getVarList(String dataClass)

static void

main(String[] args)

void

processModelData(String id, String data, String type, String base, String last, float modelScale, float vibScale, boolean isFirst)

String

rd()

void

setSpectrumPeaks(int nH, String peakXLabel, String peakYlabel)

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Method Details
- getVarList
  
  public static String getVarList(String dataClass)
- createJDXSourceFromStream
  
  public static JDXSource createJDXSourceFromStream(InputStream in, boolean obscure, boolean loadImaginary, float nmrMaxY) throws Exception
  
  used only for preferences display and Android
  
  Parameters:
  
  in -
  
  obscure -
  
  loadImaginary -
  
  nmrMaxY -
  
  Returns:
  
  source
  
  Throws:
  
  Exception
- getHeaderMap
  
  public static Map<String,String> getHeaderMap(InputStream in, Map<String,String> map) throws Exception
  
  Throws:
  
  Exception
- getHeaderMapS
  
  public static Map<String,String> getHeaderMapS(InputStream in, Map<String,String> map, int index, String suffix) throws Exception
  
  Parameters:
  
  in -
  
  map - may be null
  
  index - >= 0 for nth block; -1 for "last block"
  
  suffix -
  
  Returns:
  
  map
  
  Throws:
  
  Exception
- createJDXSource
  
  public static JDXSource createJDXSource(GenericFileInterface file, Object in, String filePath, boolean obscure, boolean loadImaginary, int iSpecFirst, int iSpecLast, float nmrMaxY) throws Exception
  
  general entrance method
  
  Parameters:
  
  file -
  
  in - one of: BufferedReader, InputStream, String, byte[]
  
  filePath -
  
  obscure -
  
  loadImaginary -
  
  iSpecFirst -
  
  iSpecLast -
  
  nmrMaxY -
  
  Returns:
  
  source
  
  Throws:
  
  Exception
- rd
  
  public String rd() throws Exception
  
  Specified by:
  
  rd in interface JmolJDXMOLReader
  
  Throws:
  
  Exception
- setSpectrumPeaks
  
  public void setSpectrumPeaks(int nH, String peakXLabel, String peakYlabel)
  
  Specified by:
  
  setSpectrumPeaks in interface JmolJDXMOLReader
- addPeakData
  
  public void addPeakData(String info)
  
  Specified by:
  
  addPeakData in interface JmolJDXMOLReader
- processModelData
  
  public void processModelData(String id, String data, String type, String base, String last, float modelScale, float vibScale, boolean isFirst) throws Exception
  
  Specified by:
  
  processModelData in interface JmolJDXMOLReader
  
  Throws:
  
  Exception
- discardLinesUntilContains
  
  public String discardLinesUntilContains(String containsMatch) throws Exception
  
  Specified by:
  
  discardLinesUntilContains in interface JmolJDXMOLReader
  
  Throws:
  
  Exception
- discardLinesUntilContains2
  
  public String discardLinesUntilContains2(String s1, String s2) throws Exception
  
  Specified by:
  
  discardLinesUntilContains2 in interface JmolJDXMOLReader
  
  Throws:
  
  Exception
- discardLinesUntilNonBlank
  
  public String discardLinesUntilNonBlank() throws Exception
  
  Specified by:
  
  discardLinesUntilNonBlank in interface JmolJDXMOLReader
  
  Throws:
  
  Exception
- main
  
  public static void main(String[] args)

Class JDXReader

Method Summary

Methods inherited from class java.lang.Object

Method Details

getVarList

createJDXSourceFromStream

getHeaderMap

getHeaderMapS

createJDXSource

rd

setSpectrumPeaks

addPeakData

processModelData

discardLinesUntilContains

discardLinesUntilContains2

discardLinesUntilNonBlank

main