no.uio.labmed.pdb
Class Test

java.lang.Object
  |
  +--no.uio.labmed.pdb.DataFileReader
        |
        +--no.uio.labmed.pdb.AbstractPDBparser
              |
              +--no.uio.labmed.pdb.PDBparser
                    |
                    +--no.uio.labmed.pdb.PDBinterpreter
                          |
                          +--no.uio.labmed.pdb.Test

public class Test
extends PDBinterpreter

Test program for PDBinterpreter.


Nested Class Summary
 class Test.AtomData
           
 class Test.SecondaryStructure
           
 
Nested classes inherited from class no.uio.labmed.pdb.PDBinterpreter
PDBinterpreter.PrimaryStructureData, PDBinterpreter.SecondaryStructure
 
Nested classes inherited from class no.uio.labmed.pdb.AbstractPDBparser
 
Field Summary
 
Fields inherited from class no.uio.labmed.pdb.PDBinterpreter
mapModRes, mapStandardRes, primaryStructure, secondaryStructures
 
Fields inherited from class no.uio.labmed.pdb.PDBparser
exceptionList, exceptionPrintStream, nullAtomicData
 
Fields inherited from class no.uio.labmed.pdb.AbstractPDBparser
forgetAtomicData, forgetSecondaryStructureData, keywordsRecognized, TYPE_HELIX, TYPE_SHEET, TYPE_TURN
 
Constructor Summary
Test()
           
 
Method Summary
 void beginPrimaryStructureSection()
           
 void beginSecondaryStructureSection()
           
 void endCoordinateSection()
           
 void endParse()
           
 void endPrimaryStructureSection()
           
 void endSecondaryStructureSection()
           
 boolean hasKey(java.lang.String key)
           
static void main(java.lang.String[] args)
           
 AbstractPDBparser.AtomicData newAtom()
           
 void newHeader(java.lang.String t)
           
 AbstractPDBparser.AtomicData newHetatm()
           
 void newModel(int modelId)
           
 AbstractPDBparser.SecondaryStructureData newSecondaryStructure(java.lang.Object type)
           
 void newTitle(java.lang.String t)
           
 java.lang.String readLine()
           
 
Methods inherited from class no.uio.labmed.pdb.PDBinterpreter
getResidue, getSecondaryStructureList, getStandardResMap, newAminoAcidMap, newAtomChain, newAtomResidue, newModifiedResidue, newResidue, newSeqresChain
 
Methods inherited from class no.uio.labmed.pdb.PDBparser
addException, addParseException, addParseException, addParseException, getChainId, getResidueID, parse, printException, setExceptionPrintStream
 
Methods inherited from class no.uio.labmed.pdb.AbstractPDBparser
alternateAtom, beginConnectivityAnnotationSection, beginConnectivitySection, beginCoordinateSection, beginCoordinateTransformationSection, beginHeterogenSection, beginMiscellaneousFeaturesSection, beginParse, beginTitleSection, endAtomChain, endAtomResidue, endConnectivityAnnotationSection, endConnectivitySection, endCoordinateTransformationSection, endHeterogenSection, endMiscellaneousFeaturesSection, endModel, endTitleSection, keywordRecognized, lineHasKnownKey, newAnisou, newAtom, newAuthor, newCaveat, newCispep, newCompnd, newConect, newCryst1, newDbref, newExpdta, newFormul, newHeader, newHelix, newHet, newHetatm, newHetnam, newHetsyn, newHydbnd, newJrnl, newKeywds, newLink, newMaster, newModres, newMtrix, newObslte, newOrigx, newRemark, newRevdat, newScale, newSeqadv, newSheet, newSigatm, newSiguij, newSite, newSltbrg, newSource, newSprsde, newSSbond, newTurn, newTvect, terChain
 
Methods inherited from class no.uio.labmed.pdb.DataFileReader
checkKey, close, getInt, getInt, getInt, getInt, getNum, getNum, getNum, getNum, getValue, hasValue, line, nextLine, open, open, pos, rest, skip, sub, sub
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Constructor Detail

Test

public Test()
Method Detail

main

public static void main(java.lang.String[] args)
                 throws java.lang.Exception
java.lang.Exception

readLine

public java.lang.String readLine()
Overrides:
readLine in class PDBparser

hasKey

public boolean hasKey(java.lang.String key)
Overrides:
hasKey in class DataFileReader

newHeader

public void newHeader(java.lang.String t)

newTitle

public void newTitle(java.lang.String t)
Overrides:
newTitle in class AbstractPDBparser

beginPrimaryStructureSection

public void beginPrimaryStructureSection()
Overrides:
beginPrimaryStructureSection in class AbstractPDBparser

endPrimaryStructureSection

public void endPrimaryStructureSection()
Overrides:
endPrimaryStructureSection in class AbstractPDBparser

beginSecondaryStructureSection

public void beginSecondaryStructureSection()
Overrides:
beginSecondaryStructureSection in class AbstractPDBparser

newSecondaryStructure

public AbstractPDBparser.SecondaryStructureData newSecondaryStructure(java.lang.Object type)
Overrides:
newSecondaryStructure in class PDBinterpreter

endSecondaryStructureSection

public void endSecondaryStructureSection()
Overrides:
endSecondaryStructureSection in class AbstractPDBparser

newModel

public void newModel(int modelId)
Overrides:
newModel in class AbstractPDBparser

newAtom

public AbstractPDBparser.AtomicData newAtom()

newHetatm

public AbstractPDBparser.AtomicData newHetatm()

endParse

public void endParse()
Overrides:
endParse in class AbstractPDBparser

endCoordinateSection

public void endCoordinateSection()
Overrides:
endCoordinateSection in class AbstractPDBparser