A B C D E F G H I J K L M N O P Q R S T V W X Y

A

a - Variable in class no.uio.labmed.util.objectinfo.Test
 
A - class no.uio.labmed.util.tree.adapter.A.
 
A(int) - Constructor for class no.uio.labmed.util.tree.adapter.A
 
AbstractAligner - class no.uio.labmed.biojava.alignment.AbstractAligner.
Abstract implementation of the AlignerInterface.
AbstractAligner() - Constructor for class no.uio.labmed.biojava.alignment.AbstractAligner
 
AbstractAminoAcid - class no.uio.labmed.pdb.AbstractAminoAcid.
 
AbstractAminoAcid() - Constructor for class no.uio.labmed.pdb.AbstractAminoAcid
 
AbstractAminoAcidMap - class no.uio.labmed.pdb.AbstractAminoAcidMap.
 
AbstractAminoAcidMap() - Constructor for class no.uio.labmed.pdb.AbstractAminoAcidMap
 
AbstractMatrise - class no.uio.labmed.linalg.AbstractMatrise.
Grunnleggende struktur for n-dimensjonale matriser.
AbstractMatrise.Faktorer - class no.uio.labmed.linalg.AbstractMatrise.Faktorer.
Faktoriseringsobjekt for aa dekomponere matrisen.
AbstractMatrise.Faktorer(AbstractMatrise, AbstractMatrise[]) - Constructor for class no.uio.labmed.linalg.AbstractMatrise.Faktorer
Konstruktor som lager et faktoriseringsobjekt med gitte vekter.
AbstractMatrise.Iterator - class no.uio.labmed.linalg.AbstractMatrise.Iterator.
Iterator for aa gaa igjennom alle posisjonene i en matrise.
AbstractMatrise.Iterator() - Constructor for class no.uio.labmed.linalg.AbstractMatrise.Iterator
Konstruktor for aa lage en ny iterator.
AbstractMatrise(int[]) - Constructor for class no.uio.labmed.linalg.AbstractMatrise
Konstruktoren.
AbstractNodeStatistic - class no.uio.labmed.util.tree.stat.AbstractNodeStatistic.
 
AbstractNodeStatistic() - Constructor for class no.uio.labmed.util.tree.stat.AbstractNodeStatistic
 
AbstractPDBparser - class no.uio.labmed.pdb.AbstractPDBparser.
Abstract PDBparser which implements empty metods, filtering functionality, and exception handling.
AbstractPDBparser.AtomicData - class no.uio.labmed.pdb.AbstractPDBparser.AtomicData.
 
AbstractPDBparser.AtomicData() - Constructor for class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
AbstractPDBparser.SecondaryStructureData - class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData.
 
AbstractPDBparser.SecondaryStructureData(Object) - Constructor for class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
AbstractPDBparser() - Constructor for class no.uio.labmed.pdb.AbstractPDBparser
 
AbstractTreeStatistic - class no.uio.labmed.util.tree.stat.AbstractTreeStatistic.
 
AbstractTreeStatistic(TreeInterface) - Constructor for class no.uio.labmed.util.tree.stat.AbstractTreeStatistic
 
action - Variable in class no.uio.labmed.molecule.SelectionNode
 
Action - class no.uio.labmed.molecule.Action.
 
action() - Method in class no.uio.labmed.molecule.SelectionNode
 
Action() - Constructor for class no.uio.labmed.molecule.Action
 
ActionPlot - class no.uio.labmed.molecule.ActionPlot.
 
ActionPlot.ActionPlotAtom - class no.uio.labmed.molecule.ActionPlot.ActionPlotAtom.
 
ActionPlot.ActionPlotAtom() - Constructor for class no.uio.labmed.molecule.ActionPlot.ActionPlotAtom
 
ActionPlot() - Constructor for class no.uio.labmed.molecule.ActionPlot
 
ActionPrint - class no.uio.labmed.molecule.ActionPrint.
 
ActionPrint() - Constructor for class no.uio.labmed.molecule.ActionPrint
 
add(Atom) - Method in class no.uio.labmed.protein.Molecule
 
add(Bond) - Method in class no.uio.labmed.molecule.AtomicBondings
 
add(Component) - Method in class no.uio.labmed.util.output.Output
 
add(double) - Method in class no.uio.labmed.linalg.Matrise
 
add(double[]) - Method in class no.uio.labmed.output.GraphPane
 
add(double[]) - Method in class no.uio.labmed.util.output.GraphPane
 
add(int[], double) - Method in class no.uio.labmed.linalg.Matrise
 
add(int, double) - Method in class no.uio.labmed.linalg.Matrise
 
add(int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
add(int, int, double) - Method in class no.uio.labmed.linalg.Matrise
 
add(int, int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
add(int, int, int, double) - Method in class no.uio.labmed.linalg.Matrise
 
add(int, int, int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
add(String, Component) - Method in class no.uio.labmed.output.Vindu
 
add(String, Component) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, double[][]) - Method in class no.uio.labmed.output.Vindu
 
add(String, double[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, double[][], Object[]) - Method in class no.uio.labmed.output.Vindu
 
add(String, double[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, float[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, float[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, int[][]) - Method in class no.uio.labmed.output.Vindu
 
add(String, int[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, int[][], Object[]) - Method in class no.uio.labmed.output.Vindu
 
add(String, int[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, Matrise) - Method in class no.uio.labmed.output.Vindu
 
add(String, Matrise, Object[]) - Method in class no.uio.labmed.output.Vindu
 
add(String, Object[][]) - Method in class no.uio.labmed.output.Vindu
 
add(String, Object[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, Object[][], Object[]) - Method in class no.uio.labmed.output.Vindu
 
add(String, Object[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(String, String) - Method in class no.uio.labmed.output.Vindu
 
add(String, String) - Method in class no.uio.labmed.util.output.TabbedFrame
 
add(TreeInterface) - Method in class no.uio.labmed.util.tree.TreeToString
Add tree to (internal) string buffer
add(TreePointerInterface) - Method in class no.uio.labmed.util.tree.TreeToString
Add subtree under node.
addAnnotation(String, String) - Method in class no.uio.labmed.protein.Protein
 
addAtomRes(int, AbstractAminoAcid) - Method in class no.uio.labmed.pdb.PDBinterpreter.PrimaryStructureData
 
addChild(SequenceReference) - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Add new child with given sequence reference.
addChildren() - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapterNode
Add children.
addChildren(JTreeAdapterNode) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Add children to node if not previously done, returning true.
addChildren(TreeAdapterNode) - Method in class no.uio.labmed.util.output.TreeAdapter
Add children to node if not previously done, returning true.
addElement(MolecularElement) - Method in class no.uio.labmed.molecule.CompoundElement
 
addElement(MolecularElement, String) - Method in class no.uio.labmed.molecule.CompoundElement
 
addElementAndTags(CompoundElement) - Method in class no.uio.labmed.molecule.CompoundElement
 
addException(Exception) - Method in class no.uio.labmed.pdb.PDBparser
 
addField(Field) - Method in class no.uio.labmed.pybliographer.Entry
 
addFile(String) - Static method in class no.uio.labmed.util.tree.Test
 
addGraph(String) - Method in class no.uio.labmed.util.output.Output
 
addGraph(String, String) - Method in class no.uio.labmed.output.Vindu
 
addGraph(String, String) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addMolecule(Molecule) - Method in class no.uio.labmed.protein.Protein
 
addNewElement(Molecule) - Method in class no.uio.labmed.molecule.Compound
 
addParseException(String) - Method in class no.uio.labmed.pdb.PDBparser
 
addParseException(String, Exception) - Method in class no.uio.labmed.pdb.PDBparser
 
addParseException(String, String) - Method in class no.uio.labmed.pdb.PDBparser
 
addPrintStream(String) - Method in class no.uio.labmed.output.Vindu
 
addPrintStream(String) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addPrintStream(String) - Method in class no.uio.labmed.util.output.Output
 
addRes(AbstractAminoAcid) - Method in class no.uio.labmed.pdb.PDBinterpreter.PrimaryStructureData
 
addSequence(SequenceReference) - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Add sequence to tree.
addSequence(SequenceReference) - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.SequenceAdder
Add sequence to tree
addSequence(SymbolList) - Static method in class no.uio.labmed.util.tree.Test
 
addStat(AbstractNodeStatistic) - Method in class no.uio.labmed.util.tree.stat.AbstractNodeStatistic
 
addString(String) - Static method in class no.uio.labmed.util.tree.Test
 
addTabbedPane(String) - Method in class no.uio.labmed.util.output.Output
 
addToView(Atom) - Method in class no.uio.labmed.molecule.ViewMolecule
 
addToView(Compound) - Method in class no.uio.labmed.molecule.ViewMolecule
 
addToView(Molecule) - Method in class no.uio.labmed.molecule.ViewMolecule
 
addTranspose(String, double[][]) - Method in class no.uio.labmed.output.Vindu
 
addTranspose(String, double[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, double[][], Object[]) - Method in class no.uio.labmed.output.Vindu
 
addTranspose(String, double[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, float[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, float[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, int[][]) - Method in class no.uio.labmed.output.Vindu
 
addTranspose(String, int[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, int[][], Object[]) - Method in class no.uio.labmed.output.Vindu
 
addTranspose(String, int[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, Object[][]) - Method in class no.uio.labmed.output.Vindu
 
addTranspose(String, Object[][]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTranspose(String, Object[][], Object[]) - Method in class no.uio.labmed.output.Vindu
 
addTranspose(String, Object[][], Object[]) - Method in class no.uio.labmed.util.output.TabbedFrame
 
addTree(String, TreeModel) - Method in class no.uio.labmed.util.output.Output
 
addTreeModelListener(TreeModelListener) - Method in class no.uio.labmed.util.output.TreeAdapter
Empty implementation
addTreeModelListener(TreeModelListener) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Empty implementation
align(SymbolList, SymbolList) - Method in class no.uio.labmed.biojava.alignment.SimpleAligner
 
align(SymbolList, SymbolList) - Method in interface no.uio.labmed.biojava.alignment.AlignerInterface
 
align(SymbolList, SymbolList) - Method in class no.uio.labmed.biojava.alignment.AbstractAligner
 
AlignerInterface - interface no.uio.labmed.biojava.alignment.AlignerInterface.
Interface defining a sequence aligner: one that is used to produce sequence alignments.
alternateAtom(AbstractPDBparser.AtomicData) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
AminoAcid - class no.uio.labmed.pdb.AminoAcid.
 
AminoAcid - class no.uio.labmed.protein.AminoAcid.
 
AminoAcidElement - class no.uio.labmed.molecule.AminoAcidElement.
Defines the amino acid molecular structures.
AminoAcidElement(String) - Constructor for class no.uio.labmed.molecule.AminoAcidElement
 
AminoAcidElement(String, MolecularType) - Constructor for class no.uio.labmed.molecule.AminoAcidElement
 
AminoAcidElement(String, MolecularType, String) - Constructor for class no.uio.labmed.molecule.AminoAcidElement
 
AminoAcidElement(String, String) - Constructor for class no.uio.labmed.molecule.AminoAcidElement
 
AminoAcidMap - class no.uio.labmed.pdb.AminoAcidMap.
 
AminoAcidMap() - Constructor for class no.uio.labmed.pdb.AminoAcidMap
 
aminoAcids - Static variable in class no.uio.labmed.pdb.AminoAcid
 
append(String) - Method in class no.uio.labmed.output.AppendOutputStream
 
append(String) - Method in class no.uio.labmed.util.output.AppendOutputStream
 
append(String) - Method in class no.uio.labmed.util.tree.TreeToString
Append string to string buffer
append(TreePointerInterface) - Method in class no.uio.labmed.util.tree.TreeToString
Append node to string buffer
AppendOutputStream - class no.uio.labmed.output.AppendOutputStream.
AppendOutputStream.java Created: Wed Jul 17 00:17:39 2002
AppendOutputStream - class no.uio.labmed.util.output.AppendOutputStream.
AppendOutputStream.java Created: Wed Jul 17 00:17:39 2002
AppendOutputStream() - Constructor for class no.uio.labmed.output.AppendOutputStream
 
AppendOutputStream() - Constructor for class no.uio.labmed.util.output.AppendOutputStream
 
Atom - class no.uio.labmed.molecule.Atom.
An actual atom: ie. and instance of an atom, not just the atomic element.
Atom - class no.uio.labmed.protein.Atom.
 
Atom() - Constructor for class no.uio.labmed.protein.Atom
 
Atom(AtomicElement) - Constructor for class no.uio.labmed.molecule.Atom
 
Atom(float, float, float) - Constructor for class no.uio.labmed.protein.Atom
 
Atomic - interface no.uio.labmed.molecule.Atomic.
Interface defining atomic elements.
AtomicBondings - class no.uio.labmed.molecule.AtomicBondings.
Object for storing a list of bonds: either those that a given atom participates in, or bonds in a given compound.
AtomicBondings() - Constructor for class no.uio.labmed.molecule.AtomicBondings
 
AtomicElement - class no.uio.labmed.molecule.AtomicElement.
Defines a general atom.
AtomicElement(String) - Constructor for class no.uio.labmed.molecule.AtomicElement
 
AtomicElement(String, String) - Constructor for class no.uio.labmed.molecule.AtomicElement
 
AtomInCompound - class no.uio.labmed.molecule.AtomInCompound.
Object to identify an atom in a compound element.
AtomInCompound(CompoundElement, int, Atomic) - Constructor for class no.uio.labmed.molecule.AtomInCompound
 

B

b - Variable in class no.uio.labmed.util.objectinfo.Test
 
beginConnectivityAnnotationSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginConnectivitySection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginCoordinateSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginCoordinateTransformationSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginHeterogenSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginMiscellaneousFeaturesSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginParse() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginPrimaryStructureSection() - Method in class no.uio.labmed.pdb.TestParser
 
beginPrimaryStructureSection() - Method in class no.uio.labmed.pdb.Test
 
beginPrimaryStructureSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginSecondaryStructureSection() - Method in class no.uio.labmed.pdb.TestParser
 
beginSecondaryStructureSection() - Method in class no.uio.labmed.pdb.Test
 
beginSecondaryStructureSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
beginTitleSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
BioSequenceReference - class no.uio.labmed.util.tree.BioSequenceReference.
Implementation of SequenceReference for BioJava DNA sequences.
BioSequenceReference(SymbolList) - Constructor for class no.uio.labmed.util.tree.BioSequenceReference
 
blank() - Method in class no.uio.labmed.molecule.ReadPDB.AtomData
 
blank() - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
Bond - class no.uio.labmed.molecule.Bond.
Abstract class of bonds between atoms specified as Atomic instances.
Bond() - Constructor for class no.uio.labmed.molecule.Bond
 
bondings - Variable in class no.uio.labmed.molecule.AtomicBondings
 
bondings() - Method in class no.uio.labmed.molecule.AtomInCompound
 
bondings() - Method in class no.uio.labmed.molecule.AtomicElement
 
bondings() - Method in interface no.uio.labmed.molecule.Atomic
 
bondings() - Method in class no.uio.labmed.molecule.Atom
 

C

calcStat(TreePointerInterface) - Method in class no.uio.labmed.util.tree.stat.AbstractTreeStatistic
 
changed(int) - Method in class no.uio.labmed.pdb.ChangeIntIndicator
 
changed(int) - Method in class no.uio.labmed.pdb.ChangeIndicator
 
changed(Object) - Method in class no.uio.labmed.pdb.ChangeObjectIndicator
 
changed(Object) - Method in class no.uio.labmed.pdb.ChangeIndicator
 
ChangeIndicator - class no.uio.labmed.pdb.ChangeIndicator.
Abstract class for returning a flag to tell if a value has been changed.
ChangeIndicator() - Constructor for class no.uio.labmed.pdb.ChangeIndicator
 
ChangeIntIndicator - class no.uio.labmed.pdb.ChangeIntIndicator.
Implementation of ChangeIndicator for values of type int.
ChangeIntIndicator() - Constructor for class no.uio.labmed.pdb.ChangeIntIndicator
 
ChangeObjectIndicator - class no.uio.labmed.pdb.ChangeObjectIndicator.
Implementation of ChangeIndicator for values of Object.
ChangeObjectIndicator() - Constructor for class no.uio.labmed.pdb.ChangeObjectIndicator
 
charAlphabet(String) - Method in class no.uio.labmed.biojava.alignment.Test
 
checkKey(String) - Method in class no.uio.labmed.pdb.DataFileReader
 
checkKey(String) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
ChildIterator - interface no.uio.labmed.util.tree.ChildIterator.
Interface specifying iterators that iterate over children of a node in a tree.
childIterator() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
childIterator() - Method in interface no.uio.labmed.util.tree.TreeNodePointerInterface
Return an iterator to iterate over the children.
childIterator() - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Return an iterator to iterate over the children.
childIterator() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
childIterator() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return iterator to iterate over children.
clear() - Method in class no.uio.labmed.util.tree.TreeToString
Clear string
clone() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
clone() - Method in interface no.uio.labmed.util.tree.TreeNodePointerInterface
Clone the pointer
clone() - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Clone the pointer
clone() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
clone() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Clone pointer.
close() - Method in class no.uio.labmed.output.AppendOutputStream
 
close() - Method in class no.uio.labmed.pdb.DataFileReader
 
close() - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
close() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
close() - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
close() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
close() - Method in class no.uio.labmed.util.output.AppendOutputStream
 
closeBody() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
closeDocument() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
cNormal(double) - Static method in class no.uio.labmed.linalg.Global
 
cNormal(double, double) - Static method in class no.uio.labmed.linalg.Global
Beregning av kumulativ normalfordeling Returns the error function of a double.
code() - Method in class no.uio.labmed.pdb.AminoAcid
 
code() - Method in class no.uio.labmed.protein.AminoAcid
 
compare(Object, Object) - Method in class no.uio.labmed.pybliographer.FieldComparator
 
compareFields(Field, Field) - Method in class no.uio.labmed.pybliographer.FieldComparator
 
complete() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Complete links of new child: ie. add failure and shortcut links.
complete() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Complete links of new node.
Compound - class no.uio.labmed.molecule.Compound.
An actual compound: ie. one refering to Atom instances.
Compound(CompoundElement) - Constructor for class no.uio.labmed.molecule.Compound
 
CompoundElement - class no.uio.labmed.molecule.CompoundElement.
Defines a general compound molecule: a compound of general molecular structure (see MolecularStructure).
CompoundElement.SubElement - class no.uio.labmed.molecule.CompoundElement.SubElement.
Container for element and index number for an element in a compound: ie. the compound is a list of subelements, which in turn refere to an element and its index in the list.
CompoundElement.SubElement(int, MolecularElement) - Constructor for class no.uio.labmed.molecule.CompoundElement.SubElement
 
CompoundElement(String) - Constructor for class no.uio.labmed.molecule.CompoundElement
 
CompoundElement(String, MolecularType) - Constructor for class no.uio.labmed.molecule.CompoundElement
 
CompoundElement(String, MolecularType, String) - Constructor for class no.uio.labmed.molecule.CompoundElement
 
copy() - Method in class no.uio.labmed.util.tree.SequenceReference
Clone the reference object
copy() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
copyValues(BioSequenceReference) - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
copyValues(ISTPointer) - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Copy values: to be used by clone.
copyValues(SequenceReference) - Method in class no.uio.labmed.util.tree.SequenceReference
Copy values of one SequenceReference to another.
CovalentBond - class no.uio.labmed.molecule.CovalentBond.
A covalent bond between two atoms.
CovalentBond(Atomic, Atomic) - Constructor for class no.uio.labmed.molecule.CovalentBond
 
createScene() - Method in class no.uio.labmed.molecule.ViewMolecule
 
createScene() - Method in class no.uio.labmed.protein.ViewMolecule
 
createSymbolList(String) - Static method in class no.uio.labmed.biojava.alignment.StringSequenceTools
 
createSymbolList(String, Alphabet) - Static method in class no.uio.labmed.biojava.alignment.StringSequenceTools
 

D

DataFileReader - class no.uio.labmed.pdb.DataFileReader.
Buffered reader with methods for reading data files.
DataFileReader - class no.uio.labmed.pybliographer.DataFileReader.
Buffered reader with methods for reading data files.
DataFileReader() - Constructor for class no.uio.labmed.pdb.DataFileReader
 
DataFileReader() - Constructor for class no.uio.labmed.pybliographer.DataFileReader
 
DataPrintStream - class no.uio.labmed.pdb.DataPrintStream.
 
DataPrintStream() - Constructor for class no.uio.labmed.pdb.DataPrintStream
 
DataPrintStream(OutputStream) - Constructor for class no.uio.labmed.pdb.DataPrintStream
 
defaultSelection - Variable in class no.uio.labmed.molecule.SelectionNode
 
destroy() - Method in class no.uio.labmed.molecule.ViewMolecule
 
destroy() - Method in class no.uio.labmed.protein.ViewMolecule
 
dim - Variable in class no.uio.labmed.linalg.AbstractMatrise
Dimensjonene til matrisen.
dim(int) - Method in class no.uio.labmed.linalg.AbstractMatrise
Gir storrelsen dimensjonene.
dims() - Method in class no.uio.labmed.linalg.AbstractMatrise
Antall dimensjoner.
drawDot(Graphics2D, double, double, int) - Method in class no.uio.labmed.output.GraphPane
 
drawDot(Graphics2D, double, double, int) - Method in class no.uio.labmed.util.output.GraphPane
 
drawKurve(Graphics2D, double[]) - Method in class no.uio.labmed.output.GraphPane
 
drawKurve(Graphics2D, double[]) - Method in class no.uio.labmed.util.output.GraphPane
 
drawKurve(Graphics2D, double[], double[]) - Method in class no.uio.labmed.output.GraphPane
 
drawKurve(Graphics2D, double[], double[]) - Method in class no.uio.labmed.util.output.GraphPane
 
drawLine(Graphics2D, double, double, double, double) - Method in class no.uio.labmed.output.GraphPane
 
drawLine(Graphics2D, double, double, double, double) - Method in class no.uio.labmed.util.output.GraphPane
 

E

element - Variable in class no.uio.labmed.molecule.CompoundElement.SubElement
 
element() - Method in class no.uio.labmed.molecule.Atom
 
element() - Method in class no.uio.labmed.molecule.CompoundElement.SubElement
 
element() - Method in class no.uio.labmed.molecule.Compound
 
element() - Method in class no.uio.labmed.molecule.Molecule
 
elements - Variable in class no.uio.labmed.linalg.IntMatrise
 
elements - Variable in class no.uio.labmed.linalg.Matrise
 
endAtomChain() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endAtomResidue() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endConnectivityAnnotationSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endConnectivitySection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endCoordinateSection() - Method in class no.uio.labmed.pdb.Test
 
endCoordinateSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endCoordinateTransformationSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endHeterogenSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endMiscellaneousFeaturesSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endModel() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endParse() - Method in class no.uio.labmed.pdb.TestParser
 
endParse() - Method in class no.uio.labmed.pdb.Test
 
endParse() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endPrimaryStructureSection() - Method in class no.uio.labmed.pdb.TestParser
 
endPrimaryStructureSection() - Method in class no.uio.labmed.pdb.Test
 
endPrimaryStructureSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endSecondaryStructureSection() - Method in class no.uio.labmed.pdb.TestParser
 
endSecondaryStructureSection() - Method in class no.uio.labmed.pdb.Test
 
endSecondaryStructureSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
endTitleSection() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
Entry - class no.uio.labmed.pybliographer.Entry.
 
Entry() - Constructor for class no.uio.labmed.pybliographer.Entry
 
EntryInfoInterface - interface no.uio.labmed.pybliographer.EntryInfoInterface.
 
eof() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
erfc(double) - Static method in class no.uio.labmed.linalg.Global
Returns the complementary error function of a double.
exceptionList - Variable in class no.uio.labmed.pdb.PDBparser
 
exceptionPrintStream - Variable in class no.uio.labmed.pdb.PDBparser
 
expBoundNormal(double, double, double, double) - Static method in class no.uio.labmed.linalg.Global
 
expUpperNormal(double) - Static method in class no.uio.labmed.linalg.Global
 
expUpperNormal(double, double) - Static method in class no.uio.labmed.linalg.Global
 
expUpperNormal(double, double, double) - Static method in class no.uio.labmed.linalg.Global
 

F

fail() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm
Go to failure node.
faktorer - Variable in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
Faktorene: en array per dimensjon samt en total
faktorer(AbstractMatrise) - Method in class no.uio.labmed.linalg.AbstractMatrise
 
faktorer(AbstractMatrise, AbstractMatrise[]) - Method in class no.uio.labmed.linalg.AbstractMatrise
Lager et nytt faktoriseringsobjekt for matrisen.
faktoriser() - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
 
faktoriser(double) - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
 
faktoriser(int) - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
 
faktoriser(int, double) - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
Faktoriserer matrisen.
Field - class no.uio.labmed.pybliographer.Field.
 
field() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
Field() - Constructor for class no.uio.labmed.pybliographer.Field
 
field(String, String) - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
field(String, String) - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
field(String, String, String) - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
field(String, String, String) - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
FieldComparator - class no.uio.labmed.pybliographer.FieldComparator.
 
FieldComparator(String) - Constructor for class no.uio.labmed.pybliographer.FieldComparator
 
fieldIterator() - Method in class no.uio.labmed.pybliographer.Entry
 
fieldName(Field) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
fieldsToString() - Method in class no.uio.labmed.util.objectinfo.ObjectInfo
 
fieldType(ObjectTree.ObjectPointer) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
fillWidth - Static variable in class no.uio.labmed.linalg.Global
Tekstfeltbredde
finish() - Method in class no.uio.labmed.molecule.Action
 
FLAG_CIRCULAR - Variable in class no.uio.labmed.util.tree.SequenceReference
 
FLAG_ITERATE - Variable in class no.uio.labmed.molecule.Selector
 
flush() - Method in class no.uio.labmed.output.AppendOutputStream
 
flush() - Method in class no.uio.labmed.util.output.AppendOutputStream
 
FOLLOW_SHORTCUTS - Variable in class no.uio.labmed.util.tree.suffixTree.ISTPointer
 
forgetAtomicData - Variable in class no.uio.labmed.pdb.AbstractPDBparser
 
forgetSecondaryStructureData - Variable in class no.uio.labmed.pdb.AbstractPDBparser
 

G

gat(String) - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
get() - Method in class no.uio.labmed.linalg.Matrise
 
get() - Method in class no.uio.labmed.util.objectinfo.ObjectInfo
 
get(AbstractMatrise.Iterator) - Method in class no.uio.labmed.linalg.AbstractMatrise
 
get(int) - Method in class no.uio.labmed.linalg.IntMatrise
 
get(int) - Method in class no.uio.labmed.linalg.Matrise
 
get(int) - Method in class no.uio.labmed.protein.Molecule
 
get(int[]) - Method in class no.uio.labmed.linalg.IntMatrise
 
get(int[]) - Method in class no.uio.labmed.linalg.AbstractMatrise
Abstrakt definert prosedyre for aa lese verdi fra matrisen.
get(int[]) - Method in class no.uio.labmed.linalg.Matrise
 
get(int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
get(int, int) - Method in class no.uio.labmed.linalg.Matrise
 
get(int, int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
get(int, int, int) - Method in class no.uio.labmed.linalg.Matrise
 
get(JTextArea) - Static method in class no.uio.labmed.output.AppendOutputStream
 
get(JTextArea) - Static method in class no.uio.labmed.util.output.AppendOutputStream
 
get(String) - Static method in class no.uio.labmed.molecule.SimpleElement
 
get(String) - Static method in class no.uio.labmed.molecule.SimpleCompoundElement
 
get(String) - Static method in class no.uio.labmed.molecule.AminoAcidElement
 
get(String) - Static method in class no.uio.labmed.molecule.AtomicElement
 
get(String) - Static method in class no.uio.labmed.molecule.MolecularType
 
get(String) - Static method in class no.uio.labmed.molecule.MolecularElement
 
get(String) - Method in class no.uio.labmed.pdb.AminoAcidMap
 
get(String) - Static method in class no.uio.labmed.pdb.AminoAcid
 
get(String) - Method in class no.uio.labmed.pdb.AbstractAminoAcidMap
 
get(String) - Static method in class no.uio.labmed.protein.AminoAcid
 
getAlphabet() - Static method in class no.uio.labmed.biojava.alignment.StringSequenceTools
 
getAnnotation(String) - Method in class no.uio.labmed.protein.Protein
 
getAtom() - Method in class no.uio.labmed.molecule.AtomInCompound
 
getAtom(String) - Method in class no.uio.labmed.pdb.AbstractAminoAcid
 
getBlosum62() - Static method in class no.uio.labmed.biojava.alignment.ScoreMatrix
 
getChainId() - Method in class no.uio.labmed.pdb.PDBparser
 
getChild(Object) - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Get the child corresponding to the given key.
getChild(Object, int) - Method in class no.uio.labmed.util.output.TreeAdapter
Get child of parent by index in 0..N-1
getChild(Object, int) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Get child of parent by index in 0..N-1
getChildCount(Object) - Method in class no.uio.labmed.util.output.TreeAdapter
Return number of children
getChildCount(Object) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Return number of children
getChildren() - Method in class no.uio.labmed.util.output.TreeAdapterNode
Get array containing the children of the node.
getChildren() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
getChildren(ChildIterator) - Method in class no.uio.labmed.util.output.TreeAdapterNode
Get array of children from iterator.
getCount() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeCount
 
getDescription() - Method in class no.uio.labmed.molecule.MolecularElement
 
getDescription() - Method in class no.uio.labmed.molecule.Molecule
 
getElement(int) - Method in class no.uio.labmed.molecule.CompoundElement
 
getElement(int) - Method in class no.uio.labmed.molecule.Compound
 
getElement(String) - Method in class no.uio.labmed.molecule.CompoundElement
 
getElement(String) - Method in class no.uio.labmed.molecule.Compound
 
getEntryInfo() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
getEntryIterator() - Method in class no.uio.labmed.pybliographer.PybReader
 
getEntryList() - Method in class no.uio.labmed.pybliographer.PybReader
 
getField(String) - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
getField(String) - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
getField(String) - Method in class no.uio.labmed.pybliographer.Entry
 
getFinalElement(String) - Method in class no.uio.labmed.molecule.CompoundElement
 
getFinalElement(String) - Method in class no.uio.labmed.molecule.Compound
 
getFrame(String) - Static method in class no.uio.labmed.util.output.Output
 
getFrameMaker() - Static method in class no.uio.labmed.util.output.Output
 
getIndex() - Method in class no.uio.labmed.molecule.AtomInCompound
 
getIndexOfChild(Object, Object) - Method in class no.uio.labmed.util.output.TreeAdapter
Return index of child or -1 if not a child.
getIndexOfChild(Object, Object) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Return index of child or -1 if not a child.
getInt() - Method in class no.uio.labmed.pdb.DataFileReader
 
getInt() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getInt(int) - Method in class no.uio.labmed.pdb.DataFileReader
 
getInt(int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getInt(int, int) - Method in class no.uio.labmed.pdb.DataFileReader
 
getInt(int, int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getInt(String) - Method in class no.uio.labmed.pdb.DataFileReader
 
getInt(String) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getKey() - Method in class no.uio.labmed.pybliographer.Field
 
getKey() - Method in class no.uio.labmed.util.tree.SequenceReference
Return value (key) of sequence at position.
getKey() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
getKey() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Return key of the node.
getMolecule(int) - Method in class no.uio.labmed.protein.Protein
 
getName() - Method in class no.uio.labmed.molecule.MolecularElement
 
getName() - Method in class no.uio.labmed.molecule.Molecule
 
getNew() - Method in class no.uio.labmed.molecule.AtomicElement
 
getNew() - Method in class no.uio.labmed.molecule.MolecularElement
 
getNew() - Method in class no.uio.labmed.molecule.CompoundElement
 
getNode() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
getNode() - Method in interface no.uio.labmed.util.tree.TreeNodePointerInterface
Return node
getNode() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
getNode() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return node.
getNode() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm
Returns the current node
getNum() - Method in class no.uio.labmed.pdb.DataFileReader
 
getNum() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getNum(int) - Method in class no.uio.labmed.pdb.DataFileReader
 
getNum(int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getNum(int, int) - Method in class no.uio.labmed.pdb.DataFileReader
 
getNum(int, int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getNum(String) - Method in class no.uio.labmed.pdb.DataFileReader
 
getNum(String) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getParent() - Method in class no.uio.labmed.molecule.AtomInCompound
 
getPointer() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm
Returns the current pointer
getPos() - Method in class no.uio.labmed.util.tree.SequenceReference
Return the position index.
getPos() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
getPrintStream() - Method in class no.uio.labmed.output.AppendOutputStream
 
getPrintStream() - Method in class no.uio.labmed.util.output.AppendOutputStream
 
getRef() - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
getRef() - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
getRef() - Method in class no.uio.labmed.pybliographer.Entry
 
getReference() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Return the sequence reference object of the node.
getReference() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return the sequence reference of the leaf.
getResidue(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
getResidueID() - Method in class no.uio.labmed.pdb.PDBparser
 
getRoot() - Method in class no.uio.labmed.util.output.TreeAdapter
Return root.
getRoot() - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Return root.
getRootPointer() - Method in interface no.uio.labmed.util.tree.TreeInterface
 
getRootPointer() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
getRootPointer() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Return clone of root.
getScore(Object, Object) - Method in class no.uio.labmed.biojava.alignment.ScoreMatrix
 
getScore(Object, Object) - Method in interface no.uio.labmed.biojava.alignment.ScoreInterface
 
getScore(Object, Object) - Method in class no.uio.labmed.biojava.alignment.ScoreIdentity
 
getSecondaryStructureList(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
getSequence(String) - Static method in class no.uio.labmed.biojava.alignment.Test
 
getSequenceAdder() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Get sequence adder: the object that parses the sequence and enters it into the tree.
getShortcut() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Get shortcut link.
getShortcutEnd() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Get link to end of shortcuts: ie. follow shortcuts till there are no more shortcuts.
getStandardResMap() - Method in class no.uio.labmed.pdb.PDBinterpreter
 
getStart() - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
getStat() - Method in interface no.uio.labmed.util.tree.stat.StatNodeInterface
 
getStat() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeStat
Return statistic.
getStat(TreePointerInterface) - Method in class no.uio.labmed.util.tree.stat.AbstractTreeStatistic
 
getStop() - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
getSubElement(String) - Method in class no.uio.labmed.molecule.CompoundElement
 
getSymbol(String) - Static method in class no.uio.labmed.biojava.alignment.StringSequenceTools
 
getToString() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Get a tree-to-string converter to give a string representation of the tree.
getType() - Method in class no.uio.labmed.molecule.MolecularElement
 
getType() - Method in class no.uio.labmed.molecule.Molecule
 
getType() - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
getType() - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
getType() - Method in class no.uio.labmed.pybliographer.Entry
 
getValue() - Method in class no.uio.labmed.pdb.DataFileReader
 
getValue() - Method in class no.uio.labmed.pybliographer.Field
 
getValue() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
getValue(String) - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
getValue(String) - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
getValue(String, String) - Method in class no.uio.labmed.pybliographer.Field
 
getWoodWorm() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Get a WoodWorm: a tree traverser for searching the tree.
getWriter() - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
Global - class no.uio.labmed.linalg.Global.
Globale konstanter, unntak og metoder.
Global() - Constructor for class no.uio.labmed.linalg.Global
 
gotoChild(Object) - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Go to child with given key and return true; otherwise, if no child exists with the given key, return false.
gotoChild(Object) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
gotoChild(Object) - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Try going to child with given key.
gotoFailure() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Try going to failure node.
gotoNext() - Method in interface no.uio.labmed.util.tree.ChildIterator
 
gotoNext() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator
 
gotoNext() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator
 
gotoNext() - Method in class no.uio.labmed.util.tree.suffixTree.ISTChildIterator
 
gotoRoot() - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Go to root
gotoRoot() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
gotoRoot() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Go to root.
gotoShortcut() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Try following shortcut one step.
gotoShortcutEnd() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Try following shortcuts till end.
graft() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
If node is leaf or has a shortcut, add child/children.
GraphPane - class no.uio.labmed.output.GraphPane.
 
GraphPane - class no.uio.labmed.util.output.GraphPane.
 
GraphPane(String) - Constructor for class no.uio.labmed.output.GraphPane
 
GraphPane(String) - Constructor for class no.uio.labmed.util.output.GraphPane
 

H

hasChildren() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
hasChildren() - Method in interface no.uio.labmed.util.tree.TreeNodePointerInterface
Return true is node has children
hasChildren() - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Return true is node has children
hasChildren() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
hasChildren() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Returns true if node has children: ie. children directly under the node, not by following shortcut.
hasChildren() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return true if it has children.
hasKey(String) - Method in class no.uio.labmed.pdb.TestParser
 
hasKey(String) - Method in class no.uio.labmed.pdb.Test
 
hasKey(String) - Method in class no.uio.labmed.pdb.DataFileReader
 
hasKey(String) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
hasMore() - Method in class no.uio.labmed.util.tree.SequenceReference
Return true if more exists not yet parsed.
hasMore() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
hasNext() - Method in class no.uio.labmed.molecule.NullIterator
 
hasNext() - Method in class no.uio.labmed.molecule.Selector.SelectorIterator
 
hasNext() - Method in class no.uio.labmed.pybliographer.PybReader.EntryIterator
 
hasNext() - Method in class no.uio.labmed.pybliographer.PybReader.FieldIterator
 
hasNext() - Method in class no.uio.labmed.util.tree.SequenceReference
Return true if sequence is not at end; always true if curcular.
hasNext() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator
 
hasNext() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator
 
hasNext() - Method in class no.uio.labmed.util.tree.suffixTree.ISTChildIterator
 
hasNext() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Returns true if this is not the last of the parent's children.
hasShortcut() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Returns true if node has shortcut: ie. a link to another part of the tree whose subtree is isomorphic to the subtree of the corresponding (non-implicit) suffix tree.
hasShortcut() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return true if it has a shortcut.
hasValue(int) - Method in class no.uio.labmed.pdb.DataFileReader
 
hasValue(int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
help() - Static method in class no.uio.labmed.util.tree.Test
 
HTMLEntryInfo - class no.uio.labmed.pybliographer.HTMLEntryInfo.
 
HTMLEntryInfo(HTMLwriter) - Constructor for class no.uio.labmed.pybliographer.HTMLEntryInfo
 
HTMLwriter - class no.uio.labmed.pybliographer.HTMLwriter.
 
HTMLwriter(String) - Constructor for class no.uio.labmed.pybliographer.HTMLwriter
 

I

ImplicitSuffixTree - class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.
Implicit suffix tree, ie. a suffix tree with failure nodes and shortcuts to isomorphic subtrees where possible (whereever a given string is always preceeded by a given token).
ImplicitSuffixTree.SequenceAdder - class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.SequenceAdder.
A sequence adder is the object that actually does the sequence parsing and adds the neccessary nodes, though part of the implementation is with the nodes.
ImplicitSuffixTree.SequenceAdder() - Constructor for class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.SequenceAdder
Constructor
ImplicitSuffixTree.WoodWorm - class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm.
A WoodWorm traverses the tree, reads the sequence following leaves, follows shortcuts.
ImplicitSuffixTree() - Constructor for class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Constructor: Default tree using ISTNode nodes.
ImplicitSuffixTree(ISTNode) - Constructor for class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Constructor: Tree using specified node type based on given root.
ImplicitSuffixTree(ISTPointer) - Constructor for class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Constructor: Tree using specified pointer as root.
index - Variable in class no.uio.labmed.molecule.CompoundElement.SubElement
 
index() - Method in class no.uio.labmed.molecule.CompoundElement.SubElement
 
index(int[]) - Method in class no.uio.labmed.linalg.AbstractMatrise
Finne indeks fra 0 til size()-1utfra posisjon.
info(MolecularElement) - Static method in class no.uio.labmed.molecule.Test
 
info(Molecule) - Static method in class no.uio.labmed.molecule.Test
 
infoOn(MolecularElement) - Static method in class no.uio.labmed.molecule.Test
 
infoOn(String) - Static method in class no.uio.labmed.molecule.Test
 
infoOn(String[]) - Static method in class no.uio.labmed.molecule.Test
 
init() - Method in class no.uio.labmed.biojava.alignment.Test
 
init() - Method in class no.uio.labmed.molecule.ViewMolecule
 
init() - Method in class no.uio.labmed.protein.ViewMolecule
 
init(ISTNode) - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Initiate pointer to given node in given tree.
innhold - Variable in class no.uio.labmed.output.Vindu
 
innhold - Variable in class no.uio.labmed.util.output.TabbedFrame
 
IntMatrise - class no.uio.labmed.linalg.IntMatrise.
 
IntMatrise(int) - Constructor for class no.uio.labmed.linalg.IntMatrise
 
IntMatrise(int, int) - Constructor for class no.uio.labmed.linalg.IntMatrise
 
IntMatrise(int, int, int) - Constructor for class no.uio.labmed.linalg.IntMatrise
 
is() - Method in class no.uio.labmed.linalg.AbstractMatrise.Iterator
Angir gjeldende posisjon.
is(int) - Method in class no.uio.labmed.linalg.AbstractMatrise.Iterator
Angir gjeldende posisjon langs dimensjon p.
isAtom() - Method in class no.uio.labmed.molecule.AtomicElement
 
isAtom() - Method in class no.uio.labmed.molecule.MolecularElement
 
isAtom() - Method in class no.uio.labmed.molecule.CompoundElement
 
isAtom() - Method in class no.uio.labmed.molecule.Molecule
 
isBonded(Atomic) - Method in class no.uio.labmed.molecule.CovalentBond
 
isBonded(Atomic) - Method in class no.uio.labmed.molecule.Bond
 
isCircular() - Method in class no.uio.labmed.util.tree.SequenceReference
Return true if sequence is circular.
isLast() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Returns true if this is the last of the parent's children.
isLeaf() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Returns true is node is leaf: ie. has neither children nor a shortcut
isLeaf() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return true if it points to a leaf.
isLeaf(Object) - Method in class no.uio.labmed.util.output.TreeAdapter
Return true if node is leaf.
isLeaf(Object) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Return true if node is leaf.
isRoot() - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Return true if root
isRoot() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
isRoot() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Returns true is node is the root: ie. has no parent.
isRoot() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return true if it points to the root.
ISTChildIterator - class no.uio.labmed.util.tree.suffixTree.ISTChildIterator.
 
ISTChildIterator(ISTPointer) - Constructor for class no.uio.labmed.util.tree.suffixTree.ISTChildIterator
 
ISTDepthPointer - class no.uio.labmed.util.tree.suffixTree.ISTDepthPointer.
 
ISTDepthPointer() - Constructor for class no.uio.labmed.util.tree.suffixTree.ISTDepthPointer
 
ISTNode - class no.uio.labmed.util.tree.suffixTree.ISTNode.
Nodes of an implicit suffix tree.
ISTNode() - Constructor for class no.uio.labmed.util.tree.suffixTree.ISTNode
Constructor
ISTNodeCount - class no.uio.labmed.util.tree.suffixTree.ISTNodeCount.
 
ISTNodeCount() - Constructor for class no.uio.labmed.util.tree.suffixTree.ISTNodeCount
 
ISTNodeStat - class no.uio.labmed.util.tree.suffixTree.ISTNodeStat.
 
ISTNodeStat() - Constructor for class no.uio.labmed.util.tree.suffixTree.ISTNodeStat
 
ISTPointer - class no.uio.labmed.util.tree.suffixTree.ISTPointer.
Pointer to nodes in an implicit suffix tree.
ISTPointer() - Constructor for class no.uio.labmed.util.tree.suffixTree.ISTPointer
 
isUnique() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm
Return true if present word is unique.
iterate() - Method in class no.uio.labmed.molecule.Selector.SelectorIterator
 
iterator() - Method in class no.uio.labmed.linalg.AbstractMatrise
Lager iterator for aa gjennomlope alle posisjonene i en matrise.
iterator() - Method in class no.uio.labmed.molecule.Atom
 
iterator() - Method in class no.uio.labmed.molecule.Compound
 
iterator() - Method in class no.uio.labmed.molecule.Molecule
 
iterator(Molecule) - Method in class no.uio.labmed.molecule.Selector
 
iterator(Selector.SelectorIterator) - Method in class no.uio.labmed.molecule.Selector
 

J

JTreeAdapter - class no.uio.labmed.util.tree.adapter.JTreeAdapter.
Adapter class for making javax.swing.JTree views of a tree.
JTreeAdapter(TreeInterface) - Constructor for class no.uio.labmed.util.tree.adapter.JTreeAdapter
 
JTreeAdapter(TreePointerInterface) - Constructor for class no.uio.labmed.util.tree.adapter.JTreeAdapter
Constructor: Initiate tree with given node as root
JTreeAdapterNode - class no.uio.labmed.util.tree.adapter.JTreeAdapterNode.
Nodes used by JTreeAdapter.

K

key() - Method in class no.uio.labmed.molecule.Selector.SelectorIterator
 
key(Molecule) - Method in class no.uio.labmed.molecule.SelectorByType
 
key(Molecule) - Method in class no.uio.labmed.molecule.SelectorByName
 
key(Molecule) - Method in class no.uio.labmed.molecule.Selector
 
keyIterator() - Method in class no.uio.labmed.molecule.CompoundElement
 
keyIterator() - Method in class no.uio.labmed.pdb.AminoAcidMap
 
keyIterator() - Method in class no.uio.labmed.pdb.AbstractAminoAcidMap
 
keywordRecognized(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
keywordsRecognized - Static variable in class no.uio.labmed.pdb.AbstractPDBparser
 
kill() - Method in class no.uio.labmed.protein.ViewMolecule
 

L

lambda(int[]) - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
Regner ut estimatoren for en gitt posisjon med og uten overganger: dvs. produktet av faktorene og vekten.
lambda0(int[]) - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
Regner ut den uvektede estimatoren med og uten overganger til en gitt posisjon:
leftFill(int) - Static method in class no.uio.labmed.linalg.Global
 
leftFill(Object) - Static method in class no.uio.labmed.linalg.Global
Fyll fra venstre til standardbredde
leftFill(Object, int) - Static method in class no.uio.labmed.linalg.Global
Fyll fra venstre til angitt bredde
line() - Method in class no.uio.labmed.pdb.DataFileReader
 
line() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
lineHasKnownKey(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
ln() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
lngat(String) - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
log(String) - Static method in class no.uio.labmed.linalg.Global
Skriv til log
logVindu - Static variable in class no.uio.labmed.linalg.Global
Log-vindu (hvis null benyttes System.out

M

main() - Method in class no.uio.labmed.pybliographer.Pybliography
 
main(String[]) - Static method in class no.uio.labmed.biojava.alignment.Test
 
main(String[]) - Static method in class no.uio.labmed.molecule.Test
 
main(String[]) - Static method in class no.uio.labmed.pdb.TestParser
 
main(String[]) - Static method in class no.uio.labmed.pdb.Test
 
main(String[]) - Static method in class no.uio.labmed.protein.Test
 
main(String[]) - Static method in class no.uio.labmed.pybliographer.Pybliography
 
main(String[]) - Static method in class no.uio.labmed.util.objectinfo.Test
 
main(String[]) - Static method in class no.uio.labmed.util.tree.Test
 
main(String[]) - Static method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
make() - Method in class no.uio.labmed.pdb.TestParser.AtomData
 
make() - Method in class no.uio.labmed.pdb.TestParser.SecondaryStructure
 
make() - Method in class no.uio.labmed.pdb.Test.AtomData
 
make() - Method in class no.uio.labmed.pdb.Test.SecondaryStructure
 
make() - Method in class no.uio.labmed.pdb.PDBinterpreter.SecondaryStructure
 
make() - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
make() - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
make(Molecule) - Method in class no.uio.labmed.molecule.ActionPrint
 
make(Molecule) - Method in class no.uio.labmed.molecule.ActionPlot.ActionPlotAtom
 
make(Molecule) - Method in class no.uio.labmed.molecule.Action
 
makeHead() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
makeProtein() - Static method in class no.uio.labmed.molecule.Test
 
makeSelection(Action) - Static method in class no.uio.labmed.molecule.Test
 
map() - Method in class no.uio.labmed.molecule.SimpleElement
 
map() - Method in class no.uio.labmed.molecule.SimpleCompoundElement
 
map() - Method in class no.uio.labmed.molecule.AminoAcidElement
 
map() - Method in class no.uio.labmed.molecule.AtomicElement
 
map() - Method in class no.uio.labmed.molecule.MolecularElement
 
mapModRes - Variable in class no.uio.labmed.pdb.PDBinterpreter
 
mapStandardRes - Variable in class no.uio.labmed.pdb.PDBinterpreter
 
MATCH_SCORE - Variable in class no.uio.labmed.biojava.alignment.ScoreIdentity
 
Matrise - class no.uio.labmed.linalg.Matrise.
 
Matrise(int) - Constructor for class no.uio.labmed.linalg.Matrise
 
Matrise(int[]) - Constructor for class no.uio.labmed.linalg.Matrise
 
Matrise(int, int) - Constructor for class no.uio.labmed.linalg.Matrise
 
Matrise(int, int, int) - Constructor for class no.uio.labmed.linalg.Matrise
 
modelList - Variable in class no.uio.labmed.molecule.ReadPDB
 
MolecularElement - class no.uio.labmed.molecule.MolecularElement.
Defines a general molecular structure or substructure which may be either an atom or compound.
MolecularElement(String) - Constructor for class no.uio.labmed.molecule.MolecularElement
 
MolecularElement(String, MolecularType) - Constructor for class no.uio.labmed.molecule.MolecularElement
 
MolecularElement(String, MolecularType, String) - Constructor for class no.uio.labmed.molecule.MolecularElement
 
MolecularElement(String, String) - Constructor for class no.uio.labmed.molecule.MolecularElement
 
MolecularType - class no.uio.labmed.molecule.MolecularType.
Molecular structure types.
Molecule - class no.uio.labmed.molecule.Molecule.
An actual molecule: ie. not just a general molecular structure, but an actual instance of a given MolecularElement refering to instances of Atom for each atom in the molecule and giving the coordinates of the atoms.
Molecule - class no.uio.labmed.protein.Molecule.
 
Molecule() - Constructor for class no.uio.labmed.molecule.Molecule
 
Molecule() - Constructor for class no.uio.labmed.protein.Molecule
 
monospacedFont - Static variable in class no.uio.labmed.output.Vindu
 
monospacedFont - Static variable in class no.uio.labmed.util.output.TabbedFrame
 
monospacedFont - Static variable in class no.uio.labmed.util.output.Output
 

N

nameOfClass(Class) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
nameOfClass(Class, int) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
nest(ChangeIndicator) - Method in class no.uio.labmed.pdb.ChangeIndicator
 
newAminoAcidMap() - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newAnisou() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newAtom() - Method in class no.uio.labmed.pdb.TestParser
 
newAtom() - Method in class no.uio.labmed.pdb.Test
 
newAtom(String) - Method in class no.uio.labmed.molecule.ReadPDB
 
newAtom(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newAtomChain(String) - Method in class no.uio.labmed.molecule.ReadPDB
 
newAtomChain(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newAtomChain(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newAtomResidue(String) - Method in class no.uio.labmed.molecule.ReadPDB
 
newAtomResidue(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newAtomResidue(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newAuthor(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newCaveat(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newChild(SequenceReference) - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Make a new child with a given sequence reference.
newChild(SequenceReference) - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Add and go to new child with given sequence reference.
newCispep() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newCompnd(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newConect() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newCryst1() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newDbref() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newEntry(Entry) - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
newEntry(Entry) - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
newExpdta(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newFormul() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHeader(String) - Method in class no.uio.labmed.pdb.TestParser
 
newHeader(String) - Method in class no.uio.labmed.pdb.Test
 
newHeader(String, String, String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHelix() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHet() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHetatm() - Method in class no.uio.labmed.pdb.TestParser
 
newHetatm() - Method in class no.uio.labmed.pdb.Test
 
newHetatm(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHetnam() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHetsyn() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newHydbnd() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newJrnl(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newKeywds(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newLink() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newMaster() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newModel(int) - Method in class no.uio.labmed.molecule.ReadPDB
 
newModel(int) - Method in class no.uio.labmed.pdb.TestParser
 
newModel(int) - Method in class no.uio.labmed.pdb.Test
 
newModel(int) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newModifiedResidue(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newModres() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newMtrix() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newNode() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeStat
Return a new node.
newNode() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeCount
Return a new node.
newNode() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
Return a new node.
newObslte(String, String, String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newOrigx() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newRemark(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newResidue(String) - Method in class no.uio.labmed.pdb.TestParser
 
newResidue(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newResidue(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newRevdat(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newScale() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSecondaryStructure(Object) - Method in class no.uio.labmed.pdb.TestParser
 
newSecondaryStructure(Object) - Method in class no.uio.labmed.pdb.Test
 
newSecondaryStructure(Object) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newSecondaryStructure(Object) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSeqadv() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSeqresChain(String) - Method in class no.uio.labmed.pdb.TestParser
 
newSeqresChain(String) - Method in class no.uio.labmed.pdb.PDBinterpreter
 
newSeqresChain(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSheet() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSigatm() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSiguij() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSite() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSltbrg() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSource(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSprsde(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newSSbond() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newStat() - Method in class no.uio.labmed.util.tree.stat.AbstractTreeStatistic
 
newTitle(String) - Method in class no.uio.labmed.pdb.TestParser
 
newTitle(String) - Method in class no.uio.labmed.pdb.Test
 
newTitle(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newTurn() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
newTvect() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
next() - Method in class no.uio.labmed.molecule.NullIterator
 
next() - Method in class no.uio.labmed.molecule.Selector.SelectorIterator
 
next() - Method in class no.uio.labmed.pybliographer.PybReader.EntryIterator
 
next() - Method in class no.uio.labmed.pybliographer.PybReader.FieldIterator
 
next() - Method in class no.uio.labmed.util.tree.SequenceReference
Go to next position and return pointer.
next() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator
 
next() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator
 
next() - Method in class no.uio.labmed.util.tree.suffixTree.ISTChildIterator
 
next(Object) - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm
Try going to child with given key following shortcuts if neccessary or parsing the sequence if at a leaf of the tree.
nextLine() - Method in class no.uio.labmed.pdb.DataFileReader
 
nextLine() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
nextNode(Object) - Method in class no.uio.labmed.molecule.SelectionNode
 
nextReference() - Method in class no.uio.labmed.util.tree.SequenceReference
Go to the next position and return pointer
nextReference() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
nextValue() - Method in interface no.uio.labmed.util.tree.ChildIterator
 
nextValue() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator
 
nextValue() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator
 
nextValue() - Method in class no.uio.labmed.util.tree.suffixTree.ISTChildIterator
 
no.uio.labmed.biojava.alignment - package no.uio.labmed.biojava.alignment
 
no.uio.labmed.linalg - package no.uio.labmed.linalg
 
no.uio.labmed.molecule - package no.uio.labmed.molecule
 
no.uio.labmed.output - package no.uio.labmed.output
 
no.uio.labmed.pdb - package no.uio.labmed.pdb
 
no.uio.labmed.protein - package no.uio.labmed.protein
 
no.uio.labmed.pybliographer - package no.uio.labmed.pybliographer
 
no.uio.labmed.util.objectinfo - package no.uio.labmed.util.objectinfo
 
no.uio.labmed.util.output - package no.uio.labmed.util.output
 
no.uio.labmed.util.tree - package no.uio.labmed.util.tree
 
no.uio.labmed.util.tree.adapter - package no.uio.labmed.util.tree.adapter
 
no.uio.labmed.util.tree.stat - package no.uio.labmed.util.tree.stat
 
no.uio.labmed.util.tree.suffixTree - package no.uio.labmed.util.tree.suffixTree
 
node - Variable in class no.uio.labmed.util.tree.suffixTree.ISTPointer
 
node() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return node.
none - Static variable in class no.uio.labmed.output.AppendOutputStream
 
none - Static variable in class no.uio.labmed.util.output.AppendOutputStream
 
NONMATCH_SCORE - Variable in class no.uio.labmed.biojava.alignment.ScoreIdentity
 
NULL_SCORE - Static variable in class no.uio.labmed.biojava.alignment.ScoreMatrix
 
NULL_SCORE - Variable in class no.uio.labmed.biojava.alignment.ScoreIdentity
 
nullAtomicData - Variable in class no.uio.labmed.pdb.PDBparser
 
NullIterator - class no.uio.labmed.molecule.NullIterator.
An 'empty' iterator: ie. one that has no elements to iterate over.
NullIterator() - Constructor for class no.uio.labmed.molecule.NullIterator
 
numberWidth - Static variable in class no.uio.labmed.linalg.Global
Tallfeltbredde

O

ObjectInfo - class no.uio.labmed.util.objectinfo.ObjectInfo.
 
ObjectInfo() - Constructor for class no.uio.labmed.util.objectinfo.ObjectInfo
 
ObjectInfo(Object) - Constructor for class no.uio.labmed.util.objectinfo.ObjectInfo
 
ObjectTree - class no.uio.labmed.util.tree.adapter.ObjectTree.
 
ObjectTree.ArrayIterator - class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator.
 
ObjectTree.ArrayIterator(Object, Field, int) - Constructor for class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator
 
ObjectTree.FieldIterator - class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator.
 
ObjectTree.FieldIterator(Object) - Constructor for class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator
 
ObjectTree.ObjectPointer - class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer.
 
ObjectTree.ObjectPointer(Object) - Constructor for class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
ObjectTree(Object) - Constructor for class no.uio.labmed.util.tree.adapter.ObjectTree
 
ObjectTreeAdapter - class no.uio.labmed.util.output.ObjectTreeAdapter.
NB: FORELDET!!!!!!!
ObjectTreeAdapter() - Constructor for class no.uio.labmed.util.output.ObjectTreeAdapter
Constructor
ObjectTreeAdapter(Object) - Constructor for class no.uio.labmed.util.output.ObjectTreeAdapter
Constructor
open() - Method in class no.uio.labmed.pybliographer.HTMLEntryInfo
 
open() - Method in interface no.uio.labmed.pybliographer.EntryInfoInterface
 
open(InputStream) - Method in class no.uio.labmed.pdb.DataFileReader
 
open(InputStream) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
open(Reader) - Method in class no.uio.labmed.pdb.DataFileReader
 
open(Reader) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
open(String) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
openBody() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
openDocument() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
oppdaterSummer() - Method in class no.uio.labmed.linalg.AbstractMatrise.Faktorer
Mellomregning: regner ut marginalsummene til matrisen.
out - Variable in class no.uio.labmed.output.AppendOutputStream
 
out - Variable in class no.uio.labmed.util.output.AppendOutputStream
 
Output - class no.uio.labmed.util.output.Output.
 

P

paintComponent(Graphics) - Method in class no.uio.labmed.output.GraphPane
 
paintComponent(Graphics) - Method in class no.uio.labmed.util.output.GraphPane
 
parse() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
parse() - Method in class no.uio.labmed.pdb.PDBparser
 
ParseException - exception no.uio.labmed.pdb.ParseException.
 
ParseException() - Constructor for class no.uio.labmed.pdb.ParseException
 
ParseException(Exception) - Constructor for class no.uio.labmed.pdb.ParseException
 
ParseException(String) - Constructor for class no.uio.labmed.pdb.ParseException
 
ParseException(String, Exception) - Constructor for class no.uio.labmed.pdb.ParseException
 
PDBinterpreter - class no.uio.labmed.pdb.PDBinterpreter.
 
PDBinterpreter.PrimaryStructureData - class no.uio.labmed.pdb.PDBinterpreter.PrimaryStructureData.
 
PDBinterpreter.PrimaryStructureData() - Constructor for class no.uio.labmed.pdb.PDBinterpreter.PrimaryStructureData
 
PDBinterpreter.SecondaryStructure - class no.uio.labmed.pdb.PDBinterpreter.SecondaryStructure.
 
PDBinterpreter.SecondaryStructure(Object) - Constructor for class no.uio.labmed.pdb.PDBinterpreter.SecondaryStructure
 
PDBinterpreter() - Constructor for class no.uio.labmed.pdb.PDBinterpreter
 
PDBparser - class no.uio.labmed.pdb.PDBparser.
PDB parser.
PDBparser() - Constructor for class no.uio.labmed.pdb.PDBparser
 
PDBreader - class no.uio.labmed.protein.PDBreader.
 
PDBreader() - Constructor for class no.uio.labmed.protein.PDBreader
 
pointerString(ObjectTree.ObjectPointer) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
pos - Variable in class no.uio.labmed.linalg.AbstractMatrise.Iterator
Array som angir naavaerende posisjon i matrisen.
pos(int) - Method in class no.uio.labmed.pdb.DataFileReader
 
pos(int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
posisjonOK(int[]) - Method in class no.uio.labmed.linalg.AbstractMatrise
Sjekker om posisjonen er innenfor matrisens dimensjoner
position(int) - Method in class no.uio.labmed.linalg.AbstractMatrise
Finner posisjon utfra index
prefix(String) - Method in class no.uio.labmed.pdb.DataPrintStream
 
prefixln(String) - Method in class no.uio.labmed.pdb.DataPrintStream
 
present(Object) - Method in class no.uio.labmed.molecule.SelectionNode
 
present(Object, SelectionNode) - Method in class no.uio.labmed.molecule.Selector
 
present(SelectionNode) - Method in class no.uio.labmed.molecule.Selector.SelectorIterator
 
primaryStructure - Variable in class no.uio.labmed.pdb.PDBinterpreter
 
print(String) - Method in class no.uio.labmed.pdb.DataPrintStream
 
printException(Exception) - Method in class no.uio.labmed.pdb.PDBparser
 
println() - Method in class no.uio.labmed.pdb.DataPrintStream
 
println() - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
println(String) - Method in class no.uio.labmed.pdb.DataPrintStream
 
Protein - class no.uio.labmed.protein.Protein.
 
Protein() - Constructor for class no.uio.labmed.protein.Protein
 
Protein(String) - Constructor for class no.uio.labmed.protein.Protein
 
proteinAligner() - Static method in class no.uio.labmed.biojava.alignment.Test
 
put(String, AbstractAminoAcid) - Method in class no.uio.labmed.pdb.AminoAcidMap
 
put(String, AbstractAminoAcid) - Method in class no.uio.labmed.pdb.AbstractAminoAcidMap
 
Pybliography - class no.uio.labmed.pybliographer.Pybliography.
 
Pybliography() - Constructor for class no.uio.labmed.pybliographer.Pybliography
 
PybReader - class no.uio.labmed.pybliographer.PybReader.
 
PybReader.EntryIterator - class no.uio.labmed.pybliographer.PybReader.EntryIterator.
 
PybReader.EntryIterator() - Constructor for class no.uio.labmed.pybliographer.PybReader.EntryIterator
 
PybReader.FieldIterator - class no.uio.labmed.pybliographer.PybReader.FieldIterator.
 
PybReader.FieldIterator() - Constructor for class no.uio.labmed.pybliographer.PybReader.FieldIterator
 
PybReader() - Constructor for class no.uio.labmed.pybliographer.PybReader
 

Q

quit() - Method in class no.uio.labmed.molecule.ViewMolecule
 

R

random(int) - Static method in class no.uio.labmed.util.tree.Test
 
read(BufferedReader) - Method in class no.uio.labmed.protein.PDBreader
 
read(String) - Static method in class no.uio.labmed.molecule.Test
 
read(String) - Method in class no.uio.labmed.protein.PDBreader
 
readLine() - Method in class no.uio.labmed.pdb.TestParser
 
readLine() - Method in class no.uio.labmed.pdb.Test
 
readLine() - Method in class no.uio.labmed.pdb.DataFileReader
 
readLine() - Method in class no.uio.labmed.pdb.PDBparser
 
readLine() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
ReadPDB - class no.uio.labmed.molecule.ReadPDB.
 
ReadPDB.AtomData - class no.uio.labmed.molecule.ReadPDB.AtomData.
 
ReadPDB.AtomData() - Constructor for class no.uio.labmed.molecule.ReadPDB.AtomData
 
ReadPDB() - Constructor for class no.uio.labmed.molecule.ReadPDB
 
remove() - Method in class no.uio.labmed.molecule.NullIterator
 
remove() - Method in class no.uio.labmed.molecule.Selector.SelectorIterator
 
remove() - Method in class no.uio.labmed.pybliographer.PybReader.EntryIterator
 
remove() - Method in class no.uio.labmed.pybliographer.PybReader.FieldIterator
 
remove() - Method in class no.uio.labmed.util.tree.SequenceReference
Empty implementation.
remove() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ArrayIterator
 
remove() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.FieldIterator
 
remove() - Method in class no.uio.labmed.util.tree.suffixTree.ISTChildIterator
 
removeTreeModelListener(TreeModelListener) - Method in class no.uio.labmed.util.output.TreeAdapter
Empty implementation
removeTreeModelListener(TreeModelListener) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Empty implementation
reset() - Method in class no.uio.labmed.pdb.ChangeIndicator
 
reset() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree.WoodWorm
Reset worm and return to root.
resetSub() - Method in class no.uio.labmed.pdb.ChangeIndicator
 
resetThis() - Method in class no.uio.labmed.pdb.ChangeObjectIndicator
 
resetThis() - Method in class no.uio.labmed.pdb.ChangeIntIndicator
 
resetThis() - Method in class no.uio.labmed.pdb.ChangeIndicator
 
rest() - Method in class no.uio.labmed.pdb.DataFileReader
 
rest() - Method in class no.uio.labmed.pybliographer.DataFileReader
 
rightFill(int) - Static method in class no.uio.labmed.linalg.Global
 
rightFill(Object) - Static method in class no.uio.labmed.linalg.Global
Fyll fra hoyre til standardbredde
rightFill(Object, int) - Static method in class no.uio.labmed.linalg.Global
Fyll fra hoyre til angitt bredde
rnd - Static variable in class no.uio.labmed.util.tree.Test
 

S

scale() - Method in class no.uio.labmed.output.GraphPane
 
scale() - Method in class no.uio.labmed.util.output.GraphPane
 
scale(double, double) - Method in class no.uio.labmed.output.GraphPane
 
scale(double, double) - Method in class no.uio.labmed.util.output.GraphPane
 
scale(double, double, double, double) - Method in class no.uio.labmed.output.GraphPane
 
scale(double, double, double, double) - Method in class no.uio.labmed.util.output.GraphPane
 
scale(double, double, double, double, double, double) - Method in class no.uio.labmed.output.GraphPane
 
scale(double, double, double, double, double, double) - Method in class no.uio.labmed.util.output.GraphPane
 
ScoreIdentity - class no.uio.labmed.biojava.alignment.ScoreIdentity.
Implementation of ScoreInterface which scores identity.
ScoreIdentity() - Constructor for class no.uio.labmed.biojava.alignment.ScoreIdentity
 
ScoreInterface - interface no.uio.labmed.biojava.alignment.ScoreInterface.
Interface defining alignment scoring.
ScoreMatrix - class no.uio.labmed.biojava.alignment.ScoreMatrix.
Alignment scoring matrix, eg.
ScoreMatrix(Object[], float[][]) - Constructor for class no.uio.labmed.biojava.alignment.ScoreMatrix
 
secondaryStructures - Variable in class no.uio.labmed.pdb.PDBinterpreter
 
select(Object, SelectionNode) - Method in class no.uio.labmed.molecule.SelectionNode
 
selectionMap - Variable in class no.uio.labmed.molecule.SelectionNode
 
SelectionNode - class no.uio.labmed.molecule.SelectionNode.
 
SelectionNode() - Constructor for class no.uio.labmed.molecule.SelectionNode
 
selector - Variable in class no.uio.labmed.molecule.SelectionNode
 
Selector - class no.uio.labmed.molecule.Selector.
Class defining a selector: adapters towards the data which defines the key and interators for subelements.
Selector.SelectorIterator - class no.uio.labmed.molecule.Selector.SelectorIterator.
 
Selector.SelectorIterator(Molecule) - Constructor for class no.uio.labmed.molecule.Selector.SelectorIterator
 
Selector() - Constructor for class no.uio.labmed.molecule.Selector
 
SelectorByName - class no.uio.labmed.molecule.SelectorByName.
Implementation of Selector which selects on molecule name.
SelectorByName() - Constructor for class no.uio.labmed.molecule.SelectorByName
 
SelectorByType - class no.uio.labmed.molecule.SelectorByType.
Implementation of Selector which selects by molecular type.
SelectorByType() - Constructor for class no.uio.labmed.molecule.SelectorByType
 
SequenceReference - class no.uio.labmed.util.tree.SequenceReference.
Abstract class for pointing to a specific position in a sequence.
SequenceReference() - Constructor for class no.uio.labmed.util.tree.SequenceReference
 
set(double) - Method in class no.uio.labmed.linalg.Matrise
 
set(int) - Method in class no.uio.labmed.molecule.AtomicElement
 
set(int[], double) - Method in class no.uio.labmed.linalg.Matrise
 
set(int, double) - Method in class no.uio.labmed.linalg.Matrise
 
set(int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
set(int, int, double) - Method in class no.uio.labmed.linalg.Matrise
 
set(int, int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
set(int, int, int, double) - Method in class no.uio.labmed.linalg.Matrise
 
set(int, int, int, int) - Method in class no.uio.labmed.linalg.IntMatrise
 
set(Object) - Method in class no.uio.labmed.util.objectinfo.ObjectInfo
 
setA(Object) - Method in class no.uio.labmed.util.objectinfo.Test
 
setAll(double) - Method in class no.uio.labmed.linalg.Matrise
 
setAll(int) - Method in class no.uio.labmed.linalg.IntMatrise
 
setAltLoc(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setB(Object) - Method in class no.uio.labmed.util.objectinfo.Test
 
setC(Object) - Method in class no.uio.labmed.util.objectinfo.Test
 
setChainId(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setChainId(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
setCircular(boolean) - Method in class no.uio.labmed.util.tree.SequenceReference
Set to true if sequence is circular.
setClass(int) - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
setCoord(float, float, float) - Method in class no.uio.labmed.molecule.ReadPDB.AtomData
 
setCoord(float, float, float) - Method in class no.uio.labmed.molecule.Atom
 
setCoord(float, float, float) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setD(Object) - Method in class no.uio.labmed.util.objectinfo.Test
 
setExceptionPrintStream(PrintStream) - Method in class no.uio.labmed.pdb.PDBparser
 
setICode(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setKey(String) - Method in class no.uio.labmed.pybliographer.Field
 
setLocalAlignment(boolean) - Method in class no.uio.labmed.biojava.alignment.SimpleAligner
 
setName(String) - Method in class no.uio.labmed.pdb.TestParser.AtomData
 
setName(String) - Method in class no.uio.labmed.pdb.Test.AtomData
 
setOccupancy(float) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setPenalties(float, float) - Method in class no.uio.labmed.biojava.alignment.SimpleAligner
 
setRef(String) - Method in class no.uio.labmed.pybliographer.Entry
 
setRememberMatrix(boolean) - Method in class no.uio.labmed.biojava.alignment.SimpleAligner
 
setResName(String) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setResSeq(int) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setScore(ScoreInterface) - Method in class no.uio.labmed.biojava.alignment.SimpleAligner
 
setSerial(int) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setSerNum(int) - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
setSheetBond(int, String, int) - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
setStartStop(int, int) - Method in class no.uio.labmed.pdb.AbstractPDBparser.SecondaryStructureData
 
setStat(AbstractNodeStatistic) - Method in interface no.uio.labmed.util.tree.stat.StatNodeInterface
 
setStat(AbstractNodeStatistic) - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeStat
Set statistic.
setSubsort(Comparator) - Method in class no.uio.labmed.pybliographer.FieldComparator
 
setTempFactor(float) - Method in class no.uio.labmed.pdb.AbstractPDBparser.AtomicData
 
setType(String) - Method in class no.uio.labmed.pybliographer.Entry
 
setValue(String[]) - Method in class no.uio.labmed.pybliographer.Field
 
setView(ViewMolecule) - Method in class no.uio.labmed.molecule.ActionPlot
 
SHORT_CLASS_NAME - Variable in class no.uio.labmed.util.tree.adapter.ObjectTree
 
SimpleAligner - class no.uio.labmed.biojava.alignment.SimpleAligner.
Implementation of the Needleman-Wunsch and Smith-Waterman algorithm for sequence alignment.
SimpleAligner() - Constructor for class no.uio.labmed.biojava.alignment.SimpleAligner
 
SimpleAligner(ScoreInterface) - Constructor for class no.uio.labmed.biojava.alignment.SimpleAligner
 
SimpleCompoundElement - class no.uio.labmed.molecule.SimpleCompoundElement.
Definitions of simple molecules that tend to be components of larger compounds: eg.
SimpleCompoundElement(String) - Constructor for class no.uio.labmed.molecule.SimpleCompoundElement
 
SimpleCompoundElement(String, String) - Constructor for class no.uio.labmed.molecule.SimpleCompoundElement
 
SimpleElement - class no.uio.labmed.molecule.SimpleElement.
Definition of a family of simple molecules and their composition.
SimpleElement(String) - Constructor for class no.uio.labmed.molecule.SimpleElement
 
SimpleElement(String, String) - Constructor for class no.uio.labmed.molecule.SimpleElement
 
size() - Method in class no.uio.labmed.linalg.AbstractMatrise
Antall elementer i matrisen: produktet av alle dimensjonene.
size() - Method in class no.uio.labmed.molecule.AtomicElement
 
size() - Method in class no.uio.labmed.molecule.MolecularElement
 
size() - Method in class no.uio.labmed.molecule.CompoundElement
 
size() - Method in class no.uio.labmed.pdb.AminoAcidMap
 
size() - Method in class no.uio.labmed.pdb.AbstractAminoAcidMap
 
skip(int) - Method in class no.uio.labmed.pdb.DataFileReader
 
skip(int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
smallFont - Static variable in class no.uio.labmed.output.Vindu
 
smallFont - Static variable in class no.uio.labmed.util.output.TabbedFrame
 
smallFont - Static variable in class no.uio.labmed.util.output.Output
 
sortFeatures(FeatureHolder) - Static method in class no.uio.labmed.biojava.alignment.Test
 
space(String) - Method in class no.uio.labmed.pdb.DataPrintStream
 
StatNodeInterface - interface no.uio.labmed.util.tree.stat.StatNodeInterface.
 
StringSequenceTools - class no.uio.labmed.biojava.alignment.StringSequenceTools.
Helper class for making sequences over the alphabet of characters.
StringSequenceTools() - Constructor for class no.uio.labmed.biojava.alignment.StringSequenceTools
 
sub - Variable in class no.uio.labmed.pdb.ChangeIndicator
 
sub(int) - Method in class no.uio.labmed.pdb.DataFileReader
 
sub(int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
sub(int, int) - Method in class no.uio.labmed.pdb.DataFileReader
 
sub(int, int) - Method in class no.uio.labmed.pybliographer.DataFileReader
 
subsize() - Method in class no.uio.labmed.molecule.AtomicElement
 
subsize() - Method in class no.uio.labmed.molecule.MolecularElement
 
subsize() - Method in class no.uio.labmed.molecule.CompoundElement
 
suffixString - Static variable in class no.uio.labmed.linalg.Global
Kolonneskilletegn

T

tabbed - Variable in class no.uio.labmed.output.Vindu
 
tabbed - Variable in class no.uio.labmed.util.output.TabbedFrame
 
TabbedFrame - class no.uio.labmed.util.output.TabbedFrame.
 
TabbedFrame() - Constructor for class no.uio.labmed.util.output.TabbedFrame
 
TabbedFrame(int, int, int, int) - Constructor for class no.uio.labmed.util.output.TabbedFrame
 
TabbedFrame(int, int, int, int, String) - Constructor for class no.uio.labmed.util.output.TabbedFrame
 
TabbedFrame(String) - Constructor for class no.uio.labmed.util.output.TabbedFrame
 
tag(String) - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
tag(String, String) - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
tagln(String) - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
tagln(String, String) - Method in class no.uio.labmed.pybliographer.HTMLwriter
 
terChain() - Method in class no.uio.labmed.pdb.AbstractPDBparser
 
Test - class no.uio.labmed.biojava.alignment.Test.
Test program.
Test - class no.uio.labmed.molecule.Test.
Test program.
Test - class no.uio.labmed.pdb.Test.
Test program for PDBinterpreter.
Test - class no.uio.labmed.protein.Test.
 
Test - class no.uio.labmed.util.objectinfo.Test.
 
Test - class no.uio.labmed.util.tree.Test.
 
Test.AtomData - class no.uio.labmed.pdb.Test.AtomData.
 
Test.AtomData() - Constructor for class no.uio.labmed.pdb.Test.AtomData
 
Test.SecondaryStructure - class no.uio.labmed.pdb.Test.SecondaryStructure.
 
Test.SecondaryStructure(Object) - Constructor for class no.uio.labmed.pdb.Test.SecondaryStructure
 
Test() - Constructor for class no.uio.labmed.biojava.alignment.Test
 
Test() - Constructor for class no.uio.labmed.molecule.Test
 
Test() - Constructor for class no.uio.labmed.pdb.Test
 
Test() - Constructor for class no.uio.labmed.protein.Test
 
Test() - Constructor for class no.uio.labmed.util.objectinfo.Test
 
Test() - Constructor for class no.uio.labmed.util.tree.Test
 
test(String[]) - Method in class no.uio.labmed.biojava.alignment.Test
 
test2() - Method in class no.uio.labmed.biojava.alignment.Test
 
TestParser - class no.uio.labmed.pdb.TestParser.
Test program for PDBparser.
TestParser.AtomData - class no.uio.labmed.pdb.TestParser.AtomData.
 
TestParser.AtomData() - Constructor for class no.uio.labmed.pdb.TestParser.AtomData
 
TestParser.SecondaryStructure - class no.uio.labmed.pdb.TestParser.SecondaryStructure.
 
TestParser.SecondaryStructure(Object) - Constructor for class no.uio.labmed.pdb.TestParser.SecondaryStructure
 
TestParser() - Constructor for class no.uio.labmed.pdb.TestParser
 
thissize() - Method in class no.uio.labmed.molecule.AtomicElement
 
thissize() - Method in class no.uio.labmed.molecule.MolecularElement
 
thissize() - Method in class no.uio.labmed.molecule.CompoundElement
 
time() - Method in class no.uio.labmed.output.Timer
Return number of milliseconds since last call
Timer - class no.uio.labmed.output.Timer.
Timer.java Timer for timing operations: returns time in miliseconds since last call.
Timer() - Constructor for class no.uio.labmed.output.Timer
Construct Timer object
token() - Method in interface no.uio.labmed.util.tree.TreePointerInterface
Token (string) describing the key
token() - Method in class no.uio.labmed.util.tree.SequenceReference
Return token representation of value.
token() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
token() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
token() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return token representation of node: typically of the key.
token(Object) - Static method in class no.uio.labmed.util.tree.BioSequenceReference
 
token(Symbol) - Static method in class no.uio.labmed.util.tree.BioSequenceReference
 
toMatrise() - Method in class no.uio.labmed.linalg.IntMatrise
 
toMatrise() - Method in class no.uio.labmed.linalg.AbstractMatrise
Konverterer/kopierer til Matrise
toNext() - Method in class no.uio.labmed.linalg.AbstractMatrise.Iterator
Gaar til neste posisjon og returnerer om denne er gyldig.
toObject(double[]) - Static method in class no.uio.labmed.output.Vindu
 
toObject(double[]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(double[][]) - Static method in class no.uio.labmed.output.Vindu
 
toObject(double[][]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(float[]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(float[][]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(int[]) - Static method in class no.uio.labmed.output.Vindu
 
toObject(int[]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(int[][]) - Static method in class no.uio.labmed.output.Vindu
 
toObject(int[][]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(Object[][], Object[][]) - Static method in class no.uio.labmed.output.Vindu
 
toObject(Object[][], Object[][]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
toObject(Object[], Object[][]) - Static method in class no.uio.labmed.output.Vindu
 
toObject(Object[], Object[][]) - Static method in class no.uio.labmed.util.output.TabbedFrame
 
topMolecule - Variable in class no.uio.labmed.molecule.ReadPDB
 
toString() - Method in class no.uio.labmed.linalg.Matrise
 
toString() - Method in class no.uio.labmed.molecule.Atom
 
toString() - Method in class no.uio.labmed.molecule.MolecularType
 
toString() - Method in class no.uio.labmed.molecule.MolecularElement
 
toString() - Method in class no.uio.labmed.molecule.Compound
 
toString() - Method in class no.uio.labmed.pdb.AminoAcid
 
toString() - Method in class no.uio.labmed.protein.Protein
 
toString() - Method in class no.uio.labmed.protein.AminoAcid
 
toString() - Method in class no.uio.labmed.util.objectinfo.Test
 
toString() - Method in class no.uio.labmed.util.objectinfo.ObjectInfo
 
toString() - Method in class no.uio.labmed.util.output.TreeAdapterNode
Return string representation of node.
toString() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
toString() - Method in class no.uio.labmed.util.tree.TreeToString
Return string
toString() - Method in class no.uio.labmed.util.tree.BioSequenceReference
 
toString() - Method in class no.uio.labmed.util.tree.adapter.ObjectTree.ObjectPointer
 
toString() - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapterNode
Return string representation of node.
toString() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeStat
Return string representation
toString() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNodeCount
 
toString() - Method in class no.uio.labmed.util.tree.suffixTree.ISTNode
 
toString() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return string representation of pointer.
toString(double) - Static method in class no.uio.labmed.linalg.Global
Konverter til String med standardbredde
toString(double[]) - Static method in class no.uio.labmed.linalg.Global
 
toString(double, int) - Static method in class no.uio.labmed.linalg.Global
Konverter til String med n desimaler
toString(int) - Static method in class no.uio.labmed.linalg.Global
Konverter til String
toString(int[]) - Static method in class no.uio.labmed.linalg.Global
 
toString(Object[]) - Static method in class no.uio.labmed.linalg.Global
Konverterer array til String
tree - Variable in class no.uio.labmed.util.tree.suffixTree.ISTPointer
 
TreeAdapter - class no.uio.labmed.util.output.TreeAdapter.
NB: FORELDET!!!!!!!!!!!!!!!!!!!!
TreeAdapter(TreeAdapterNode) - Constructor for class no.uio.labmed.util.output.TreeAdapter
Constructor: Initiate tree with given node as root
TreeAdapter(TreePointerInterface) - Constructor for class no.uio.labmed.util.output.TreeAdapter
Constructor: Initiate tree with given node as root
TreeAdapterNode - class no.uio.labmed.util.output.TreeAdapterNode.
NB: FORELDET!!!!!!!!!!!!!!!!!!!!!!
TreeInterface - interface no.uio.labmed.util.tree.TreeInterface.
 
TreeNodeInterface - interface no.uio.labmed.util.tree.TreeNodeInterface.
 
TreeNodePointerInterface - interface no.uio.labmed.util.tree.TreeNodePointerInterface.
A minimal interface for pointing to tree nodes and parsing it's children.
TreePointerInterface - interface no.uio.labmed.util.tree.TreePointerInterface.
A tree pointer is basically a pointer to a node in a tree.
treeString() - Method in class no.uio.labmed.molecule.Molecule
 
treeString(int) - Method in class no.uio.labmed.molecule.Molecule
 
treeString(StringBuffer, String, int) - Method in class no.uio.labmed.molecule.Molecule
 
TreeToString - class no.uio.labmed.util.tree.TreeToString.
Class for producing string representation of tree.
treeToString() - Method in class no.uio.labmed.util.tree.suffixTree.ImplicitSuffixTree
Get a string representation of the tree.
TreeToString() - Constructor for class no.uio.labmed.util.tree.TreeToString
Constructor
TYPE_HELIX - Static variable in class no.uio.labmed.pdb.AbstractPDBparser
 
TYPE_SHEET - Static variable in class no.uio.labmed.pdb.AbstractPDBparser
 
TYPE_TURN - Static variable in class no.uio.labmed.pdb.AbstractPDBparser
 

V

value() - Method in class no.uio.labmed.util.output.ObjectTreeAdapter
 
value(ObjectTree.ObjectPointer) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
valueForPathChanged(TreePath, Object) - Method in class no.uio.labmed.util.output.TreeAdapter
Empty implementation
valueForPathChanged(TreePath, Object) - Method in class no.uio.labmed.util.tree.adapter.JTreeAdapter
Empty implementation
valueType(ObjectTree.ObjectPointer) - Method in class no.uio.labmed.util.tree.adapter.ObjectTree
 
vectorString() - Method in class no.uio.labmed.molecule.Atom
 
view(Molecule) - Static method in class no.uio.labmed.molecule.ViewMolecule
 
view(Molecule) - Static method in class no.uio.labmed.protein.ViewMolecule
 
view(Molecule, ActionPlot, SelectionNode) - Static method in class no.uio.labmed.molecule.ViewMolecule
 
viewFile(String, int) - Static method in class no.uio.labmed.molecule.Test
 
viewH2O() - Static method in class no.uio.labmed.molecule.Test
 
ViewMolecule - class no.uio.labmed.molecule.ViewMolecule.
 
ViewMolecule - class no.uio.labmed.protein.ViewMolecule.
 
ViewMolecule(Molecule) - Constructor for class no.uio.labmed.protein.ViewMolecule
 
ViewMolecule(Molecule, ActionPlot, SelectionNode) - Constructor for class no.uio.labmed.molecule.ViewMolecule
 
Vindu - class no.uio.labmed.output.Vindu.
 
Vindu() - Constructor for class no.uio.labmed.output.Vindu
 
Vindu(int, int, int, int) - Constructor for class no.uio.labmed.output.Vindu
 
Vindu(int, int, int, int, String) - Constructor for class no.uio.labmed.output.Vindu
 
Vindu(String) - Constructor for class no.uio.labmed.output.Vindu
 

W

word() - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return the string of tokens from root to this node.
word(ISTNode) - Method in class no.uio.labmed.util.tree.suffixTree.ISTPointer
Return the string of tokens from root to given node.
write(int) - Method in class no.uio.labmed.output.AppendOutputStream
 
write(int) - Method in class no.uio.labmed.util.output.AppendOutputStream
 

X

x(double) - Method in class no.uio.labmed.output.GraphPane
 
x(double) - Method in class no.uio.labmed.util.output.GraphPane
 
xtoString() - Method in class no.uio.labmed.molecule.Molecule
 

Y

y(double) - Method in class no.uio.labmed.output.GraphPane
 
y(double) - Method in class no.uio.labmed.util.output.GraphPane
 

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