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## G

generateTraceRecord(MultiAlignment, Sequence) - Method in class jprotein.tree.tools.ET
genericAtomCoordinatesExtraction() - Method in class jprotein.io.file.PdbFileReader2
getAction() - Method in class jprotein.ProgressIndicator
getAlignment(int) - Method in class jprotein.data.datatype.MultiAlignment
getAlignmentComposition(Vector, Sequence) - Static method in class jprotein.data.dataformat.parser.BlastPairwise
getAlignmentComposition(Sequence) - Method in class jprotein.data.datatype.MultiAlignment
getAlignmentComposition() - Method in class jprotein.data.datatype.MultiPairwiseAlignment
getAllAtoms() - Method in class jprotein.data.datatype.Residue3D
getAtomAccessibleSurfaceArea() - Method in class jprotein.data.datatype.Atom
  Retourne la surface de l'atome qui est accessible.
getAtomAccessibleSurfaceArea() - Method in class jprotein.data.datatype.Atom1
getAtomIndex(char) - Static method in class jprotein.data.datatype.Atom
  Methodes statiques retournant des caractéristiques générale des atomes
getAtomIndex() - Method in class jprotein.data.datatype.Atom
getAtomIndex(char) - Static method in class jprotein.data.datatype.Atom1
getAtomIndex() - Method in class jprotein.data.datatype.Atom1
getAtomSurfaceArea() - Method in class jprotein.data.datatype.Atom
getAtomSurfaceArea() - Method in class jprotein.data.datatype.Atom1
getBackTrace() - Method in class jprotein.tree.data.Leaf
getCanvas() - Method in class jprotein.rasmol.ProteinEngine3D
getCarbonAlphaCoordinates() - Method in class jprotein.data.datatype.Residue3D
  Coordonnees du carbone alpha qui est en position 0 du squelette
getCenterGravityCoordinates() - Method in class jprotein.data.datatype.Residue3D
  Calcul du centre de gravite
getChainId() - Method in class jprotein.data.datatype.Sequence3D
getChild() - Method in class jprotein.tree.data.VisualLeaf
getChild() - Method in class jprotein.tree.data.VisualNode
getColor(int) - Method in class jprotein.rasmol.SequenceAppearance
getCompositionFrequencies(Vector) - Static method in class jprotein.data.dataformat.parser.BlastPairwise
getCompositionFrequencies(Vector) - Static method in class jprotein.data.datatype.MultiAlignment
getCompositionFrequencies(Vector) - Static method in class jprotein.data.datatype.MultiPairwiseAlignment
getConservedResidue() - Method in class jprotein.tree.data.Leaf
getCoordinates() - Method in class jprotein.data.datatype.Atom
getCoordinates() - Method in class jprotein.data.datatype.Atom1
getCoreIndex() - Method in class jprotein.cluster.data.Cluster
getCoreResidues() - Method in class jprotein.cluster.data.Cluster
getData() - Method in interface jprotein.data.dataformat.Format
getData() - Method in class jprotein.io.file.BlastFileReader
getData() - Method in class jprotein.io.file.ClustalFileReader
getData() - Method in class jprotein.io.file.PdbFileReader
  Methode de lecture ligne par ligne heritee de FileIO retournant un vecteur.
getData() - Method in class jprotein.io.net.BlastClient
getData() - Method in class jprotein.io.net.PdbCodeClient
  Envoi de la requ�te et r�cup�ration des infos
getData() - Method in class jprotein.io.net.PsiBlastClient
getData() - Method in class jprotein.io.net.PsiBlastClientOld
getDatabase() - Method in class jprotein.io.net.BlastClient
getDatabase() - Method in class jprotein.io.net.PsiBlastClient
getDatabase() - Method in class jprotein.io.net.PsiBlastClientOld
getDistance() - Method in class jprotein.cluster.data.ProxNode
getDistance(int) - Method in class jprotein.tree.data.Leaf
getDistance(Residue, Residue) - Method in class jprotein.tree.tools.SubstitutionMatrix
getDistanceMatrix() - Method in class jprotein.tree.tools.NJ
getDistantCouple() - Method in class jprotein.tree.tools.DistanceMatrix
getDoubleDistance(int) - Method in class jprotein.tree.data.Leaf
getDoubleParam(String, String) - Method in class jprotein.ConfigFile
getEndOverlap() - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
getEndOverlap() - Method in class jprotein.data.datatype.SequenceInformation
getEValue() - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
getExpectedValue() - Method in class jprotein.io.net.BlastClient
getExpectedValue() - Method in class jprotein.io.net.PsiBlastClient
getExpectedValue() - Method in class jprotein.io.net.PsiBlastClientOld
getExpectedValue() - Method in class jprotein.tree.tools.SubstitutionMatrix
getExpectValue() - Method in class jprotein.data.datatype.SequenceInformation
getFormat() - Method in class jprotein.io.net.PsiBlastClient
getGapCosts() - Method in class jprotein.io.net.BlastClient
getGapCosts() - Method in class jprotein.io.net.PsiBlastClient
getGapCosts() - Method in class jprotein.io.net.PsiBlastClientOld
getHeader() - Method in class jprotein.data.datatype.Sequence3D
getId() - Method in class jprotein.cluster.data.ProxList
getIdentity() - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
getIdentity() - Method in class jprotein.data.datatype.SequenceInformation
getIndex() - Method in class jprotein.data.datatype.IndexedResidue
getIndex() - Method in class jprotein.rasmol.model.ResidueModel
getInformationContent(Vector) - Static method in class jprotein.data.dataformat.parser.BlastPairwise
getInformationContent(Vector) - Static method in class jprotein.data.datatype.MultiAlignment
getInformationContent(Vector) - Static method in class jprotein.data.datatype.MultiPairwiseAlignment
getInterface(Sequence3D, Sequence3D, double) - Static method in class jprotein.TestAccess
  interface method
getIntParam(String, String) - Method in class jprotein.ConfigFile
getLeaf() - Method in class jprotein.tree.data.VisualLeaf
getLeaf(int) - Method in class jprotein.tree.tools.DistanceMatrix
getLeaf(SimpleNode, Sequence) - Method in class jprotein.tree.tools.Tree
getLeaf(SimpleNode, int) - Method in class jprotein.tree.tools.Tree
getLeftSpan() - Method in class jprotein.tree.data.VisualLeaf
getLeftSpan() - Method in class jprotein.tree.data.VisualNode
getLeftVertice() - Method in class jprotein.tree.data.SimpleNode
getLength() - Method in class jprotein.cluster.data.DistanceMap
getLength() - Method in class jprotein.cluster.data.ProxList
getLimit() - Method in class jprotein.tree.VisualTree
getLowerLimitScore(int, int) - Method in class jprotein.tree.tools.DistanceMatrix
getMatrix() - Method in class jprotein.io.net.BlastClient
getMatrix() - Method in class jprotein.io.net.PsiBlastClient
getMatrix() - Method in class jprotein.io.net.PsiBlastClientOld
getMaxIteration() - Method in class jprotein.io.net.PsiBlastClient
getMaxLevels() - Method in class jprotein.tree.data.TreeRecord
getMaxResults() - Method in class jprotein.io.net.BlastClient
getMaxResults() - Method in class jprotein.io.net.PsiBlastClient
getMaxResults() - Method in class jprotein.io.net.PsiBlastClientOld
getName() - Method in class jprotein.data.datatype.Atom
getName() - Method in class jprotein.data.datatype.Atom1
getNeighbourResidues() - Method in class jprotein.cluster.data.Cluster
getNeighbourResidues(float) - Method in class jprotein.cluster.data.ProxList
getNodeDistance(SimpleNode, double) - Method in class jprotein.tree.tools.Tree
getNodePartition(SimpleNode, double) - Method in class jprotein.tree.tools.Tree
getNonGappedAlignedLength(int, int) - Method in class jprotein.tree.tools.DistanceMatrix
getNonGappedPosition(int) - Method in class jprotein.data.datatype.Sequence
getNonGappedSequenceLength() - Method in class jprotein.data.datatype.Sequence
getNumAlignments() - Method in class jprotein.io.net.PsiBlastClient
getNumDescriptions() - Method in class jprotein.io.net.PsiBlastClient
getNumIteration() - Method in class jprotein.io.net.PsiBlastClientOld
getNumLevels(int) - Method in class jprotein.tree.data.TreeRecord
getOverlapLength() - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
getPairwiseAlignment(int) - Method in class jprotein.data.datatype.MultiPairwiseAlignment
getPairwiseInfo(Format) - Static method in class jprotein.data.dataformat.parser.BlastPairwise
getParam(String, String) - Method in class jprotein.ConfigFile
getPath() - Method in class jprotein.io.file.ETtoHTML
getPath() - Method in class jprotein.io.file.FastaFileReader
getPath() - Method in class jprotein.io.file.PdbFileReader
getPathDistance(SimpleNode, PathIndex) - Method in class jprotein.tree.tools.Tree
getPathIndex(SimpleNode, Leaf) - Method in class jprotein.tree.tools.Tree
getPDBCode() - Method in class jprotein.io.net.PdbCodeClient
getPercentAccessibility() - Method in class jprotein.data.datatype.Atom
  Retourne le pourcentage de la surface de l'atome qui est accessible.
getPercentAccessibility() - Method in class jprotein.data.datatype.Atom1
getPosition() - Method in class jprotein.data.datatype.Residue
getPosition() - Method in class jprotein.rasmol.model.ResidueModel
getPrevRID() - Method in class jprotein.io.net.PsiBlastClient
getPrevRID() - Method in class jprotein.io.net.PsiBlastClientOld
getProgress() - Method in class jprotein.ProgressIndicator
getProjection(int) - Method in class jprotein.data.datatype.Atom
getProjection(int) - Method in class jprotein.data.datatype.Atom1
getPropertyColor(int) - Method in class jprotein.rasmol.Property
getPropertyData() - Method in class jprotein.data.dataformat.info.PdbSequenceInfo
getPropertyValue(int) - Method in class jprotein.rasmol.Property
getProxList(int) - Method in class jprotein.cluster.data.DistanceMap
getProxNode(int) - Method in class jprotein.cluster.data.ProxList
getPsiThreshhold() - Method in class jprotein.io.net.PsiBlastClient
getPsiThreshhold() - Method in class jprotein.io.net.PsiBlastClientOld
getQuerySequence() - Method in class jprotein.io.net.BlastClient
getQuerySequence() - Method in class jprotein.io.net.PsiBlastClient
getQuerySequence() - Method in class jprotein.io.net.PsiBlastClientOld
getRadius(char) - Static method in class jprotein.data.datatype.Atom
getRadius() - Method in class jprotein.data.datatype.Atom
getRadius(char) - Static method in class jprotein.data.datatype.Atom1
getRadius() - Method in class jprotein.data.datatype.Atom1
getRadius() - Method in class jprotein.data.datatype.Residue3D
  Calcul du rayon max par rapport au centre de gravite
getRef() - Method in class jprotein.cluster.data.ProxNode
getRefSequence() - Method in class jprotein.data.dataformat.info.BlastPairwiseInfo
getRefSequence() - Method in class jprotein.data.datatype.PairwiseAlignment
getRelativeTraceDepth(Vector, double) - Method in class jprotein.tree.tools.ET
getResidue() - Method in class jprotein.cluster.data.ProxList
getResidue() - Method in class jprotein.cluster.data.ProxNode
getResidue(int) - Method in class jprotein.data.datatype.Sequence
getResidue(int, int) - Method in class jprotein.data.datatype.Sequence3D
getResidue() - Method in class jprotein.rasmol.model.ResidueModel
getResidueCode(int) - Static method in class jprotein.data.datatype.Residue
getResidueCode() - Method in class jprotein.data.datatype.Residue
getResidueIndex() - Method in class jprotein.data.datatype.Residue
getResidueIndex(char) - Static method in class jprotein.data.datatype.Residue
getResidueIndex(String) - Static method in class jprotein.data.datatype.Residue
getResidueInfo(Sphere) - Method in class jprotein.rasmol.model.SqueletonModel
getResidueSymbol(int) - Static method in class jprotein.data.datatype.Residue
getResidueSymbol() - Method in class jprotein.data.datatype.Residue
getRightSpan() - Method in class jprotein.tree.data.VisualLeaf
getRightSpan() - Method in class jprotein.tree.data.VisualNode
getRightVertice() - Method in class jprotein.tree.data.SimpleNode
getRoot() - Method in class jprotein.tree.VisualTree
getRTOE() - Method in class jprotein.io.net.PsiBlastClient
getRTOE() - Method in class jprotein.io.net.PsiBlastClientOld
getScaleX() - Method in class jprotein.tree.VisualTree
getScaleY() - Method in class jprotein.tree.VisualTree
getSequence() - Method in class jprotein.data.dataformat.info.PdbSequenceInfo
getSequence() - Method in class jprotein.data.datatype.Sequence
getSequence() - Method in class jprotein.tree.data.Leaf
getSequenceBegin() - Method in class jprotein.data.datatype.Sequence3D
getSequenceData(Format) - Static method in class jprotein.data.dataformat.parser.Clustal
getSequenceData() - Method in class jprotein.io.file.FastaFileReader
getSequenceData() - Method in class jprotein.io.file.PdbFileReader2
getSequenceHeader() - Method in class jprotein.io.file.PdbFileReader2
getSequenceInfo(Format) - Static method in class jprotein.data.dataformat.parser.Blast
getSequenceInfo(Format) - Static method in class jprotein.data.dataformat.parser.PDB
  Parseur d'un fichier pdb, retourne une liste de jprotein.data.dataformat.info.PdbSequenceInfo.
getSequenceLength() - Method in class jprotein.data.datatype.Sequence
getSequenceLength() - Method in class jprotein.data.datatype.Sequence3D
getSequenceName() - Method in class jprotein.data.datatype.Sequence
getSequencePosition(int) - Method in class jprotein.data.datatype.Alignment
getSideChainAtom(int) - Method in class jprotein.data.datatype.Residue3D
getSideChainSize() - Method in class jprotein.data.datatype.Residue3D
  Accesseurs de la chaine laterale
getSpan() - Method in class jprotein.tree.data.VisualLeaf
getSpan() - Method in class jprotein.tree.data.VisualNode
getSphereList() - Method in class jprotein.rasmol.model.ResidueModel
getSqueletonAtom(int) - Method in class jprotein.data.datatype.Residue3D
  Accesseurs d'atomes (dans la chaine laterale et le squelette
getSqueletonAtom(String) - Method in class jprotein.data.datatype.Residue3D
getSqueletonSize() - Method in class jprotein.data.datatype.Residue3D
  Accesseurs de la chaine squelette
getStartOverlap() - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
getStartOverlap() - Method in class jprotein.data.datatype.SequenceInformation
getStatus() - Method in class jprotein.ProgressIndicator
getSum() - Method in class jprotein.tree.data.Leaf
getSymbol() - Method in class jprotein.data.datatype.Atom
getSymbol() - Method in class jprotein.data.datatype.Atom1
getTrace(Vector) - Method in class jprotein.tree.tools.Tree
getTraceAnalysis(SimpleNode) - Method in class jprotein.tree.tools.Tree
getTransX() - Method in class jprotein.tree.VisualTree
getTransY() - Method in class jprotein.tree.VisualTree
getTree() - Method in class jprotein.tree.tools.NJ
getUpperLimitScore(int, int) - Method in class jprotein.tree.tools.DistanceMatrix
getURL() - Method in class jprotein.io.net.WebClient
getVertice(SimpleNode, int) - Method in class jprotein.tree.tools.Tree
getVision() - Method in class jprotein.rasmol.ProteinEngine3D
getVMaxX() - Method in class jprotein.tree.data.VisualLeaf
getVMaxX() - Method in class jprotein.tree.data.VisualNode
getVMaxY() - Method in class jprotein.tree.data.VisualLeaf
getVMaxY() - Method in class jprotein.tree.data.VisualNode
getVMinX() - Method in class jprotein.tree.data.VisualLeaf
getVMinX() - Method in class jprotein.tree.data.VisualNode
getVX() - Method in class jprotein.tree.data.VisualLeaf
getVY() - Method in class jprotein.tree.data.VisualLeaf
goLeft() - Method in class jprotein.tree.data.SimpleNode
goLeft() - Method in class jprotein.tree.data.VisualNode
goRight() - Method in class jprotein.tree.data.SimpleNode
goRight() - Method in class jprotein.tree.data.VisualNode

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A B C D E F G H I J L M N O P R S T U V W Z