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

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
 

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