Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
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
Overview
Package
Class
Use
Tree
Deprecated
Index
Help
PREV LETTER
NEXT LETTER
FRAMES
NO FRAMES
All Classes
A
B
C
D
E
F
G
H
I
J
L
M
N
O
P
R
S
T
U
V
W
Z