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## S

select(Vector) - Method in class jprotein.rasmol.SequenceAppearance
select() - Method in class jprotein.tree.data.VisualLeaf
selectAll() - Method in class jprotein.rasmol.SequenceAppearance
sendCommand() - Method in class jprotein.io.net.PdbCodeClient
sendCommand() - Method in class jprotein.io.net.WebClient
sendCommand(String) - Method in class jprotein.io.net.WebClient
sendGetCommand() - Method in class jprotein.io.net.BlastClient
sendInitialPsiGetCommand() - Method in class jprotein.io.net.PsiBlastClientOld
sendInitialPsiPutCommand() - Method in class jprotein.io.net.PsiBlastClient
sendIterPsiGetCommand() - Method in class jprotein.io.net.PsiBlastClientOld
sendPsiGetCommand() - Method in class jprotein.io.net.PsiBlastClient
sendPutCommand() - Method in class jprotein.io.net.BlastClient
sendPutCommand() - Method in class jprotein.io.net.PsiBlastClientOld
Sequence - Class in jprotein.data.datatype
Sequence() - Constructor for class jprotein.data.datatype.Sequence
Sequence(String) - Constructor for class jprotein.data.datatype.Sequence
Sequence(String, String) - Constructor for class jprotein.data.datatype.Sequence
Sequence3D - Class in jprotein.data.datatype
Sequence3D() - Constructor for class jprotein.data.datatype.Sequence3D
Sequence3D(String, String) - Constructor for class jprotein.data.datatype.Sequence3D
SequenceAppearance - Class in jprotein.rasmol
SequenceAppearance(Sequence3D) - Constructor for class jprotein.rasmol.SequenceAppearance
SequenceAppearance(Sequence3D, Property) - Constructor for class jprotein.rasmol.SequenceAppearance
SequenceInformation - Class in jprotein.data.datatype
SequenceInformation() - Constructor for class jprotein.data.datatype.SequenceInformation
setAccessibility(Atom) - Method in class jprotein.data.datatype.Atom
  Méthode pour calculer les points accessibles de l'atome courant par un atome par défaut (oxygène) sachant que l'espace est aussi encombré par l'atome atom.
setAccessibility(Atom, float) - Method in class jprotein.data.datatype.Atom
  Méthode pour calculer les points accessibles de l'atome courant par un atome sonde de rayon probeRadius sachant que l'espace est aussi encombré par l'atome atom.
setAccessibility(Atom, float, float) - Method in class jprotein.data.datatype.Atom
  Méthode pour calculer les points accessibles de l'atome courant par un atome sonde de rayon probeRadius sachant que l'espace est aussi encombré par l'atome atom en spécifiant un bruit (?).
setAccessibility(Atom) - Method in class jprotein.data.datatype.Atom1
setAccessibility(Atom, float) - Method in class jprotein.data.datatype.Atom1
setAccessibility(Atom, float, float) - Method in class jprotein.data.datatype.Atom1
setAccessibility(boolean) - Method in class jprotein.data.datatype.Residue
setAccessible(boolean, int) - Method in class jprotein.data.datatype.Atom
setAccessible(boolean, int) - Method in class jprotein.data.datatype.Atom1
setAction(String) - Method in class jprotein.ProgressIndicator
setAppearance(Vector) - Method in class jprotein.rasmol.model.SqueletonModel
setBackTrace(Vector) - Method in class jprotein.tree.data.Leaf
setChainId(String) - Method in class jprotein.data.datatype.Sequence3D
setColor(int, Color3f) - Method in class jprotein.rasmol.SequenceAppearance
setColors(Color3f, Color3f, Color3f) - Method in class jprotein.rasmol.Property
setConservedResidue(Vector) - Method in class jprotein.tree.data.Leaf
setCoordinates(Point3f) - Method in class jprotein.data.datatype.Atom
setCoordinates(Point3f) - Method in class jprotein.data.datatype.Atom1
setDatabase(String) - Method in class jprotein.io.net.BlastClient
setDatabase(String) - Method in class jprotein.io.net.PsiBlastClient
setDatabase(String) - Method in class jprotein.io.net.PsiBlastClientOld
setDistance(float) - Method in class jprotein.cluster.data.ProxNode
setDistantCouple(Sequence, Sequence) - Method in class jprotein.tree.tools.DistanceMatrix
setEndOverlap(int) - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
setEndOverlap(int) - Method in class jprotein.data.datatype.SequenceInformation
setEValue(double) - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
setExpectedValue(double) - Method in class jprotein.io.net.BlastClient
setExpectedValue(double) - Method in class jprotein.io.net.PsiBlastClient
setExpectedValue(double) - Method in class jprotein.io.net.PsiBlastClientOld
setExpectValue(double) - Method in class jprotein.data.datatype.SequenceInformation
setFileName(String) - Method in class jprotein.io.file.ClustalFileReader
setGapCosts(int, int) - Method in class jprotein.io.net.BlastClient
setGapCosts(int, int) - Method in class jprotein.io.net.PsiBlastClient
setGapCosts(int, int) - Method in class jprotein.io.net.PsiBlastClientOld
setHeader(String) - Method in class jprotein.data.datatype.Sequence3D
setId(int) - Method in class jprotein.cluster.data.ProxList
setIdentity(int) - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
setIdentity(int) - Method in class jprotein.data.datatype.SequenceInformation
setIndex(int) - Method in class jprotein.rasmol.model.ResidueModel
setLeaf(SimpleNode, int, Leaf) - Method in class jprotein.tree.tools.Tree
setLeft(Leaf) - Method in class jprotein.tree.data.SimpleNode
setLeftVertice(double) - Method in class jprotein.tree.data.SimpleNode
setLimit(double) - Method in class jprotein.tree.VisualTree
setMatrix(String) - Method in class jprotein.io.net.BlastClient
setMatrix(String) - Method in class jprotein.io.net.PsiBlastClient
setMatrix(String) - Method in class jprotein.io.net.PsiBlastClientOld
setMaxIteration(int) - Method in class jprotein.io.net.PsiBlastClient
setMaxResults(int) - Method in class jprotein.io.net.BlastClient
setMaxResults(int) - Method in class jprotein.io.net.PsiBlastClient
setMaxResults(int) - Method in class jprotein.io.net.PsiBlastClientOld
setMultipleAlignment(MultiAlignment) - Method in class jprotein.tree.tools.DistanceMatrix
setName(String) - Method in class jprotein.data.datatype.Atom
setName(String) - Method in class jprotein.data.datatype.Atom1
setNumIteration(int) - Method in class jprotein.io.net.PsiBlastClientOld
setOverlapLength(int) - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
setPath(String) - Method in class jprotein.io.file.ETtoHTML
setPath(String) - Method in class jprotein.io.file.FastaFileReader
setPath(String) - Method in class jprotein.io.file.PdbFileReader
setPDBCode(String) - Method in class jprotein.io.net.PdbCodeClient
setPosition(int) - Method in class jprotein.data.datatype.Residue
setPrevRID(String) - Method in class jprotein.io.net.PsiBlastClient
setPrevRID(String) - Method in class jprotein.io.net.PsiBlastClientOld
setProgress(double) - Method in class jprotein.ProgressIndicator
setProperty(Vector) - Method in class jprotein.rasmol.Property
setProperty(Property) - Method in class jprotein.rasmol.SequenceAppearance
setPropertyData(Vector) - Method in class jprotein.data.dataformat.info.PdbSequenceInfo
setQuerySequence(Sequence) - Method in class jprotein.io.net.BlastClient
setQuerySequence(String) - Method in class jprotein.io.net.BlastClient
setQuerySequence(Sequence) - Method in class jprotein.io.net.PsiBlastClient
setQuerySequence(String) - Method in class jprotein.io.net.PsiBlastClient
setQuerySequence(Sequence) - Method in class jprotein.io.net.PsiBlastClientOld
setQuerySequence(String) - Method in class jprotein.io.net.PsiBlastClientOld
setRef(ProxList) - Method in class jprotein.cluster.data.ProxNode
setRefSequence(Sequence) - Method in class jprotein.data.dataformat.info.BlastPairwiseInfo
setRefSequence(Sequence) - Method in class jprotein.data.datatype.PairwiseAlignment
setResidue(Residue3D) - Method in class jprotein.cluster.data.ProxList
setRetrieveMode(boolean) - Method in class jprotein.io.net.PsiBlastClient
setRight(Leaf) - Method in class jprotein.tree.data.SimpleNode
setRightVertice(double) - Method in class jprotein.tree.data.SimpleNode
setRoot(Leaf) - Method in class jprotein.tree.VisualTree
setRTOE(String) - Method in class jprotein.io.net.PsiBlastClient
setRTOE(String) - Method in class jprotein.io.net.PsiBlastClientOld
setScale(double, double) - Method in class jprotein.tree.data.VisualLeaf
setSelected(int, boolean) - Method in class jprotein.rasmol.SequenceAppearance
setSequence(String) - Method in class jprotein.data.datatype.Sequence
setSequenceBegin(int) - Method in class jprotein.data.datatype.Sequence3D
setSequenceBreak(boolean) - Method in class jprotein.data.datatype.Residue3D
setSequenceName(String) - Method in class jprotein.data.datatype.Sequence
setStartOverlap(int) - Method in class jprotein.data.dataformat.info.BlastSequenceInfo
setStartOverlap(int) - Method in class jprotein.data.datatype.SequenceInformation
setStatus(String) - Method in class jprotein.ProgressIndicator
setSubstitutionMatrix(SubstitutionMatrix) - Method in class jprotein.tree.tools.DistanceMatrix
setSymbol(char) - Method in class jprotein.data.datatype.Atom
setSymbol(char) - Method in class jprotein.data.datatype.Atom1
setTransparent(int, boolean) - Method in class jprotein.rasmol.SequenceAppearance
setURL(String) - Method in class jprotein.io.net.WebClient
setVertice(SimpleNode, int, double) - Method in class jprotein.tree.tools.Tree
setVisible(int, boolean) - Method in class jprotein.rasmol.SequenceAppearance
setVX(double) - Method in class jprotein.tree.data.VisualLeaf
setVX(double) - Method in class jprotein.tree.data.VisualNode
setVY(double) - Method in class jprotein.tree.data.VisualLeaf
setVY(double) - Method in class jprotein.tree.data.VisualNode
shiftRoot(SimpleNode, int, int) - Method in class jprotein.tree.tools.Tree
SimpleNode - Class in jprotein.tree.data
SimpleNode(Leaf, Leaf) - Constructor for class jprotein.tree.data.SimpleNode
Squeleton - Class in jprotein.rasmol.model
Squeleton() - Constructor for class jprotein.rasmol.model.Squeleton
SqueletonModel - Class in jprotein.rasmol.model
SqueletonModel(Vector, Vector) - Constructor for class jprotein.rasmol.model.SqueletonModel
standardError(Vector) - Static method in class jprotein.tools.Statistic
standardError(Vector) - Static method in class jprotein.tree.tools.Statistic
Statistic - Class in jprotein.tools
Statistic() - Constructor for class jprotein.tools.Statistic
Statistic - Class in jprotein.tree.tools
Statistic() - Constructor for class jprotein.tree.tools.Statistic
stop() - Method in class jprotein.ProgressIndicator
SubstitutionMatrix - Class in jprotein.tree.tools
SubstitutionMatrix(String) - Constructor for class jprotein.tree.tools.SubstitutionMatrix
sumAlignmentComposition(Vector, Vector) - Static method in class jprotein.data.datatype.MultiAlignment
sumAlignmentComposition(Vector, Vector) - Static method in class jprotein.data.datatype.MultiPairwiseAlignment

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