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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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