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A
ActiveSiteProfile
- Class in
dasp.model
ActiveSiteProfile(List<ActiveSiteSignature>, Align)
- Constructor for class dasp.model.
ActiveSiteProfile
ActiveSiteSignature
- Class in
dasp.model
ActiveSiteSignature(String)
- Constructor for class dasp.model.
ActiveSiteSignature
ActiveSiteSignature(DaspStructure, List<Residue>)
- Constructor for class dasp.model.
ActiveSiteSignature
addFragRes(Residue)
- Method in class dasp.model.
Fragment
addSequence(String)
- Method in class dasp.model.
Alignment
addSequence can be used to add an addtional sequence to the alignment.
addSequences(List<String>)
- Method in class dasp.model.
Alignment
addSequences can be used to add a list of addtional sequences to the alignment.
Align
- Interface in
dasp.algorithms
align(List<String>)
- Method in interface dasp.algorithms.
Align
align actually performs the alignment.
align(List<String>)
- Method in class dasp.algorithms.
ClustalAlign
align actually performs the alignment.
Alignment
- Class in
dasp.model
Alignment()
- Constructor for class dasp.model.
Alignment
Alignment(List<String>, Align)
- Constructor for class dasp.model.
Alignment
alignment
- Variable in class dasp.model.
Alignment
C
ClustalAlign
- Class in
dasp.algorithms
ClustalAlign()
- Constructor for class dasp.algorithms.
ClustalAlign
Will need to store the alignment or files the alignemnt is saved to?
D
dasp
- package dasp
Dasp
- Class in
dasp
Dasp()
- Constructor for class dasp.
Dasp
dasp.algorithms
- package dasp.algorithms
dasp.model
- package dasp.model
DaspStructure
- Class in
dasp.model
DaspStructure(String)
- Constructor for class dasp.model.
DaspStructure
Create a new structure from a pdb file.
DaspStructure(String, String)
- Constructor for class dasp.model.
DaspStructure
Create a new structure from a pdb file.
deleteSequence(String)
- Method in class dasp.model.
Alignment
deleteSequence can be used to remove a sequence from the alignment.
dist(Residue, Residue)
- Method in class dasp.model.
ActiveSiteSignature
Calculates the Euclidean distance between two residue centers
doAlign()
- Method in class dasp.model.
Alignment
F
Fragment
- Class in
dasp.model
Fragment()
- Constructor for class dasp.model.
Fragment
G
getAA()
- Method in class dasp.model.
Residue
getAlignment()
- Method in interface dasp.algorithms.
Align
Return the alignment itself as a list of aligned sequences with dashes to account for insertions.
getAlignment()
- Method in class dasp.algorithms.
ClustalAlign
Return the alignment itself with each sequence as a single string and with dashes inserted to account for insertions.
getAlignment()
- Method in class dasp.model.
Alignment
Return the alignment itself as a list of strings with dashes inserted to account for insertions.
getAlignmentAsString()
- Method in class dasp.model.
Alignment
Return the alignment itself as a string with newlines between sequences and dashes inserted to account for insertions.
getAlignmentByIndex(int)
- Method in class dasp.model.
Alignment
Return the alignment string for just one of the proteins in the alignment.
getAlignmentByName(String)
- Method in class dasp.model.
Alignment
Return the alignment string for just one of the proteins in the alignment.
getASPscore(String, int)
- Method in interface dasp.algorithms.
Align
Return the ASP score as defined in Cammer et al for this alignment.
getASPscore(String, int)
- Method in class dasp.algorithms.
ClustalAlign
Return the ASP score as defined in Cammer et al for this alignment.
getCenter()
- Method in class dasp.model.
Residue
getFragFormattedAlignment()
- Method in class dasp.model.
ActiveSiteProfile
Modify alignment to reflect fragments of signatures.
getFragmentsInContext()
- Method in class dasp.model.
ActiveSiteSignature
getFragRes(int)
- Method in class dasp.model.
Fragment
getHTMLAlignment(List<String>)
- Method in interface dasp.algorithms.
Align
Return the alignment itself as an HTML-formatted string to account for insertions.
getHTMLAlignment(List<String>)
- Method in class dasp.algorithms.
ClustalAlign
Return the alignment itself as an HTML-formatted string to account for insertions.
getHTMLAlignment()
- Method in class dasp.model.
Alignment
Return the alignment itself as an HTML-formatted string to account for insertions.
getIdentity()
- Method in interface dasp.algorithms.
Align
Return the % identity for all of the sequences in the alignment.
getIdentity()
- Method in class dasp.algorithms.
ClustalAlign
Return the % identity for all of the sequences in the alignment.
getIdentity()
- Method in class dasp.model.
Alignment
Return the % identity for all of the sequences in the alignment.
GetOpt
- Class in
dasp
GetOpt(String[], String)
- Constructor for class dasp.
GetOpt
getopt()
- Method in class dasp.
GetOpt
getOptLetter()
- Method in class dasp.
GetOpt
getPdbId()
- Method in class dasp.model.
ActiveSiteSignature
getPdbId()
- Method in class dasp.model.
DaspStructure
Return the pbd id and chain as a string for this sequence Does not account ofr a possible 'pdb' in front of the pdb id.
getResidue(String)
- Method in class dasp.model.
DaspStructure
Return a Residue object for a residue within this PDB file.
getScore()
- Method in class dasp.model.
Alignment
Return the alignment score that results from the alignment.
getSeqLength()
- Method in class dasp.model.
DaspStructure
Returns the number of residues in the sequence.
getSequence()
- Method in class dasp.model.
DaspStructure
Return the amino acid sequence for this PDB file.
getSequence(boolean)
- Method in class dasp.model.
Fragment
getSequences()
- Method in class dasp.model.
Alignment
Return all of the sequences as FASTA-formatted strings
getSignature(int)
- Method in class dasp.model.
ActiveSiteSignature
getX()
- Method in class dasp.model.
Location
getY()
- Method in class dasp.model.
Location
getZ()
- Method in class dasp.model.
Location
H
hasMoreResidues()
- Method in class dasp.model.
DaspStructure
Tests to see if there is at least one more Residue object in the sequence
L
Location
- Class in
dasp.model
Location(double, double, double)
- Constructor for class dasp.model.
Location
M
main(String[])
- Static method in class dasp.
Dasp
main(String[])
- Static method in class dasp.model.
ActiveSiteSignature
makeUpper(String)
- Method in class dasp.model.
Fragment
method
- Variable in class dasp.model.
Alignment
N
nameMap
- Variable in class dasp.model.
Alignment
nextResidue()
- Method in class dasp.model.
DaspStructure
Enumerates through sequence of residues and returns the next Residue object.
O
optArg
- Variable in class dasp.
GetOpt
optInd
- Variable in class dasp.
GetOpt
P
PSSM
- Class in
dasp.model
PSSM()
- Constructor for class dasp.model.
PSSM
R
resetEnum()
- Method in class dasp.model.
DaspStructure
Resets the enumerator variable to -1
Residue
- Class in
dasp.model
Residue(AminoAcid)
- Constructor for class dasp.model.
Residue
S
seqs
- Variable in class dasp.model.
Alignment
sortN2C(List<Fragment>)
- Static method in class dasp.model.
Fragment
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