Class AfpChainWriter
- java.lang.Object
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- org.biojava.nbio.structure.align.model.AfpChainWriter
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public class AfpChainWriter extends java.lang.Object
A class to convert the data in an AfpChain object to various String outputs.- Author:
- Andreas Prlic
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Field Summary
Fields Modifier and Type Field Description static java.lang.String
newline
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Constructor Summary
Constructors Constructor Description AfpChainWriter()
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static java.lang.String
toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Prints the alignment in the simplest form: a list of aligned residues.static java.lang.String
toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static java.lang.String
toDBSearchResult(AFPChain afpChain)
static java.lang.String
toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static java.lang.String
toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock)
Output in FatCatCore formatstatic java.lang.String
toRotMat(AFPChain afpChain)
static java.lang.String
toScoresList(AFPChain afpChain)
static java.lang.String
toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.static java.lang.String
toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showAlignmentBlock)
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.
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Method Detail
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toScoresList
public static java.lang.String toScoresList(AFPChain afpChain)
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toFatCatCore
public static java.lang.String toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock)
Output in FatCatCore formatNote that if a circular permutation has occured the residue numbers may be innaccurate.
- Parameters:
afpChain
-ca1
-ca2
-printLegend
-longHeader
-showHTML
-showAlignmentBlock
-- Returns:
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toWebSiteDisplay
public static java.lang.String toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.- Parameters:
afpChain
-ca1
-ca2
-- Returns:
- a String representation as it is used on the RCSB PDB web site for display.
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toWebSiteDisplay
public static java.lang.String toWebSiteDisplay(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showAlignmentBlock)
Prints the afpChain as a nicely formatted alignment, including alignment statistics, the aligned sequences themselves, and information about the superposition.- Parameters:
afpChain
-ca1
-ca2
-- Returns:
- a String representation as it is used on the RCSB PDB web site for display.
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toAlignedPairs
public static java.lang.String toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
Prints the alignment in the simplest form: a list of aligned residues. Format is one line per residue pair, tab delimited:- 1. PDB number. Includes insertion code
- 1. Chain.
- 1. Amino Acid. Three letter code.
- 2. PDB number.
- 2. Chain.
- 2. Amino Acid.
152 A ALA 161S A VAL
Note that this format loses information about blocks.
- Parameters:
afpChain
-ca1
-ca2
-- Returns:
- a String representation of the aligned pairs.
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toDBSearchResult
public static java.lang.String toDBSearchResult(AFPChain afpChain)
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toRotMat
public static java.lang.String toRotMat(AFPChain afpChain)
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