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 void
printScoresInLines(AFPChain afpChain, int blockNum, int optLength, double totalRmsdOpt, double alignScore, int alnLength, int gapLen, double identity, double similarity, java.lang.StringBuffer txt)
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
toPrettyAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showHTML, boolean showAlignmentBlock)
static 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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printScoresInLines
public static void printScoresInLines(AFPChain afpChain, int blockNum, int optLength, double totalRmsdOpt, double alignScore, int alnLength, int gapLen, double identity, double similarity, java.lang.StringBuffer txt)
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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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toPrettyAlignment
public static java.lang.String toPrettyAlignment(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showHTML, boolean showAlignmentBlock)
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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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