org.biojava.nbio.structure.align.model

Class AfpChainWriter

java.lang.Object

org.biojava.nbio.structure.align.model.AfpChainWriter

public class AfpChainWriter
extends java.lang.Object

A class to convert the data in an AfpChain object to various String outputs.

Author:

Andreas Prlic

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	newline

Constructor Summary

Constructors

Constructor and Description
AfpChainWriter()

Method Summary

Modifier and Type	Method and 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 format
static 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.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

newline

public static final java.lang.String newline

Constructor Detail

AfpChainWriter

public AfpChainWriter()

Method Detail

toFatCat

public static java.lang.String toFatCat(AFPChain afpChain,
                                        Atom[] ca1,
                                        Atom[] ca2)

toScoresList

public static java.lang.String toScoresList(AFPChain afpChain)

toFatCatCore

public static java.lang.String toFatCatCore(AFPChain afpChain,
                                            Atom[] ca1,
                                            Atom[] ca2,
                                            boolean printLegend,
                                            boolean longHeader,
                                            boolean showHTML,
                                            boolean showAlignmentBlock)

Output in FatCatCore format

Note that if a circular permutation has occured the residue numbers may be innaccurate.

Parameters:

afpChain -

ca1 -

ca2 -

printLegend -

longHeader -

showHTML -

showAlignmentBlock -

Returns:

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)

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.

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.

toPrettyAlignment

public static java.lang.String toPrettyAlignment(AFPChain afpChain,
                                                 Atom[] ca1,
                                                 Atom[] ca2,
                                                 boolean showHTML,
                                                 boolean showAlignmentBlock)

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.

example: 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.

toDBSearchResult

public static java.lang.String toDBSearchResult(AFPChain afpChain)

toRotMat

public static java.lang.String toRotMat(AFPChain afpChain)

toCE

public static java.lang.String toCE(AFPChain afpChain,
                                    Atom[] ca1,
                                    Atom[] ca2)