org.biojava.bio.structure.align.model
Class AfpChainWriter

java.lang.Object
  extended by org.biojava.bio.structure.align.model.AfpChainWriter

public class AfpChainWriter
extends Object

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

Author:
Andreas Prlic

Field Summary
static String newline
           
 
Constructor Summary
AfpChainWriter()
           
 
Method Summary
static String toAlignedPairs(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
          Prints the alignment in the simplest form: a list of aligned residues.
static String toCE(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
           
static String toDBSearchResult(AFPChain afpChain)
           
static String toFatCat(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
           
static String toFatCatCore(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean printLegend, boolean longHeader, boolean showHTML, boolean showAlignmentBlock)
          Output in FatCatCore format
static String toRotMat(AFPChain afpChain)
           
static String toScoresList(AFPChain afpChain)
           
static 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 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 String newline
Constructor Detail

AfpChainWriter

public AfpChainWriter()
Method Detail

toFatCat

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

toScoresList

public static String toScoresList(AFPChain afpChain)

toFatCatCore

public static 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:

toWebSiteDisplay

public static 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 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.

toAlignedPairs

public static 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: 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 String toDBSearchResult(AFPChain afpChain)

toRotMat

public static String toRotMat(AFPChain afpChain)

toCE

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