Package org.biojava.nbio.structure.align.model

Class 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 Description
      static java.lang.String newline  

    • Constructor Summary

      Constructors 
      Constructor Description
      AfpChainWriter()  

    • 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 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)