org.biojava.nbio.structure.align.util

Class AFPAlignmentDisplay

java.lang.Object

org.biojava.nbio.structure.align.util.AFPAlignmentDisplay

public class AFPAlignmentDisplay
extends Object

Constructor Summary

Constructors

Constructor and Description
AFPAlignmentDisplay()

Method Summary

Methods

Modifier and Type	Method and Description
static int	aaScore(char a, char b)
static Map<String,Double>	calcIdSimilarity(char[] seq1, char[] seq2, int alnLength)
static Structure	createArtificalStructure(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static void	getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2) Extract the alignment output
static void	getAlign(AFPChain afpChain, Atom[] ca1, Atom[] ca2, boolean showSeq) Sets the following properties: The alignment strings alnseq1, alnseq2, and alnsymb alnbeg1 and 2 alnLength and gapLen
static Atom[]	getAlignedAtoms1(AFPChain afpChain, Atom[] ca1)
static Atom[]	getAlignedAtoms2(AFPChain afpChain, Atom[] ca2)
static int	getBlockNrForAlignPos(AFPChain afpChain, int aligPos) get the block number for an aligned position
static Matrix	getRotMax(AFPChain afpChain, Atom[] ca1, Atom[] ca2)
static Atom	getTranslation(AFPChain afpChain, Atom[] ca1, Atom[] ca2)

Methods inherited from class java.lang.Object

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

Constructor Detail

AFPAlignmentDisplay

public AFPAlignmentDisplay()

Method Detail

getRotMax

public static Matrix getRotMax(AFPChain afpChain,
               Atom[] ca1,
               Atom[] ca2)
                        throws StructureException

Throws:

StructureException

getTranslation

public static Atom getTranslation(AFPChain afpChain,
                  Atom[] ca1,
                  Atom[] ca2)
                           throws StructureException

Throws:

StructureException

getAlignedAtoms1

public static Atom[] getAlignedAtoms1(AFPChain afpChain,
                      Atom[] ca1)

getAlignedAtoms2

public static Atom[] getAlignedAtoms2(AFPChain afpChain,
                      Atom[] ca2)

getAlign

public static void getAlign(AFPChain afpChain,
            Atom[] ca1,
            Atom[] ca2)

Extract the alignment output

eg

 STWNTWACTWHLKQP--WSTILILA
 111111111111     22222222
 SQNNTYACSWKLKSWNNNSTILILG
 

Those position pairs labeled by 1 and 2 are equivalent positions, belongs to two blocks 1 and 2. The residues between labeled residues are non-equivalent, with '-' filling in their resulting gaps.

The three lines can be accessed using AFPChain.getAlnseq1(), AFPChain.getAlnsymb(), and AFPChain.getAlnseq2().

getAlign

public static void getAlign(AFPChain afpChain,
            Atom[] ca1,
            Atom[] ca2,
            boolean showSeq)

Sets the following properties:

• The alignment strings alnseq1, alnseq2, and alnsymb
• alnbeg1 and 2
• alnLength and gapLen

Expects the following properties to be previously computed:

• AFPChain.getOptAln() and lengths

Known Bugs

Expects the alignment to have linear topology. May give odd results for circular permutations and other complicated topologies.

Parameters:

afpChain - Alignment between ca1 and ca2

ca1 - CA atoms of the first protein

ca2 - CA atoms of the second protein

showSeq - Use symbols reflecting sequence similarity: '|' for identical, ':' for similar, '.' for dissimilar. Otherwise, use the block number to show aligned residues.

aaScore

public static int aaScore(char a,
          char b)

calcIdSimilarity

public static Map<String,Double> calcIdSimilarity(char[] seq1,
                                  char[] seq2,
                                  int alnLength)

createArtificalStructure

public static Structure createArtificalStructure(AFPChain afpChain,
                                 Atom[] ca1,
                                 Atom[] ca2)
                                          throws ClassNotFoundException,
                                                 NoSuchMethodException,
                                                 InvocationTargetException,
                                                 IllegalAccessException

Parameters:

afpChain -

ca1 -

ca2 -

Returns:

Throws:

ClassNotFoundException - If an error occurs when invoking jmol

NoSuchMethodException - If an error occurs when invoking jmol

InvocationTargetException - If an error occurs when invoking jmol

IllegalAccessException - If an error occurs when invoking jmol

getBlockNrForAlignPos

public static int getBlockNrForAlignPos(AFPChain afpChain,
                        int aligPos)

get the block number for an aligned position

Parameters:

afpChain -

aligPos -

Returns: