org.biojava.bio.structure.align.util
Class AFPAlignmentDisplay

java.lang.Object
  extended by org.biojava.bio.structure.align.util.AFPAlignmentDisplay

public class AFPAlignmentDisplay
extends Object


Constructor Summary
AFPAlignmentDisplay()
           
 
Method Summary
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:

Expects the following properties to be previously computed:

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 Exception
Throws:
Exception

getBlockNrForAlignPos

public static int getBlockNrForAlignPos(AFPChain afpChain,
                                        int aligPos)
get the block number for an aligned position

Parameters:
afpChain -
aligPos -
Returns: