'STRAP:multiple sequence alignments '

charite.christo.interfaces
Interface ProteinWriter

All Known Implementing Classes:
ProteinWriter1

public interface ProteinWriter

A ProteinWriter is used to export a protein to a text file using a certain format such as pdb or fasta.


Field Summary
static long ATOM_LINES
           
static long COMPLETE_PDB
           
static long FASTA
           
static long HELIX_SHEET
           
static long HETEROS
           
static long MET_INSTEAD_OF_MSE
           
static long NUCLEOTIDE_STRUCTURE
           
static long NUCLEOTIDES
           
static long PDB
           
static long SEQRES
           
static long SEQRES_IF_COORDINATES
           
static long SIDE_CHAIN_ATOMS
           
 
Method Summary
 String getFileSuffix()
          Extension ".pdb" forPDB-files and ".fa" for fasta-files
 void selectResidues(boolean[] isSelected)
          do not write all residues but only a certain subset.
 void setResidueRange(int indexOfFirstAmino, int indexOfLastPlus1)
          index of first and last amino acid
 boolean toText(Protein p, Matrix3D[] m3d, long mode, ByteArray sb)
          Gets the text representation of the protein e.g.
 

Field Detail

PDB

static final long PDB
See Also:
Constant Field Values

FASTA

static final long FASTA
See Also:
Constant Field Values

ATOM_LINES

static final long ATOM_LINES
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Constant Field Values

SIDE_CHAIN_ATOMS

static final long SIDE_CHAIN_ATOMS
See Also:
Constant Field Values

SEQRES

static final long SEQRES
See Also:
Constant Field Values

SEQRES_IF_COORDINATES

static final long SEQRES_IF_COORDINATES
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HETEROS

static final long HETEROS
See Also:
Constant Field Values

NUCLEOTIDE_STRUCTURE

static final long NUCLEOTIDE_STRUCTURE
See Also:
Constant Field Values

NUCLEOTIDES

static final long NUCLEOTIDES
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HELIX_SHEET

static final long HELIX_SHEET
See Also:
Constant Field Values

MET_INSTEAD_OF_MSE

static final long MET_INSTEAD_OF_MSE
See Also:
Constant Field Values

COMPLETE_PDB

static final long COMPLETE_PDB
See Also:
Constant Field Values
Method Detail

toText

boolean toText(Protein p,
               Matrix3D[] m3d,
               long mode,
               ByteArray sb)
Gets the text representation of the protein e.g. in fasta or PDB format and appends it to the StringBuffer.

Returns:
true: was able to produce the text, false: unable to produce the text because information is not set in the protein model. A ProteinWriter for protein structures returns false if the coordinate fields in the Protein instance are empty.

getFileSuffix

String getFileSuffix()
Extension ".pdb" forPDB-files and ".fa" for fasta-files


setResidueRange

void setResidueRange(int indexOfFirstAmino,
                     int indexOfLastPlus1)
index of first and last amino acid


selectResidues

void selectResidues(boolean[] isSelected)
do not write all residues but only a certain subset.


'STRAP:multiple sequence alignments '

'The most important classes are StrapAlign, StrapProtein and StrapEvent.'