'STRAP:multiple sequence alignments '

charite.christo.strap.interfaces
Interface AlignmentWriter

All Known Implementing Classes:
AlignmentWriterHSSP, ExportAlignment

public interface AlignmentWriter


Field Summary
static long CLUSTALW
           
static long CSS_BROWSER
           
static long EXTRA_SPACE
           
static long FASTA
           
static long FILE_SUFFIX
           
static long HTML
           
static long HTML_HEAD_BODY
           
static long MSF
           
static long NO_GAPS
           
static long NUCLEOTIDE_TRIPLET
           
static long PDB_RESIDUE_NUMBER
           
static long PROTEIN_ICONS
           
static long SECONDARY_STRUCTURE
           
static long SEQUENCE_FEATURES
           
static long UNDERLINE_ANNOTATIONS
           
 
Method Summary
 String getFileExtension()
          A file name suffix like msf of fa or fasta or clustalW
 void getText(long mode, StringBuffer sb)
          The alignment text is written into the StringBuffer.
 void setCharForGapAndTerminalBlanks(char gap, char left, char right)
           
 void setColumnRange(int firstColumn, int LastColumn)
          The alignment column index starts at zero.
 void setNames(String[] names)
          The names for the row headers.
 void setProteins(StrapProtein... proteins)
           
 void setResiduesPerLine(int resPerLine)
          Typically 50 to 70 residues are printed in one line.
 

Field Detail

HTML

static final long HTML
See Also:
Constant Field Values

MSF

static final long MSF
See Also:
Constant Field Values

CLUSTALW

static final long CLUSTALW
See Also:
Constant Field Values

FASTA

static final long FASTA
See Also:
Constant Field Values

FILE_SUFFIX

static final long FILE_SUFFIX
See Also:
Constant Field Values

EXTRA_SPACE

static final long EXTRA_SPACE
See Also:
Constant Field Values

NUCLEOTIDE_TRIPLET

static final long NUCLEOTIDE_TRIPLET
See Also:
Constant Field Values

NO_GAPS

static final long NO_GAPS
See Also:
Constant Field Values

PDB_RESIDUE_NUMBER

static final long PDB_RESIDUE_NUMBER
See Also:
Constant Field Values

UNDERLINE_ANNOTATIONS

static final long UNDERLINE_ANNOTATIONS
See Also:
Constant Field Values

SECONDARY_STRUCTURE

static final long SECONDARY_STRUCTURE
See Also:
Constant Field Values

CSS_BROWSER

static final long CSS_BROWSER
See Also:
Constant Field Values

HTML_HEAD_BODY

static final long HTML_HEAD_BODY
See Also:
Constant Field Values

SEQUENCE_FEATURES

static final long SEQUENCE_FEATURES
See Also:
Constant Field Values

PROTEIN_ICONS

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

setProteins

void setProteins(StrapProtein... proteins)

setColumnRange

void setColumnRange(int firstColumn,
                    int LastColumn)
The alignment column index starts at zero. Note in STRAP only those columns are displayed where at least one protein has a residue. Common gaps are suppressed in the display.

See Also:
StrapProtein.getResidueColumn()

setResiduesPerLine

void setResiduesPerLine(int resPerLine)
Typically 50 to 70 residues are printed in one line. If MAX_INT is given, each protein is printed in one line.


getText

void getText(long mode,
             StringBuffer sb)
The alignment text is written into the StringBuffer.


setNames

void setNames(String[] names)
The names for the row headers. Usually the protein names.


setCharForGapAndTerminalBlanks

void setCharForGapAndTerminalBlanks(char gap,
                                    char left,
                                    char right)

getFileExtension

String getFileExtension()
A file name suffix like msf of fa or fasta or clustalW


'STRAP:multiple sequence alignments '

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