charite.christo.strap.extensions
Class AlignmentWriterHSSP

java.lang.Object
  charite.christo.strap.extensions.AlignmentWriterHSSP

All Implemented Interfaces:

AlignmentWriter

public class AlignmentWriterHSSP
extends java.lang.Object
implements AlignmentWriter

HELP Example

## PROTEINS : EMBL/SWISSPROT identifier and alignment statistics
NR.   ID    STRID %IDE %WSIM IFIR ILAS JFIR JLAS LALI NGAP LGAP LSEQ2 ACCNUM
1:cram_craab 1CRN 1.00  1.00   1   46    1   46   46    0    0   46  P01542
2:thn_pyrpu       0.53  0.59   2   46    2   47   45    1    1   47  P07504
3:thn_dencl       0.53  0.69   2   44    2   44   43    0    0   46  P01541
4:thn3_visal      0.49  0.66   2   46   28   72   45    0    0  111  P01538
5:thn_pholi       0.47  0.61   2   46    2   46   45    0    0   46  P01540
6:thnl_horvu      0.44  0.61   2   46   30   74   45    0    0  137  P09617
7:thnb_visal      0.44  0.61   2   46    8   52   45    0    0  103  P08943
8:thn6_horvu      0.40  0.57   2   46    2   46   45    0    0   46  P09618
Part 3) the aligned sequences. Residues 10-39 have been deleted to save space.
## ALIGNMENTS    1 -    8
 SeqNo  PDBNo AA STRUCTURE BP1 BP2  ACC NOCC  VAR  ....:....1....:....2....:
     1    1   T              0   0   77    2    0  T
     2    2   T  E     -A   34   0A  21    9   23  TSSSSSSS
     3    3   a  E     -A   33   0A   0    9    0  CCCCCCCC
     4    4   b        -     0   0    0    9    0  CCCCCCCC
     5    5   P  S    S+     0   0   52    9   28  PRPPPKPK
     6    6   S  S  > S-     0   0   48    9   35  SNTNSNND
     7    7   I  H  > S+     0   0  123    9   25  ITTTTTTT
     8    8   V  H  > S+     0   0   98    9   47  VWATTTTL
     9    9   A  H  > S+     0   0    6    9   15  AAAGAGGA
...
Part 4) the profile. The profile values for 16 residues have been
removed to save space.
## SEQUENCE PROFILE AND ENTROPY
 SeqNo PDBNo   V   L   N   D  NOCC NDEL NINS ENTROPY RELENT WEIGHT
    1    1     0   0   0   0     2    0    0   0.000      0  1.00
    2    2     0   0   0   0     9    0    0   0.530     24  1.00
    3    3     0   0   0   0     9    0    0   0.000      0  1.33
    4    4     0   0   0   0     9    0    0   0.000      0  1.33
    5    5     0   0   0   0     9    0    0   0.849     39  0.79
    6    6     0   0  44  11     9    0    0   1.215     55  0.75
    7    7     0   0   0   0     9    0    0   0.530     24  0.98
    8    8    22  11   0   0     9    0    0   1.427     65  0.47
    9    9     0   0   0   0     9    0    0   0.637     29  1.01
...

Field Summary

Fields inherited from interface charite.christo.strap.AlignmentWriter

CLUSTALW, CSS_BROWSER, EXTRA_SPACE, FASTA, FILE_SUFFIX, HTML, HTML_HEAD_BODY, MSF, NO_GAPS, NUCLEOTIDE_TRIPLET, PDB_RESIDUE_NUMBER, PROTEIN_ICONS, SECONDARY_STRUCTURE, UNDERLINE_ANNOTATIONS

Constructor Summary

AlignmentWriterHSSP()

Method Summary

java.lang.String	getFileExtension() A file name suffix like msf of fa or fasta or clustalW
void	getText(long options, BA sb) The alignment text is written into the StringBuffer.
void	setCharForGapAndTerminalBlanks(char m, char n, char c)
void	setColumnRange(int first, int last) The alignment column index starts at zero.
void	setNames(java.lang.String[] names) The names for the row headers.
void	setProteins(Protein... pp)
void	setResiduesPerLine(int resPerLine) Typically 50 to 70 residues are printed in one line.

Methods inherited from class java.lang.Object

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

Constructor Detail

AlignmentWriterHSSP

public AlignmentWriterHSSP()

Method Detail

setProteins

public void setProteins(Protein... pp)

Specified by:

setProteins in interface AlignmentWriter

setNames

public void setNames(java.lang.String[] names)

Description copied from interface: AlignmentWriter

The names for the row headers. Usually the protein names.

Specified by:

setNames in interface AlignmentWriter

setColumnRange

public void setColumnRange(int first,
                           int last)

Description copied from interface: AlignmentWriter

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.

Specified by:

setColumnRange in interface AlignmentWriter

See Also:

Protein.getResidueColumn()

setResiduesPerLine

public void setResiduesPerLine(int resPerLine)

Description copied from interface: AlignmentWriter

Typically 50 to 70 residues are printed in one line. If MAX_INT is given, each protein is printed in one line.

Specified by:

setResiduesPerLine in interface AlignmentWriter

setCharForGapAndTerminalBlanks

public void setCharForGapAndTerminalBlanks(char m,
                                           char n,
                                           char c)

Specified by:

setCharForGapAndTerminalBlanks in interface AlignmentWriter

getFileExtension

public java.lang.String getFileExtension()

Description copied from interface: AlignmentWriter

A file name suffix like msf of fa or fasta or clustalW

Specified by:

getFileExtension in interface AlignmentWriter

getText

public void getText(long options,
                    BA sb)

Description copied from interface: AlignmentWriter

The alignment text is written into the StringBuffer.

Specified by:

getText in interface AlignmentWriter