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'STRAP:multiple sequence alignments ' | ||||||||
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SUMMARY: NESTED | FIELD | CONSTR | METHOD | DETAIL: FIELD | CONSTR | METHOD |
public interface AlignmentWriter
Field Summary | |
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static long |
CLUSTALW
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static long |
CSS_BROWSER
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static long |
EXTRA_SPACE
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static long |
FASTA
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static long |
FILE_SUFFIX
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static long |
HTML
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static long |
HTML_HEAD_BODY
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static long |
MSF
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static long |
NO_GAPS
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static long |
NUCLEOTIDE_TRIPLET
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static long |
PDB_RESIDUE_NUMBER
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static long |
PROTEIN_ICONS
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static long |
SECONDARY_STRUCTURE
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static long |
SEQUENCE_FEATURES
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static long |
UNDERLINE_ANNOTATIONS
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Method Summary | |
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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)
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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)
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void |
setResiduesPerLine(int resPerLine)
Typically 50 to 70 residues are printed in one line. |
Field Detail |
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static final long HTML
static final long MSF
static final long CLUSTALW
static final long FASTA
static final long FILE_SUFFIX
static final long EXTRA_SPACE
static final long NUCLEOTIDE_TRIPLET
static final long NO_GAPS
static final long PDB_RESIDUE_NUMBER
static final long UNDERLINE_ANNOTATIONS
static final long SECONDARY_STRUCTURE
static final long CSS_BROWSER
static final long HTML_HEAD_BODY
static final long SEQUENCE_FEATURES
static final long PROTEIN_ICONS
Method Detail |
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void setProteins(StrapProtein... proteins)
void setColumnRange(int firstColumn, int LastColumn)
StrapProtein.getResidueColumn()
void setResiduesPerLine(int resPerLine)
void getText(long mode, StringBuffer sb)
void setNames(String[] names)
void setCharForGapAndTerminalBlanks(char gap, char left, char right)
String getFileExtension()
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