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'STRAP:multiple sequence alignments ' | ||||||||
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java.lang.Object charite.christo.strap.ExportAlignment
public class ExportAlignment
HELP
Field Summary |
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Fields inherited from interface charite.christo.strap.AlignmentWriter |
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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 | |
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ExportAlignment()
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Method Summary | |
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static BA |
colorMark(ResidueSelection s,
BA sb)
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int |
compare(java.lang.Object o1,
java.lang.Object o2)
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java.lang.String |
getFileExtension()
A file name suffix like msf of fa or fasta or clustalW |
java.lang.String[] |
getNames()
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Protein[] |
getProteins()
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void |
getText(long opts,
BA sb)
The alignment text is written into the StringBuffer. |
static void |
img(java.lang.String url,
BA sb)
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void |
setCharForGapAndTerminalBlanks(char gap,
char blankN,
char blankC)
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void |
setColumnRange(int first,
int last)
The alignment column index starts at zero. |
ExportAlignment |
setIdentThreshold(int percent)
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void |
setNames(java.lang.String[] names)
The names for the row headers. |
void |
setProteins(Protein... pp)
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void |
setResiduesPerLine(int n)
Typically 50 to 70 residues are printed in one line. |
void |
setSecondaryStructure(int iP)
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Methods inherited from class java.lang.Object |
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equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait |
Methods inherited from interface java.util.Comparator |
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equals |
Constructor Detail |
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public ExportAlignment()
Method Detail |
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public Protein[] getProteins()
public java.lang.String[] getNames()
public void setProteins(Protein... pp)
setProteins
in interface AlignmentWriter
public void setNames(java.lang.String[] names)
AlignmentWriter
setNames
in interface AlignmentWriter
public void setColumnRange(int first, int last)
AlignmentWriter
setColumnRange
in interface AlignmentWriter
Protein.getResidueColumn()
public void setResiduesPerLine(int n)
AlignmentWriter
setResiduesPerLine
in interface AlignmentWriter
public void setCharForGapAndTerminalBlanks(char gap, char blankN, char blankC)
setCharForGapAndTerminalBlanks
in interface AlignmentWriter
public java.lang.String getFileExtension()
AlignmentWriter
getFileExtension
in interface AlignmentWriter
public ExportAlignment setIdentThreshold(int percent)
public void getText(long opts, BA sb)
AlignmentWriter
getText
in interface AlignmentWriter
public static BA colorMark(ResidueSelection s, BA sb)
public void setSecondaryStructure(int iP)
public static void img(java.lang.String url, BA sb)
public int compare(java.lang.Object o1, java.lang.Object o2)
compare
in interface java.util.Comparator
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