charite.christo.strap
Class ExportAlignment

java.lang.Object
  charite.christo.strap.ExportAlignment

All Implemented Interfaces:

AlignmentWriter, java.util.Comparator

public class ExportAlignment
extends java.lang.Object
implements AlignmentWriter, java.util.Comparator

HELP

This alignment view has been generated with the sequence alignment program Strap. Send problems, HTML errors and suggestions to the author of Strap.
The HTML alignment output

• Sequence features like Glycosylation are underlined. They have a balloon message.
• Residue annotations are underlined.

User Interaction

• Proteins with an accession ID have a link to the protein file database.

Word Processors The alignment can be edited in text processors such as Word. Unfortunately copy and paste from the browser works only for IE. Therefore, the entire html file needs to be loaded into the text processor. Most text processors accept a web address instead of a file name in the file open dialog.

Supported text processors: MS-Word, kompozer (Macintosh), gwrite (Linux).
Not Supported: OpenOffice, Abiword, TextEdit.

Tips and Tricks

• Rectangular selections in MS-Word: This html output can be processed in MS-Word. In MS-Word it is relatively easy to cut out a section of the alignment by using the MS-Word feature of selecting columns in a Word text: Drag the mouse with the alt-key to select columns.
• Setting icon images of proteins: Search in Google for the desired image. Then drag the image from the browser to the protein in Strap (See Dragging Web links). They appear as protein icon in the alignment.

This alignment view has been generated with Strap LINK_TO_STRAP

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

ExportAlignment()

Method Summary

static BA	colorMark(ResidueSelection s, BA sb)
int	compare(java.lang.Object o1, java.lang.Object o2)
java.lang.String	getFileExtension() A file name suffix like msf of fa or fasta or clustalW
java.lang.String[]	getNames()
Protein[]	getProteins()
void	getText(long opts, BA sb) The alignment text is written into the StringBuffer.
static void	img(java.lang.String url, BA sb)
void	setCharForGapAndTerminalBlanks(char gap, char blankN, char blankC)
void	setColumnRange(int first, int last) The alignment column index starts at zero.
ExportAlignment	setIdentThreshold(int percent)
void	setNames(java.lang.String[] names) The names for the row headers.
void	setProteins(Protein... pp)
void	setResiduesPerLine(int n) Typically 50 to 70 residues are printed in one line.
void	setSecondaryStructure(int iP)

Methods inherited from class java.lang.Object

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

Methods inherited from interface java.util.Comparator

equals

Constructor Detail

ExportAlignment

public ExportAlignment()

Method Detail

getProteins

public Protein[] getProteins()

getNames

public java.lang.String[] getNames()

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 n)

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 gap,
                                           char blankN,
                                           char blankC)

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

setIdentThreshold

public ExportAlignment setIdentThreshold(int percent)

getText

public void getText(long opts,
                    BA sb)

Description copied from interface: AlignmentWriter

The alignment text is written into the StringBuffer.

Specified by:

getText in interface AlignmentWriter

colorMark

public static BA colorMark(ResidueSelection s,
                           BA sb)

setSecondaryStructure

public void setSecondaryStructure(int iP)

img

public static void img(java.lang.String url,
                       BA sb)

compare

public int compare(java.lang.Object o1,
                   java.lang.Object o2)

Specified by:

compare in interface java.util.Comparator