- Annote Cascading Style Sheet (CSS)
This file contains the style sheet to personalize the appearance of the HTML
notes generated by the cb2Bib. The cb2Bib distribution includes the
tex2html.css file as a CSS template.
- MathJax Header File
The mathematical notation in the text notes is displayed by jsMath. or its
successor MathJax. The
MathJax is a Java Script library. Its location and configuration must be
specified inside the HTML files in order to be known by the browser.
- Include CSS in HTML
Styles for the notes will be included, if checked, into the HTML file. In this
way, all the information, text and layout, is contained in one single file.
- Use relative links
If checked, linked local files will be set relative to the current HTML
- Annote Viewer Fonts
Selects default and monospaced fonts for the Annote viewer. Changes in the fonts
might need restarting the viewer unless using some of the latest QtWebKit
libraries. The viewer is disabled if the cb2Bib was not compiled and linked
against WebKit. Note also that fonts specified in the CSS prevail over this
- CiteID Pattern
Specifies the pattern for formatting cite's ID. Predefined placeholders are
available as a context menu, by right-clicking this edit line. Placeholders will
be substituted by the actual reference field values. See Predefined cite and document ID placeholders
- Author and Editor Name Format
Sets Authors and Editor names in abbreviated or full form, if the latter is
- Journal Name Format
Sets output journal names in abbreviated or full form. Note that this feature
only works if journal names are found in the
Journal Abbreviation List
- Number Separator
Sets number separator, e.g., ' - ' or ' -- '. Spaces count. It applies to
- Convert entry strings to LaTeX
If checked, cb2Bib converts special characters to LaTeX commands. Most BibTeX
import filters do not process LaTeX escaped characters. Therefore, keeping this
box unchecked can be appropriate when using cb2Bib as a temporary media to
transfer references to non BibTeX reference managers.
- Set 'title' in double braces
If checked, it writes extra braces in title. This will keep capitalization as is,
when processed by BibTeX.
- Postprocess 'month'
If checked, cb2Bib elaborates the 'month' string on a BibTeX fashion. E.g.,
'April 1' becomes '"1~" # apr'. No processing is done if the input string is not
written in English.
- Try Heuristic Guess if recognition fails
If checked, when automatic recognition fails, cb2Bib tries to catch some of the
fields of the reference through an heuristic set of rules. See Field Recognition Rules.
- Check Repeated On Save
If checked, cb2Bib looks for existing references in the BibTeX directory similar
to the one being saved. The search is based on exact cite ID match, or on
reference contents, by considering title and author field values, or, if empty,
booktitle and editor, and using the approximate string search pattern. If similar references are
found, the current reference is not saved, and the similar ones are displayed.
Pressing the save button one second time will proceed to actually saving the
current reference. Note that this feature is not applied in command line
mode, when using
cb2bib --txt2bib or
See also Additional, Keyboard
- External BibTeX Postprocessing
Use this box to select a BibTeX postprocessing external tool. The name of the
executable, the command arguments and the output file extension are required
fields. Arguments, any number, are passed to the executable. For the sake of
generality, it is required to specify the
%foutput placeholders. The first one is later substituted by the
current BibTeX filename. The second one is substituted by the current filename
with the specified output extension. Caution: Be careful if using the same
file extension for input and output, e.g., using
bib because you
want to use a beautifier or a sorting script. The cb2Bib has no control on
external disk modifications. Therefore, if the script failed, the input data
would possibly be lost. See also Additional, Keyboard Functionality.
- Replace/Remove from Input Stream
If checked, input stream is preprocessed by performing a customizable set of
string substitutions/removals. This option is mainly intended to remove image
alt tags. Although not visible,
alt tags reach the
clipboard when selecting and copying text. Author lists with email icons may
alt strings that would interfere with the author names
processing. In addition, this option is also appropriate to help translating
special characters to Unicode and LaTeX. Use it carefully, as to avoid unwanted
or unsuspected substitutions. See also Extracting data from the clipboard.
- External Clipboard Preparsing Command
Preparses input stream through an external, user-defined tool. Use the box bellow
to specify its name and path. cb2Bib executes the command
tmp_inputfile tmp_outputfile. You might consider a wrapper shell script to
fullfill this particular syntax requirement. Two examples,
ris2bib are provided. To test them, make sure the BibUtils Package is available
on your machine. Otherwise, modify these scripts according to your needs. See
also Additional, Keyboard
Functionality, Extracting data from
the clipboard, and the examples ISI Reference Format and RIS Reference Format.
- Perform always, as part of an automatic extraction
Performs preparsing each time the recognition engine is invoked. Caution:
cb2Bib, when not in disconnected mode, starts the recognition engine each time
the clipboard changes. Thus, it might send arbitrary data to the external parsing
tool. The tool might not be prepared to handle 'any data' and might fall
into a sort of 'infinite loop'. cb2Bib kills the external tool after a
reasonable waiting. But, if the tool is called through a wrapper script, killing
the script will not end the tool itself. Therefore, check this box only when
needed. If you write your own preparser, design it as to write no data to
output file whenever it can not process an input properly. When the preparser
produces no data, the cb2Bib sends instead the input stream to the recognition
engine. In this way, preparsing and normal cb2Bib functioning will work
- Do not show log
If unchecked, the external process messages, and the input and output streams are
shown in a log window. Showing output logs is useful for debugging purposes.
- Add document metadata to Input Stream
When checked, if the document linked to a reference contains relevant metadata,
then metadata will be added to the current clipboard contents. The metadata is
included at the time of adding the document to the current reference, e. g., when
dropping a file into the cb2Bib panel. If the document has BibTeX information,
the cb2Bib will automatically set the corresponding fields. If it has not, but
relevant bibliographic information is found, this data is only added to the
clipboard panel. To insert it in the edit lines, activate the Heuristic Guess
(Alt+G). The option Prepend or Append to the clipboard contents is
provided for conveniently writing regular expressions considering metadata
contents. File documents are linked to the references by the BibTeX tag 'file'.
See also Reading and writing
- Rename and Copy/Move document files to Directory
If selected, each file 'drag and dropped' onto the cb2Bib main window is renamed
DocumentID.pdf (or DocumentID.ps, DocumentID.dvi, etc.) and moved
to the storage directory. If unselected, the file URL is written to the
file BibTeX keyword, without any renaming or moving of the file. The
actual copy/move action is scheduled and performed once the reference is
accepted, e.g., once it is saved.
- Copy or Move document files
Choose whether copy or move Network Files dropped onto the cb2Bib main window.
See also Use External Network Client.
- Set directory relative to the BibTeX File Directory
If checked, the document file is copied/moved to the current BibTeX file
directory. If the Documents Directory box contains a relative directory it
will be added to the file name. For example, if it contains
articles, files will be copied to
/current_bibtex_path/articles/. An absolute path in the Documents
Directory box will be ignored in this context. Note that the file dialog returns
here relative file addresses. Consequently, only the necessary portion of the
full name, instead of the fullpath filename, is written to the BibTeX entry. File
retrieving from within the cb2Bib browser will be relative to the BibTeX file
Use this option if you plan to store in a same or a related directory the BibTeX
and document files. This option is appropriate for storing bibliographic
collections in removal devices. Likewise, when the cb2Bib is launched in USB
mode, by means of the command line switch '--conf', the alternate option is not
available. See Release
Note cb2Bib 0.8.4 and Export Selected Entries.
- Insert BibTeX metadata to document files
If checked, the cb2Bib will write bibliographic metadata to the linked document,
once the current reference is accepted and saved. See also Reading and writing bibliographic metadata.
- DocumentID Pattern
Specifies the pattern for formatting the document's filenames. Predefined
placeholders are available as a context menu, by right-clicking this edit line.
Placeholders will be substituted by the actual reference field values. See
Predefined cite and document ID
placeholders for descriptions.
- ExifTool Metadata writer
The cb2Bib uses ExifTool for writing bibliographic metadata to the attached
documents. Select here the ExifTool path name. On Windows, remember renaming
exiftool.exe for command line use.
See also Writing
- Journal Abbreviation List File
This file contains a list of journal names equivalences: a capital-letter
acronym, standard abbreviated form, and full name of the journal. If an input
journal name is recognized, cb2Bib will use the standard abbreviated form for the
journal bibkey. If your usual journal were not within the
abbreviations.txt, you could edit this file, or
point to a personalized abbreviation file. Note: Changes in the
abbreviation file only take place after reestarting cb2Bib.
- Regular Expression List File
The cb2Bib distribution includes the file
regexps.txt with a few set
of rules for reference extraction. This includes most of the scientific
literature. Extracting from email alerts or publisher abstract pages is a
volatile task. Information does not follow a standardized structure.
Extraction pattern may then change as often as the web design needs to. Besides,
such extraction from the clipboard is system dependent, in a way that produces
different formatting of the text copies on different systems. You can use your
regexps.txt file, for testing, debugging -regular
expressions are reloaded each time the automatic recognition engine executes-,
and fullfiling your particular extraction needs.
- Bookmarks and Network Query Info File
The cb2Bib distribution includes the file
netqinf.txt that contains
bookmarks data, and server related information for bibliographic querying. Note
that the cb2Bib treats bibliographic queries as generalized net bookmarks. This
allows accessing almost any online bibliographic resource. Check this file for
implementations details and customization.
- Browser Cascading Style Sheet (CSS)
This file contains the style sheet to configure the appearance of the
bibliographic references when viewed in browser mode. The cb2Bib distribution
file as a CSS examples.
- Part Of Speech (POS) Lexicon
This box must contain the address to the cb2Bib distribution file
lexicon.pos. This file contains a set of patterns and related POS
information required to Index Documents, i. e., to extract keywords from
documents for the c2bCiter module.
- Search In Files Cache Directory
Directory containing internal data for Search In Files functionality. If an
existing directory is selected the cb2Bib will write all internal data on it. If
otherwise, cache data will be written on the same directory from where BibTeX are
searched. It might be, therefore, convenient to group all this files in a
separate directory that does not need to be backup, and that can easily be
deleted whenever desired.
- Font Selector
Selects the main window and editor font family and size.
- Context Colors
Doubleclick on context color items to select syntax highlighter font color.
Besides syntax highlighting, and to ease manual bibliographic extractions, cb2Bib
has the following coloring convention. 'cb2Bib unrelevant text' colors non-word,
non-digit, and cb2Bib's internal tags. 'cb2Bib relevant text' refers to the
reference's year. 'cb2Bib highly relevant' attempts to guess text sectioning,
highlighting 'abstract', 'introduction', and 'keywords'.
- Use External Network Client
The cb2Bib manages local and network files in an equivalent manner. Network file
retrieving, however, requires sometimes password and/or cookies administration.
The KDE desktop incorporates
kfmclient utility. A command
kfmclient (copy|move|exec) source [destination] permits copying or
moving files, with
kfmclient taking care of advanced browsing
preferences. By checking this box, cb2Bib will use the specified file manger
- Use Proxy
If checked, the cb2Bib will access the network through a proxy host. Set the Host
name, the Port, and the proxy Type. A login dialog will appear if the proxy
requires authentication. Login data is not stored, it must be entered at each
- Perform Network Queries after automatic reference extractions
Network queries can be used to complete a partial reference extraction. For
instance, provided a reference 'J. Name, 25, 103' and an appropriate pattern to
extract it, cb2Bib will attempt to complete the reference automatically. No query
is performed if automatic reference extraction was tagged as BibTeX.
- Download document if available
If checked, cb2Bib downloads document files to the directory specified in
Rename and Copy/Move document files to Directory. See also the file
netqinf.txt for details. Download is scheduled and performed once
the reference is accepted, e.g., once it is saved. Note that when document file
is local, e.g., when PDFImport or switch
--doc2bib is used, no
document is downloaded.
- Keep Query temporary files (Debug Only)
cb2Bib may use up to three temporary files to perform a network query. If this
box is checked, the temporary files are not deleted. This facilitates the testing
and customization of the information file
- Customizes most key sequences for actions shortcuts. Concretely, cb2Bib
specific actions are configurable, but not standard actions such as 'Open',
'Exit', 'Copy', or 'Paste', which are already predefined to the standard,
specific key sequences for each platform. Shortcuts are customizable for the
cb2Bib main panel, editor, and reference list actions. Single-key shortcuts,
i.e., for manual reference extraction and shortcuts in c2bCiter, are
non-configurable, since they they closely map non-translatable BibTeX
- To plain text converter
Selects the external
some_format_to_text tool that cb2Bib uses to
convert document files prior to reference extraction and searching. cb2Bib
executes the line command
converter [options] inputfile
[options] are user defined arguments.
As a default, cb2Bib launches
pdf2cb, a modified PDF to text utility
found in the XPDF package. Modifications are available at xpdf/ directory in the
cb2Bib sources. Default arguments are
-q -f 1 -l 1 to extract only
the first, title page when used within PDFImport, and
-q, to convert
the complete document when used within Search in Files. Appropriate for PDFImport
could also be a document metadata extractor. Often metadata contains structured
information regarding document authors, title, and source. A simple shell script
wrapper could be the following
# Convert documents to text according to filename extension
# any2text_search input_fn.ext output_fn.txt
set ext = $1:e
if ( $ext == 'djvu' ) then
/usr/bin/djvutxt "$1" "$2"
if ($status) exit 1
else if ( $ext == 'chm' ) then
(/usr/local/bin/archmage -c text "$1" "$2") >& /dev/null
if ($status) exit 1
# If using pdf2cb
/path/to/pdf2cb -q "$1" "$2"
# If using pdftotex
# /usr/bin/pdftotext -enc UTF-8 "$1" "$2"
if ($status) exit 1