From a3dad48b74c25a965e0aeac772cd22a4ee4a0e23 Mon Sep 17 00:00:00 2001 From: "n.hoffmann" Date: Wed, 29 Feb 2012 16:38:46 +0000 Subject: [PATCH] added name parser documentation to help content --- .gitattributes | 19 ++--- .../html/concepts/maintopic.html | 13 ---- .../html/concepts/subtopic.html | 13 ---- .../html/concepts/subtopic2.html | 13 ---- .../html/nameparser/authorship_part.html | 26 +++++++ .../html/nameparser/name_part.html | 69 +++++++++++++++++++ .../nameparser/nomenclatural_status_part.html | 20 ++++++ .../html/nameparser/overview.html | 51 ++++++++++++++ .../html/nameparser/reference_part.html | 50 ++++++++++++++ .../html/reference/maintopic.html | 13 ---- .../html/reference/subtopic.html | 13 ---- .../html/reference/subtopic2.html | 13 ---- .../html/samples/maintopic.html | 13 ---- .../html/samples/subtopic.html | 13 ---- .../html/samples/subtopic2.html | 13 ---- .../html/tasks/maintopic.html | 13 ---- .../html/tasks/subtopic.html | 13 ---- .../html/tasks/subtopic2.html | 13 ---- eu.etaxonomy.taxeditor.help/html/toc.html | 13 ---- eu.etaxonomy.taxeditor.help/plugin.xml | 7 +- eu.etaxonomy.taxeditor.help/toc.xml | 5 +- eu.etaxonomy.taxeditor.help/tocnameparser.xml | 12 ++++ 22 files changed, 244 insertions(+), 184 deletions(-) delete mode 100644 eu.etaxonomy.taxeditor.help/html/concepts/maintopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/concepts/subtopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/concepts/subtopic2.html create mode 100644 eu.etaxonomy.taxeditor.help/html/nameparser/authorship_part.html create mode 100644 eu.etaxonomy.taxeditor.help/html/nameparser/name_part.html create mode 100644 eu.etaxonomy.taxeditor.help/html/nameparser/nomenclatural_status_part.html create mode 100644 eu.etaxonomy.taxeditor.help/html/nameparser/overview.html create mode 100644 eu.etaxonomy.taxeditor.help/html/nameparser/reference_part.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/reference/maintopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/reference/subtopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/reference/subtopic2.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/samples/maintopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/samples/subtopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/samples/subtopic2.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/tasks/maintopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/tasks/subtopic.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/tasks/subtopic2.html delete mode 100644 eu.etaxonomy.taxeditor.help/html/toc.html create mode 100644 eu.etaxonomy.taxeditor.help/tocnameparser.xml diff --git a/.gitattributes b/.gitattributes index 64368233e..e1e8195c4 100644 --- a/.gitattributes +++ b/.gitattributes @@ -513,9 +513,6 @@ eu.etaxonomy.taxeditor.help/.classpath -text eu.etaxonomy.taxeditor.help/.project -text eu.etaxonomy.taxeditor.help/META-INF/MANIFEST.MF -text eu.etaxonomy.taxeditor.help/build.properties -text -eu.etaxonomy.taxeditor.help/html/concepts/maintopic.html -text -eu.etaxonomy.taxeditor.help/html/concepts/subtopic.html -text -eu.etaxonomy.taxeditor.help/html/concepts/subtopic2.html -text eu.etaxonomy.taxeditor.help/html/gettingstarted/a_succesful_parsed_taxon_record.html -text eu.etaxonomy.taxeditor.help/html/gettingstarted/about_bulk_editing.html -text eu.etaxonomy.taxeditor.help/html/gettingstarted/about_the_manual.html -text @@ -778,22 +775,18 @@ eu.etaxonomy.taxeditor.help/html/img/cybergate.jpg -text eu.etaxonomy.taxeditor.help/html/img/fileicon.jpg -text eu.etaxonomy.taxeditor.help/html/img/orangewarning.jpg -text eu.etaxonomy.taxeditor.help/html/img/redwarning.jpg -text -eu.etaxonomy.taxeditor.help/html/reference/maintopic.html -text -eu.etaxonomy.taxeditor.help/html/reference/subtopic.html -text -eu.etaxonomy.taxeditor.help/html/reference/subtopic2.html -text -eu.etaxonomy.taxeditor.help/html/samples/maintopic.html -text -eu.etaxonomy.taxeditor.help/html/samples/subtopic.html -text -eu.etaxonomy.taxeditor.help/html/samples/subtopic2.html -text -eu.etaxonomy.taxeditor.help/html/tasks/maintopic.html -text -eu.etaxonomy.taxeditor.help/html/tasks/subtopic.html -text -eu.etaxonomy.taxeditor.help/html/tasks/subtopic2.html -text -eu.etaxonomy.taxeditor.help/html/toc.html -text +eu.etaxonomy.taxeditor.help/html/nameparser/authorship_part.html -text +eu.etaxonomy.taxeditor.help/html/nameparser/name_part.html -text +eu.etaxonomy.taxeditor.help/html/nameparser/nomenclatural_status_part.html -text +eu.etaxonomy.taxeditor.help/html/nameparser/overview.html -text +eu.etaxonomy.taxeditor.help/html/nameparser/reference_part.html -text eu.etaxonomy.taxeditor.help/original_document/Taxonomic_Editor_User_Manual_Version_4.doc -text eu.etaxonomy.taxeditor.help/plugin.xml -text eu.etaxonomy.taxeditor.help/pom.xml -text eu.etaxonomy.taxeditor.help/src/eu/etaxonomy/taxeditor/help/Activator.java -text eu.etaxonomy.taxeditor.help/toc.xml -text eu.etaxonomy.taxeditor.help/tocgettingstarted.xml -text +eu.etaxonomy.taxeditor.help/tocnameparser.xml -text eu.etaxonomy.taxeditor.navigation/.classpath -text eu.etaxonomy.taxeditor.navigation/.project -text eu.etaxonomy.taxeditor.navigation/META-INF/MANIFEST.MF -text diff --git a/eu.etaxonomy.taxeditor.help/html/concepts/maintopic.html b/eu.etaxonomy.taxeditor.help/html/concepts/maintopic.html deleted file mode 100644 index a476078ac..000000000 --- a/eu.etaxonomy.taxeditor.help/html/concepts/maintopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Main Topic - - - -

Main Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/concepts/subtopic.html b/eu.etaxonomy.taxeditor.help/html/concepts/subtopic.html deleted file mode 100644 index 8a61c501d..000000000 --- a/eu.etaxonomy.taxeditor.help/html/concepts/subtopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic - - - -

Sub Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/concepts/subtopic2.html b/eu.etaxonomy.taxeditor.help/html/concepts/subtopic2.html deleted file mode 100644 index 86bcbf9cd..000000000 --- a/eu.etaxonomy.taxeditor.help/html/concepts/subtopic2.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic 2 - - - -

Sub Topic 2

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/nameparser/authorship_part.html b/eu.etaxonomy.taxeditor.help/html/nameparser/authorship_part.html new file mode 100644 index 000000000..f8a29d8f9 --- /dev/null +++ b/eu.etaxonomy.taxeditor.help/html/nameparser/authorship_part.html @@ -0,0 +1,26 @@ +

Authorship Part

+ +

The authorship part is divided into the original combination authorship and the combination authorship. +The earlier is put in brackets.

+ +
+Example (bot.): (L.) Mill. 
+Example (zoo.): (XXX, 1830) XXX, 1845
+
+ +

You can use either no authorship (only if not followed by any other part), the original combination +authorship, the combination authorship or both.

+ +

The parser differentiates botanical and zoological authorship. The later has a year following the +author, separated by a comma. Botanical names only have authors. +Authorship may include single persons and teams. Team members are separated by & . A placeholder al. +may be used for further team members. Both authorships may include ex-authors separated by ex or ex. +Some valid author strings are:

+
+Example (bot.): (Greuther & L'Hiver & al. ex Müller & Schmidt) Clark ex Ciardelli 
+Example (zoo.):
+
+ +

The number of allowed special characters like ' or - at the moment is beyond the scope of this +documentation and will change in the future.

+ diff --git a/eu.etaxonomy.taxeditor.help/html/nameparser/name_part.html b/eu.etaxonomy.taxeditor.help/html/nameparser/name_part.html new file mode 100644 index 000000000..4fc3b1dca --- /dev/null +++ b/eu.etaxonomy.taxeditor.help/html/nameparser/name_part.html @@ -0,0 +1,69 @@ +

Name Part

+ +

The name part recognizes uninomials, binomials and trinomials. The first epithet must start +with a capital letter; all other words (except for infrageneric epitheta) can only contain +lower-case letters. Only latin letters are allowed in names (except for ï). +The name part parser differentiates 6 different syntaxes.

+ +

Uninomials

+

One word starting with a capital letter. As the rank is usually ambiguous for uninomials, +the rank represents the parser's best guess and a warning is returned to check the rank.

+
Example: Cichorieae
+ + +

Infrageneric Names

+

Capital word followed by the infrageneric marker followed by the infrageneric epitheton. +Valid markers are: +

+

+
Example: Desmometopa subg. LitoXXX
+ + +

Species Aggregates

+

Species aggregates are recognized similarly to species except they are followed by a group +marker. Valid markers are: +

+

+
Example: XXX
+ + +

Species

+

Species names have a genus part (capital letter) and a species part (lower case letter).

+
Examples are: Abies alba
+ +

Infraspecific names

+

Infraspecific names have four parts: the genus part, the species part, the infraspecific +marker and the infraspecific part. All but the first may not start with a capital letter. +Recognized markers are: +

+ +

+
Example:
+ +

Infraspecific names (old markers)

+

Some older names (not valid according to the nomenclatural code) use other infraspecific +markers. The recognition of these older names is not yet implemented.

+ + diff --git a/eu.etaxonomy.taxeditor.help/html/nameparser/nomenclatural_status_part.html b/eu.etaxonomy.taxeditor.help/html/nameparser/nomenclatural_status_part.html new file mode 100644 index 000000000..e3c5fb10a --- /dev/null +++ b/eu.etaxonomy.taxeditor.help/html/nameparser/nomenclatural_status_part.html @@ -0,0 +1,20 @@ +

Nomenclatural Status

+ +

The nomeclatural status is separated from the preceding text by a comma. Current valid values for a status:

+ + + +

Multiple values separated by comma are possible.

\ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/nameparser/overview.html b/eu.etaxonomy.taxeditor.help/html/nameparser/overview.html new file mode 100644 index 000000000..ba52dd453 --- /dev/null +++ b/eu.etaxonomy.taxeditor.help/html/nameparser/overview.html @@ -0,0 +1,51 @@ +

Name Parser Documentation

+ + +

The taxonomic name parser analyzes a free text taxonomic reference for the following four components:

+ + + +

Not all of them are required.

+ +

The four parts are separated by the following separators:

+ + + + + + + + + + + + + + + + + + + + + + + + + + +
partseparatorexample
authorshipany whitespaceAbies alba_L.
referencecommata with following whitespace OR whitespace+'in'+whitespaceAbies alba L.,_Sp. Pl... or Pinus alba_in_Bull. Soc....
nom. statuscommata with following whitespacein Bull. Bot. 3: 99. 1987., nom illeg.
+ +

Some valid name texts fully recognized by the parser are:

+ +
+Abies alba (L.) Mill., Sp. Pl.: 105. 1846., nom illeg. 
+Abies alba (L.) Mill. in Bull. Bot. 3: 99. 1987., nom illeg.
+
+ +

The name part is required. The authorship part is required only if followed by the reference part. The reference part as well as the status part are not required. In the following sections, the four parts are described in detail:

\ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/nameparser/reference_part.html b/eu.etaxonomy.taxeditor.help/html/nameparser/reference_part.html new file mode 100644 index 000000000..bc9ac8c01 --- /dev/null +++ b/eu.etaxonomy.taxeditor.help/html/nameparser/reference_part.html @@ -0,0 +1,50 @@ +

Reference Part

+ +

The reference part follows the syntax: {separator}{authorship{,}}{titleEditionVolume}{:}{detail}{.}{year}

+ +

Zoological new combinations should not have a reference part, since in zoology, it is not common +to mention the new combination reference.

+ +

Separator

+ +

The separator between the reference part and the preceding authorship may be a comma , or +an 

 in
(surrounded by whitespaces). The comma indicates a book whereas the in stands either +for a journal article or a book section. If the in is not followed by a comma, the parser +interprets the reference as an article; otherwise, as a book section. Reference type parsing +should be improved in future.

+ +

Reference Authorship

+ +

An author is only available for book sections. Articles and book sections are differentiated +from each other by comparing the first four words that follow the separator. If these words +include a comma and the words before the comma are likely to represent an author, the reference +is recognized as a book section. Otherwise, it will be treated as an article. In both cases, +a warning is thrown that differentiation is not possible.

+ +

TitleEditionVolume

+ +

The TitleEditionVolume part includes the title itself as well as optional edition part +and volume parts. The title itself allows most character combinations but care must be taken +if a : is included as this is the separator for the subsequent detail part. Special characters +like & and - are only allowed if preceded and followed immediately by ordinary characters. +Ordinary brackets are allowed. Edition and volume are separated by whitespace if only one +of them exists. If both exist the later is separated by a comma. Both are optional, so all +four of the following formats are valid:

+ +
+Sp. Pl.
+Sp. Pl. ed. 3
+Sp. Pl. ed. 3, 4
+Sp. Pl. 4
+
+ +

As can be seen, the edition is recognized by a preceding ed., whereas the volume is just +a number (or a number followed by another number in brackets - e.g. 4(5) ).

+ +

The detail part is separated by a column : from the preceding titleEditonVolume part and +is separated from the year by . (botanical names only). A number of typical detail information +is recognized as either pure page numbers (345) or ranges (345-348). Page numbers may be +preceded by p.(e.g. p. 345) or pp.(e.g. pp. 345-348). Abbreviations indicating special parts of a +reference such as fig. or tab. are recognized as well. Roman numbers are not detected +at the moment.

+ diff --git a/eu.etaxonomy.taxeditor.help/html/reference/maintopic.html b/eu.etaxonomy.taxeditor.help/html/reference/maintopic.html deleted file mode 100644 index a476078ac..000000000 --- a/eu.etaxonomy.taxeditor.help/html/reference/maintopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Main Topic - - - -

Main Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/reference/subtopic.html b/eu.etaxonomy.taxeditor.help/html/reference/subtopic.html deleted file mode 100644 index 8a61c501d..000000000 --- a/eu.etaxonomy.taxeditor.help/html/reference/subtopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic - - - -

Sub Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/reference/subtopic2.html b/eu.etaxonomy.taxeditor.help/html/reference/subtopic2.html deleted file mode 100644 index 86bcbf9cd..000000000 --- a/eu.etaxonomy.taxeditor.help/html/reference/subtopic2.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic 2 - - - -

Sub Topic 2

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/samples/maintopic.html b/eu.etaxonomy.taxeditor.help/html/samples/maintopic.html deleted file mode 100644 index a476078ac..000000000 --- a/eu.etaxonomy.taxeditor.help/html/samples/maintopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Main Topic - - - -

Main Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/samples/subtopic.html b/eu.etaxonomy.taxeditor.help/html/samples/subtopic.html deleted file mode 100644 index 8a61c501d..000000000 --- a/eu.etaxonomy.taxeditor.help/html/samples/subtopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic - - - -

Sub Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/samples/subtopic2.html b/eu.etaxonomy.taxeditor.help/html/samples/subtopic2.html deleted file mode 100644 index 86bcbf9cd..000000000 --- a/eu.etaxonomy.taxeditor.help/html/samples/subtopic2.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic 2 - - - -

Sub Topic 2

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/tasks/maintopic.html b/eu.etaxonomy.taxeditor.help/html/tasks/maintopic.html deleted file mode 100644 index a476078ac..000000000 --- a/eu.etaxonomy.taxeditor.help/html/tasks/maintopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Main Topic - - - -

Main Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/tasks/subtopic.html b/eu.etaxonomy.taxeditor.help/html/tasks/subtopic.html deleted file mode 100644 index 8a61c501d..000000000 --- a/eu.etaxonomy.taxeditor.help/html/tasks/subtopic.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic - - - -

Sub Topic

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/tasks/subtopic2.html b/eu.etaxonomy.taxeditor.help/html/tasks/subtopic2.html deleted file mode 100644 index 86bcbf9cd..000000000 --- a/eu.etaxonomy.taxeditor.help/html/tasks/subtopic2.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Sub Topic 2 - - - -

Sub Topic 2

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/html/toc.html b/eu.etaxonomy.taxeditor.help/html/toc.html deleted file mode 100644 index 326f0a9ff..000000000 --- a/eu.etaxonomy.taxeditor.help/html/toc.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - Table of Contents - - - -

Table of Contents

-Please enter your text here. - - \ No newline at end of file diff --git a/eu.etaxonomy.taxeditor.help/plugin.xml b/eu.etaxonomy.taxeditor.help/plugin.xml index 027ed0fee..db9b794ef 100644 --- a/eu.etaxonomy.taxeditor.help/plugin.xml +++ b/eu.etaxonomy.taxeditor.help/plugin.xml @@ -9,7 +9,12 @@ primary="true"> + file="tocgettingstarted.xml" + primary="false"> + + diff --git a/eu.etaxonomy.taxeditor.help/toc.xml b/eu.etaxonomy.taxeditor.help/toc.xml index 011941785..92e4369ca 100644 --- a/eu.etaxonomy.taxeditor.help/toc.xml +++ b/eu.etaxonomy.taxeditor.help/toc.xml @@ -1,8 +1,11 @@ - + + + + diff --git a/eu.etaxonomy.taxeditor.help/tocnameparser.xml b/eu.etaxonomy.taxeditor.help/tocnameparser.xml new file mode 100644 index 000000000..b249a5a59 --- /dev/null +++ b/eu.etaxonomy.taxeditor.help/tocnameparser.xml @@ -0,0 +1,12 @@ + + + + + + + + + + + + -- 2.34.1