Documentation Update for Proteios SE 2.15.0.

[olle]

This ticket collects various changes in the Proteios SE documentation made for the release of Proteios SE 2.15.0. Some modifications in the documentation may address changes made prior to version 2.15.0, if the documentation has not been updated earlier.

[olle]

Ticket accepted.

[olle]

Cautionary Note:

• There is no guarantee that all changes in the documentation made for the release of Proteios SE 2.15.0 are collected here. The intention of the ticket is to make it easier to follow major additions and rewrites made for the release.

[olle]

(In ​[22]) Proteios SE manual wiki page ​Proteios SE server administration updated by addition of introductory section for configuration of Proteios SE access to external programs. Previous section "Search Engine configuration" renamed "Search Engine Configuration - General" and placed as subsection to the new section. The change was motivated by only part of the supported external programs being "search engines" in the strict sense.

[olle]

(In ​[23]) Proteios SE manual wiki page ​Proteios SE server administration updated by addition of new section on configuration of msInspect feature detection.

[olle]

(In ​[24]) Proteios SE manual wiki page ​Proteios SE server administration updated in section "Tomcat memory settings" by adding info for SuSE Linux 11 and Tomcat 6.

[olle]

(In ​[25]) Proteios SE manual wiki page ​Proteios SE server administration updated by addition of new section on configuration of OpenMS feature detection.

[olle]

(In ​[6]) Proteios SE manual wiki page ​Working With Files expanded and info on demo file upload updated.

[olle]

(In ​[41]) Proteios SE manual wiki page ​User Guide updated on running plug-ins and importing peaklist files.

[olle]

(In ​[42]) Proteios SE manual wiki page ​User Guide updated in section "Protein identification reports" regarding menu selections.

[olle]

(In ​[4]) Proteios SE manual wiki page ​Sitemap updated by added entry for LabelFree (Label-free quantitative analysis).

[olle]

(In ​[7]) Proteios SE manual wiki page ​Working With Files updated with page outline command at top.

[olle]

(In ​[4]) Proteios SE manual wiki page ​Working With Projects expanded and existing info updated.

[olle]

(In ​[43]) Proteios SE manual wiki page ​User Guide updated in section "Working with projects" regarding menu selections.

[olle]

(In ​[44]) Proteios SE manual wiki page ​User Guide updated in section "Working with projects" in text for active project.

[olle]

(In ​[4]) Proteios SE manual wiki page ​PRIDE 2.1 XML Export updated in section "How to Export Hits Data to PRIDE XML" regarding menu selections.

[olle]

(In ​[45]) Proteios SE manual wiki page ​User Guide updated in section "For Users" with new link for Hits Comparison Report.

[olle]

(In ​[5]) Proteios SE manual wiki page ​Sitemap updated by added entry for HitsComparisonReport (Hits Comparison Report).

[olle]

(In ​[6]) Proteios SE manual wiki page ​Sitemap updated by added entry for NonQuantitativeHitsComparisonReport (Non-Quantitative Hits Comparison Report).

[olle]

(In ​[7]) Proteios SE manual wiki page ​Sitemap updated by added entry for QuantitativeHitsComparisonReport (Quantitative Hits Comparison Report).

[olle]

(In ​[46]) Proteios SE manual wiki page ​User Guide updated in section "For Users" with new link for Feature Detection.

[olle]

(In ​[8]) Proteios SE manual wiki page ​Sitemap updated by added entry for FeatureDetection (Feature Detection).

[olle]

Ticket description updated with disclaimer that some modifications in the documentation may address changes made prior to version 2.15.0, if the documentation has not been updated earlier.

[olle]

(In [4165]) Refs #668. Refs #746. Class/file plugins/RunMsInspectPlugin.java in plugin/ updated in javadoc:

1. Public method void setInputFileSizeInBytes(long inputFileSizeInBytes) updated in javadoc by fix of typo.

[olle]

(In [4166]) Refs #744. Refs #746. Class/file plugins/RunOpenMsPlugin.java in plugin/ updated in javadoc:

1. Public method void setInputFileSizeInBytes(long inputFileSizeInBytes) updated in javadoc by fix of typo.

[olle]

(In [4167]) Refs #746. Classes/files in api/core/ updated in javadoc by removal of obsolete links:

1. Class/file core/Protocol.java in api/core/ updated in javadoc for public method boolean isUsed() by removal of obsolete link.

2. Class/file core/ProtocolType.java in api/core/ updated in javadoc for public method boolean isUsed() by removal of obsolete link.

3. Class/file core/data/MappingCoordinate.java in api/core/ updated in javadoc for class by removal of obsolete link.

[olle]

Ticket closed as the documentation wiki has been updated.