Opened 10 years ago

Closed 10 years ago

Last modified 9 years ago

#639 closed (fixed)

Enhancement of protein list comparisons

Reported by: Fredrik Levander Owned by: olle
Milestone: Proteios SE 2.11 Keywords:
Cc:

Description (last modified by Fredrik Levander)

The current hits comparison report (#535) will compare all hits found in the hits reports on protein or peptide level. However, often there are several proteins in a group, which in most cases should only be counted as one protein. When Proteios protein assembly (#484,#495) is performed, in each group of Proteios proteins there will be one leading protein which gets firstInCombination==null, while the other proteins will have firstInCombination pointing to the leading protein.

There should be a check box "only use leading proteins" on the protein level comparison, which should impose a filter, so that only hits with firstInCombination==null are queried for.

Change History (9)

comment:1 Changed 10 years ago by Fredrik Levander

Description: modified (diff)

comment:2 Changed 10 years ago by olle

Traceability note.

Summary of tickets referenced in the ticket description:

  • Ticket #535 (Comparison of Hits reports).
  • Ticket #484 (Generate protein report from peptide entries).
  • Ticket #495 (Isobaric label support).

comment:3 Changed 10 years ago by olle

Design info:

  • Class/file core/data/HitData.java in api/core/ has an instance variable HitData firstInCombination mapped to database column firstHitInCombination (note the difference in name).

comment:4 Changed 10 years ago by olle

(In [3529]) Refs #639. Refs #535. Refs #287. Hits comparison of protein lists updated with option to only use leading proteins when comparing proteins:

  1. Class/file action/hit/HitsComparisonReport.java in client/servlet/

updated with new public valid parameter VBoolean VONLYUSELEADINGPROTEINS.

  1. Class/file gui/form/FormFactory.java in client/servlet/ updated in

public method Form getHitsComparisonReportForm(Project project, Project project1, Project project2, String filenamePrefixDefault) by adding check-box coupled to valid parameter HitsComparisonReport.VONLYUSELEADINGPROTEINS.

  1. Class/file action/hit/CreateHitsComparisonReportJob.java in

client/servlet/ updated:

  1. Protected method void runMe() updated by obtaining value of

new valid VBoolean parameter HitsComparisonReport.VONLYUSELEADINGPROTEINS and setting it as values of new job parameter "onlyUseLeadingProteins".

  1. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated:
  2. Private inner class HitsComparisonData updated with new instance

variable boolean onlyUseLeadingProteins with public accessor methods. The default value is false.

  1. Public method

void run(Request request, Response response, ProgressReporter progress) updated to obtain value of new job parameter "onlyUseLeadingProteins" and transferring it to new instance of HitsComparisonData.

  1. Public method

void doExport(DbControl dc, HitsComparisonData hcd, File outCoreFile, ProgressReporter progress) updated by giving value of onlyUseLeadingProteins flag as argument when calling private method List<Hit> ofetchHitSelectionHitList(DbControl dc, Project theProject, ...). If the comparison is not of proteins, the value has first been reset to false.

  1. Private method

List<Hit> fetchHitSelectionHitList(DbControl dc, Project theProject, ...) updated with new argument Boolean onlyUseLeadingProteins, that is given as argument when calling private method private ItemQuery<Hit> createBasicHitQuery(Project theProject, ...).

  1. Private method

ItemQuery<Hit> createBasicHitQuery(Project theProject, ...) updated with new argument Boolean onlyUseLeadingProteins. If its value is true, the query is restricted to entries with property "firstInCombination" being equal to null.

  1. English dictionary file locale/en/dictionary in client/servlet/

updated with new string key.

comment:5 Changed 10 years ago by olle

(In [3530]) Refs #639. Refs #535. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated in java-doc for private method List<Hit> fetchHitSelectionHitList(DbControl dc, Project theProject, ...).

comment:6 Changed 10 years ago by olle

(In [3531]) Refs #639. Refs #535. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated in java-doc for private method ItemQuery<Hit> createBasicHitQuery(Project theProject, ...).

comment:7 Changed 10 years ago by Fredrik Levander

Resolution: fixed
Status: newclosed

comment:8 Changed 10 years ago by Fredrik Levander

(In [3771]) Refs #639. Also writing precursor quantity to report.

comment:9 Changed 9 years ago by olle

(In [4162]) Refs #639. Refs #535. Hits comparison updated to set MIME type of created output file in tab-separated format to "text/plain", in order to make it easier to inspect directly:

  1. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated in public method void doExport(DbControl dc, HitsComparisonData hcd, Directory outCoreDir, String filename, ProgressReporter progress) to set MIME type of created output file in tab-separated format to "text/plain", in order to make it easier to inspect directly.
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