Support for comparison of technical replicates

[Fredrik Levander]

The hits comparison reports should be extended to support comparison of individual technical replicates. There should be an option to select whether technical replicates should be treated separately or as one when comparing samples using the Hits Comparison Reports (quantitative and qualitative). The replicate functionality was introduced in #772.

[olle]

Ticket assigned to olle.

[olle]

Ticket accepted.

[olle]

Traceability note:

• Comparison of Hits reports was introduced in Ticket #535 (Comparison of Hits reports), and was updated in Ticket #639 (Enhancement of protein list comparisons).
• GUI layout of Hits Comparison Report was updated in Ticket #730 (HitComparisonReport labels and fieldset titles need rephrasing).
• Comparison of Hits reports was updated in Ticket #737 (Hits Comparison should have Option to Include Peptide Modifications).
• Quantitative hits comparison was introduced in Ticket #736 (quantitative comparison report).
• Quantitative hits comparison was updated to work better when data sets are large in Ticket #790 (Quantitative hits comparison optimisation).
• Technical replicates were introduced in Ticket #772 (Replicate distinction), where non-gel hits import was updated to support import of a replicate ID in the hits table from annotation "replicate" for the mass spectrum file.
• Import of a replicate ID by parsing the mass spectrum filename was introduced in Ticket #802 (Hits import for replicates).

[olle]

Design update:

General:

• Step 1 of the hits comparison form should be updated with a check box to indicate if technical replicates should be treated separately. Default value should be false (check box unchecked).
• If technical replicates should not be treated separately, hits comparison should be performed as usual.

When technical replicates should be treated separately:

• Step 2 of the hits comparison form should for each hit selection include a multi-selection box for selecting what replicate ID values to use. The multi-selection boxes should contain available replicate ID values for the respective hit selection projects. Missing replicate ID values, i.e. null values, should also be supported, if present, and indicated in the multi-selection box as option with name "(no replicate ID)".
• Only hits with selected replicate ID values should be used for the comparison.
• Quantitative hits comparison should be updated to report values for each replicate ID of a local sample ID. A replicate for a local sample ID will be indicated by concatenating the local sample ID and the replicate ID separated by a colon ":", e.g. replicate "02" of local sample ID "Sample_A" in hit selection 1 will be denoted "HS1:Sample_A:02".
• Combinations of the selected local sample ID and replicate ID values that do not exist will be ignored, e.g. if local sample ID values [Sample_A, Sample_B] and replicate ID values [01, 02, 03] are selected, but Sample_B only has replicates 01 and 02, no entry will be made for Sample_B:03.

[olle]

(In [4462]) Refs #792. First version of support for comparison of technical replicates. This version should be considered as experimental, until tested thoroughly.

1. XML file conf/common-queries.xml in api/core/ updated with two new pre-defined queries, "GET_UNIQUE_REPLICATEIDS_IN_HITS_FOR_PROJECT" and "GET_UNIQUE_PEPTIDE_SEQUENCES_IN_HITS_FOR_PROJECT"".

2. Class/file core/Hit.java in api/core/ updated with two new public static methods, List<String> getUniqueReplicateIds(Project project, DbControl dc) and List<String> getUniqueReplicateIdsForLocalSampleId(Project project, String localSampleId, DbControl dc).

3. Class/file gui/form/HitComparisonStep1Form.java in client/servlet/ updated with check box for selecting replicate-wise comparison. The check box state is coupled to valid parameter VBoolean HitsComparisonReport.VREPLICATEWISECOMPARISONREPORT.

4. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated with new valid parameters and transfer of value of VBoolean VREPLICATEWISECOMPARISONREPORT from HitComparisonStep1Form to HitComparisonForm.

5. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated to add multi-selection boxes for replicate id values, if replicate-wise comparison id used.

6. Class/file action/hit/CreateHitsComparisonReportJob.java in client/servlet/ updated to obtain selected replicate id values and find existing combinations of selected local sample id and replicate id values in the hits table, and transfer the found pairs to the created job via job parameters.

7. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated to allow filtering of hits for selected replicate id values, when replicate-wise comparison is used.

8. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated to allow filtering of hits for selected replicate id values, when replicate-wise comparison is used. In addition, for replicate-wise comparison values are reported for each existing pair of selected local sample id and replicate id values in the hits table.

9. English dictionary file locale/en/dictionary in client/servlet/ updated with new entries for various string keys.

[olle]

Ticket closed as the requested functionality has been added.