Opened 9 years ago

Closed 9 years ago

Last modified 7 years ago

#736 closed (fixed)

quantitative comparison report

Reported by: Fredrik Levander Owned by: olle
Milestone: Proteios SE 2.15.0 Keywords:
Cc:

Description

It should be possible to create a tab-separated table from the Hits report:

Peptide sequenceChargeSample1Sample2Sample3
ABCDEF21000020000N/A
ABCDEF3200350N/A
GHIJKL3120003000050000

The user selects any number of available local sample ids. Then keys (sequence + charge for peptides or external id for proteins), and what to write as quantities below each sample(precursorQuantity or totalIntensity).

Presumably the Protein comparison report could be extended with another writer to allow for this new functionality, since it already deals with redundancy problems.

Change History (32)

comment:1 Changed 9 years ago by olle

Status: newassigned

Ticket accepted.

comment:2 Changed 9 years ago by 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).
Last edited 9 years ago by olle (previous) (diff)

comment:3 Changed 9 years ago by olle

Design update:

  • Since many input selections for the quantitative report also appear for the existing hits comparison report, the first version of quantitative hits comparison report should be designed as a special type of hits comparison report, together with the previous choice of "Peptide" or "Protein" comparison type.
  • Two hits selections should be supported for the quantitative report, just as for the existing report.
  • The quantitative report table should contain the following columns:
    1. Peptide sequence.
    2. Charge.
    3. External ID.
    4. Columns with quantity values for local sample id values of hit selection 1.
    5. Columns with quantity values for local sample id values of hit selection 2.
    6. Ratio of mean values for hit selections.
    7. t-test p-values.

Discussion of report format:

If hit selection 1 contains local sample id "Sample1" and "Sample2", while hit selection 2 contains "Sample3" and "Sample4", a table row for sequence "ABCDEF" might look something like this (top header line with hit selections only shown for reference here, with hit selections 1 and 2 specified as "Group 1" and "Group 2", respectively):




Group 1Group 2

Peptide sequenceChargeExternal IDSample1Sample2Sample3Sample4Ratiot-test p-value
ABCDEF2IPI00169383.3101020200.5(specified later)

Note that what local sample id values belong to what hit selection is important for the statistics calculation, e.g. the ratio displayed is that of the mean values for the two selections. In the above example, ratio = ((10 + 10)/2)/((20 + 20)/2) = 10/20 = 0.5. However, if hit selection 1 contains local sample id "Sample1", while hit selection 2 contains "Sample2", "Sample3" and "Sample4", ratio = ((10/1)/((10 + 20 + 20)/3) = 10/16.667 = 0.6:




Group 1Group 2

Peptide sequenceChargeExternal IDSample1Sample2Sample3Sample4Ratiot-test p-value
ABCDEF2IPI00169383.3101020200.6(specified later)

It is therefore essential that the report specifies what local sample id values belong to each of the hit selections. In the current Hits Comparison Report this is done in the header section before the table itself. This should be kept for the quantitative hits comparison report, but whether the relationship should somehow be displayed in the table itself has not yet been decided.

Last edited 9 years ago by olle (previous) (diff)

comment:4 Changed 9 years ago by olle

Design update of GUI for Hit Comparison:

  • Current GUI for comparing hits is divided into two steps, where step 1 consists of selecting projects for hit selection 1 and 2 (the reason for the two-step process was that available options for the two projects could then be shown in step 2, when the two projects were known). The following additions/changes should be made for the two steps:

    1. Step 1 should be extended with selecting whether a quantitative comparison report should be created, as this affects options in step 2.
    2. Selection of whether comparison should be performed for peptides or proteins, currently made in step 2, should also be moved to step 1, as this information may be used to simplify the form in step 2, by only showing relevant options.
    3. Step 2 should be extended with a header section showing the comparison type settings selected in step 1 (non-quantitative/quantitative and peptide/protein).
    4. Step 2 should be updated to show options that are relevant for the chosen comparison type (non-quantitative/quantitative and peptide/protein).

  • The form for step 1 is currently managed by class ProjectComparisonForm, but as the changes above make this name inappropriate, this class should be replaced by one named HitComparisonStep1Form.

comment:5 Changed 9 years ago by olle

(In [4101]) Refs #736. Refs #535. Hits comparison updated to use a class with a more appropriate name than ProjectComparisonForm for the form of the first step when selecting comparison parameters, as more selections than projects are now made:

  1. Class/file action/hit/HitsComparisonReportStep1.java in client/servlet/ updated to use new form class HitComparisonStep1Form instead of previous ProjectComparisonForm.
  1. New class/file gui/form/HitComparisonStep1Form.java in client/servlet/ added. In its initial version, its functionality is a copy of previous file gui/form/ProjectComparisonForm.java in client/servlet/.

comment:6 Changed 9 years ago by olle

(In [4102]) Refs #736. Refs #535. Refs #287. Hits comparison report updated in GUI by placing general selections on first selection page, and display relevant options on second selection page, based on the initial selections. Option to select quantitative comparison report added, but no functionality for this alternative added:

  1. Class/file action/hit/HitsComparisonReportStep1.java in client/servlet/ updated in instruction text.
  1. Class/file gui/form/HitComparisonStep1Form.java in client/servlet/ updated by adding new initial fieldset for selecting general hits comparison settings.
  1. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated. New valid parameter VBoolean VQUANTITATIVECOMPARISONREPORT added. Protected method void runMe() updated to retrieve values of general hits comparison settings from valid parameters and transfer them to form class HitComparisonForm. Instruction text updated.
  1. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated by adding arguments Boolean quantitativeComparison and String comparisonType to constructor. GUI updated by addition of new initial fieldset reporting values of general hits comparison settings, and only displaying relevant options, based on the initial selections.
  1. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

comment:7 Changed 9 years ago by olle

Design update:

  • GUI layout for selection step 2 should be updated to place comparison type specific selections directly after display of general settings, where the comparison type is shown. Future selections specific for quantitative comparison reports should also be placed here, before selecting filters for hit selections.
  • Output selections will be kept at the end, after filter selections, as it is customary to place output settings last.

comment:8 Changed 9 years ago by olle

(In [4103]) Refs #736. Refs #535. Hits comparison report updated in GUI layout to place comparison type specific selections directly after display of general settings. Instruction text modified to be compatible with the new layout, and simplify addition of more selections:

  1. Class/file action/hit/HitsComparisonReportStep1.java in client/servlet/ updated in instruction text.
  1. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated in instruction text.
  1. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated to place comparison type specific selections directly after display of general settings.

comment:9 Changed 9 years ago by olle

Design update for quantitative comparison report:

  • Since currently quantitative comparison report is only defined for non gel-based data, selection of gel external id for the two hit selections should be removed for quantitative comparison report.
  • A new plug-in class will be introduced for quantitative comparison report, HitsComparisonQuantitativeReportPlugin, in addition to the existing class HitsComparisonReportPlugin, which will be kept for non-quantitative comparison reports.
  • For "Peptide" comparison type, the report table will be created as follows:

    a. For each hit selection project, a list of available unique peptide sequence strings and a list of available charge values will be obtained by database queries. The initial sequence lists will be based on the full description data, and will therefore include potential modifications.

    b. For each list type (sequence and charge), the two lists will then be combined into one list with unique entries. If peptide modifications should not be included, raw sequence strings are shortened to the pure sequence strings before the combined list is created. The combined lists are then sorted before being used in the quantitative comparison report table creation.

    c. The report table is created by looping over the sorted sequence values, and for each sequence value looping over all sorted charge values, to create a pair of sequence/charge values used as index.

    d. For each such index pair, the lists of hits obtained for the two hit selections are checked for hits having the same values for the index variables. The found hits are collected into a new hit list for the current index combination. A hit is only entered once in the combined hit list, even if it appears in both hit selections.

    e. If hits are found for an index pair, a single table row is printed for that index combination, otherwise no table row will be printed.

    f. Values of the chosen quantity variable (precursorQuantity or totalIntensity) for the found hits are then entered in the table row in the column for the local sample id of the hit.

    g. In case several hits exist for the current index parameter(s) and local sample id, with possibly different values for the chosen quantity variable, the user should be given the option of choosing whether the highest value or the sum of values should be used as entry in the table cell.

    h. In the quantitative comparison report table, the string "N/A" will be used as entry for a quantity if no valid data exists. A "N/A" entry will also be made if for the current index parameter(s) several values exist for a quantity other than the selected quantity variable.

    i. For the statistics variables, a ratio value is only considered valid if at least one valid quantity variable value exists for each hit selection, while for the t-test p-value at least two valid quantity variable values for each hit selection are required.

  • For "Protein" comparison type, the same procedure is followed, except that the external id is used as single index variable. A single combined list is created for unique external id values for the two selected projects.
  • Statistics for t-test in quantitative comparison report will be performed using routines from the math library apache.commons.math.stat (for more information on this library, see http://commons.apache.org/math/userguide/stat.html).
Last edited 9 years ago by olle (previous) (diff)

comment:10 Changed 9 years ago by olle

(In [4104]) Refs #736. Refs #535. Class Hit updated to facilitate database queries needed for quantitative comparison report:

  1. Class/file core/Hit.java in api/core/ updated by adding new public static methods List<String> getUniquePeptideSequences(Project project, DbControl dc), List<Integer> getUniqueCharges(Project project, DbControl dc), and List<String> getUniqueExternalIds(Project project, DbControl dc). The new methods use new predefined queries to obtain the result lists.
  1. XML file conf/common-queries.xml in api/core/ updated with new predefined queries "GET_UNIQUE_PEPTIDE_SEQUENCES_IN_HITS_FOR_PROJECT", "GET_UNIQUE_CHARGES_IN_HITS_FOR_PROJECT", and "GET_UNIQUE_EXTERNALIDS_IN_HITS_FOR_PROJECT".

comment:11 Changed 9 years ago by olle

(In [4105]) Refs #736. Refs #535. Refs #287. First preliminary version of hits comparison report with support for quantitative comparison report:

  1. Class/file action/hit/HitsComparisonReport.java in client/servlet/ updated by addition of new valid parameters VString VQUANTITYVARIABLE and VString VQUANTITYENTRY. Displayed instruction text is now modified depending on whether a non-quantitative or quantitative comparison report should be created.
  1. Class/file gui/form/HitComparisonForm.java in client/servlet/ updated to display different option depending on whether a non-quantitative or quantitative comparison report should be created. Selection of gel external id for the two hit selections is not available for quantitative comparison report. New private convenience method Select<VString> fillStringMultiSelectionBox(Select<VString> selectBox, List<String> optionStringList, String optionVariableName) added to simplify to create string multi-selection boxes.
  1. Class/file action/hit/CreateHitsComparisonReportJob.java in client/servlet/ updated to support quantitative comparison report. Input data consistency checks modified depending on whether a non-quantitative or quantitative comparison report should be created. Values of new valid parameters HitsComparisonReport.VQUANTITYVARIABLE and HitsComparisonReport.VQUANTITYENTRY are retrieved from request and transfered to the job by new job parameters. Different plug-in classes are used for the created job depending on whether a non-quantitative or quantitative comparison report should be created (HitsComparisonReportPlugin for non-quantitative and new plug-in class HitsComparisonQuantitativeReportPlugin for quantitative). New key strings needed for quantitative comparison report added to list used to obtain localized strings used by the plug-in.

  1. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated by removal of unused private instance variable boolean gelBasedExport and related public accessor methods.
  1. New class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ added. It is based on existing class HitsComparisonReportPlugin, but modified for quantitative comparison report. Hit selection and report generation completely re-written. Unused methods from class HitsComparisonReportPlugin kept in code for now, in case they should be needed later.
  1. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.
Last edited 9 years ago by olle (previous) (diff)

comment:12 Changed 9 years ago by olle

Design update:

  • For "Protein" comparison type, the column title "Peptide Sequence" in the table header should be exchanged for the much more relevant title "Description", as the data is obtained from the description field of the current hit (for peptides, this field contains the sequence plus optional modification information, explaining the original title of the column).

comment:13 Changed 9 years ago by olle

(In [4108]) Refs #736. Refs #535. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated to exchange column title "Peptide Sequence" for "Description" for comparison type "protein"", as the data is obtained from the description field of the current hit (for peptides, this field contains the sequence plus optional modification information, explaining the original title of the column):

  1. Private method String fetchTabDelimitedHitTableHeaderForQuantitativeReport(List<String> hitSelection1LocalSampleIdList, List<String> hitSelection2LocalSampleIdList) updated by added initial argument String comparisonType. If value of new argument comparisonType is "protein", column title "Peptide Sequence" is exchanged for "Description".
  1. Public method void doExport(DbControl dc, HitsComparisonData hcd, File outCoreFile, ProgressReporter progress) update to include new argument String comparisonType when calling private method String fetchTabDelimitedHitTableHeaderForQuantitativeReport(String comparisonType, ...).

comment:14 Changed 9 years ago by olle

(In [4109]) Refs #736. Refs #535. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated by fix of bug, that made t-test p-value be printed, when less than two valid entries for the quantity variable existed for each hit selection:

  1. Private method void printQuantitativeReportTableRow(...) updated by using variables hitSelection1Items and hitSelection2Items to check if more than one valid entry for the quantity variable exist for each hit selection, when deciding if a t-test p-value should be printed. Previously these numbers were taken from Apache statistics library objects ssa and ssb via calls ssa.getN() and ssb.getN(), but if one of the latter values was initially > 1 and the other == 0, two extra entries were made to the object with the smaller count before the t-test p-value calculation, resulting in both objects having a count larger than 1, when checked if the t-test p-value should be printed.

comment:15 Changed 9 years ago by olle

Design update for quantitative comparison report:

  • Table header title for "Ratio" should be exchanged for "Ratio (mean(HS1)/mean(HS2))", in order to clarify what ratio is used.
  • After each column specifying a quantity value for a local sample id, a new column should be added specifying how many hits were used to compile the printed value. The new column should have a table header title constructed from the specification of the corresponding local sample id in the preceding column plus " (N)", e.g. "HS1:Sample1 (N)".
  • The statistical calculation should be simplified to never add any dummy values (nullvalue) for local sample id without valid value. This makes it possible to revert to calculating the ratio as ssa.getMean()/ssb.getMean() after normal check that ssb.getMean() differs from 0. This will increase consistency of the statistical calculations, as both ratio and t-test p-value will be calculated from the Apache statistics library objects ssa and ssb.
  • The ratio presentation should be updated in case no valid quantity values exist for local sample id for one of the hit selections (there must exist at least one valid value for one sample, as otherwise no table row would have been printed). Instead of printing "N/A", "+" should be printed if mean for hit selection 1 differs from 0, while hit selection 2 equals 0, and "-" if the other way around.

comment:16 Changed 9 years ago by olle

Design update for quantitative comparison report:

  • The statement the "there must exist at least one valid value for one sample, as otherwise no table row would have been printed" is NOT necessarily true in the current version, as a table row is printed if at least one hit in the hit selections is found that has the current index variable values (peptide sequence/charge for "peptide" comparison type, and external id for "protein"), without checking that any valid value for the quantity variable (precursorQuantity or totalIntensity) exist. In case no valid quantity value exists for any of the hit selections, "N/A" will be printed for the ratio.
Last edited 9 years ago by olle (previous) (diff)

comment:17 Changed 9 years ago by olle

Design update note added 2011-02-07 09:42:34 updated in place by correcting errors.

Last edited 9 years ago by olle (previous) (diff)

comment:18 Changed 9 years ago by olle

(In [4110]) Refs #736. Refs #535. Refs #287. Quantitative comparison report updated by clarification of table header titles, addition of a column after each quantity value column for a local sample id showing the number of entries used to obtain the value, simplification of statistical calculations by omitting use of dummy values when values are missing, and use of ratio entry "+" in case values exist for hit selection 1 but not for hit selection 2, and "-" if it is the other way around:

  1. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated:
    a. Addition of string constants for string selection values, in order to avoid risk of wrong functionality due to misspellings in the source code (provided the constants themselves are given the correct values :)).
    b. Table header titles have been clarified.
    c. Private method Double processHitValue(Hit hit, Double columnValue, String quantityVariable, String quantityEntry) exchanged for new private methods, Double fetchHitQuantityValue(Hit hit, String quantityVariable) and Double updateColumnValue(Double columnValue, Double newValue, String quantityEntry), that together give the same functionality, but in addition allow the number of valid quantity values to be counted for a local sample id, which is reported in a new column after the column with the quantity value.
    d. Simplification of statistical calculations by omitting use of dummy values when values are missing (meaning that there is no need for variables statisticsNullValue and nullvalue). The ratio calculations are now performed using the Apache statistics library objects ssa and ssb.
    e. Ratio presentation updated to show entry "+" in case values exist for hit selection 1 but not for hit selection 2, and "-" if it is the other way around.
  1. Class/file action/hit/CreateHitsComparisonReportJob.java in client/servlet/ updated by addition of new string keys to list used to obtain localized strings used by the plug-in.
  1. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

comment:19 Changed 9 years ago by olle

(In [4120]) Refs #737. Refs #736. Hits comparison updated to ignore any "delta" data in a hit description string when obtaining a sequence string:

  1. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated:
    a. Private method String fetchCompareString(String compareStr, String comparisonType, Boolean modificationsIncluded) renamed String pruneCompareString(String compareStr, String comparisonType, Boolean modificationsIncluded).
    b. Private method String pruneCompareString(String compareStr, String comparisonType, Boolean modificationsIncluded) (after name change) updated to cut off the part of the string after " delta", when modifications are included.
    c. Private method String fetchCompareString(Hit hit, boolean gelBasedComparison, String comparisonType, Boolean modificationsIncluded) updated to call renamed method String pruneCompareString(String compareStr, ...) to perform any truncation of the initial string.
  1. Class/file plugins/HitsComparisonReportPlugin.java in plugin/ updated to be consistent with class/file plugins/HitsComparisonQuantitativeReportPlugin.java.

comment:20 Changed 9 years ago by olle

Design update clarification:

  • When previously was stated that when modifications are included, the peptide sequence string should be obtained from the hit description string by cutting off the part of the string after
    " delta", was meant that the string " delta" should also be cut off.

comment:21 Changed 9 years ago by olle

(In [4163]) Refs #736. Quantitative 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/HitsComparisonQuantitativeReportPlugin.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.

comment:22 Changed 9 years ago by olle

Resolution: fixed
Status: assignedclosed

Ticket closed as the first version of support for quantitative hit comparison report has been added.

Last edited 9 years ago by olle (previous) (diff)

comment:23 Changed 9 years ago by olle

Resolution: fixed
Status: closedreopened

Ticket reopened to address modification in report generation.

comment:24 Changed 9 years ago by olle

Design update:

  • The quantity values used to calculate a report value for a local sample id for a hit selection should come from hits belonging to that hit selection. Previously, when the two hit selections contained some local sample id that was identical, quantity values from another hit selection could be used to calculate a report value, as long as the local sample id was correct. An example is when the two hit selections only differ in fraction id values.

comment:25 Changed 9 years ago by olle

(In [4202]) Refs #736. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated to ensure that the quantity values used to calculate a report value for a local sample id for a hit selection come from hits belonging to that specific hit selection:

  1. Private method void printQuantitativeReportTableRow(...) updated with two new arguments, List<Hit> hitSelection1HitList and List<Hit> hitSelection2HitList. They are used to ensure that the quantity values used to calculate a report value for a local sample id for a hit selection come from hits belonging to that specific hit selection.
  1. Private method void createQuantitativeReportPeptideTable(...) updated to supply two new arguments List<Hit> hitSelection1HitList and List<Hit> hitSelection2HitList when calling method void printQuantitativeReportTableRow(...) to create a report table row.
  1. Private method void createQuantitativeReportProteinTable(...) updated to supply two new arguments List<Hit> hitSelection1HitList and List<Hit> hitSelection2HitList when calling method void printQuantitativeReportTableRow(...) to create a report table row.

comment:26 Changed 9 years ago by olle

Resolution: fixed
Status: reopenedclosed

Ticket closed again as the report generation has been updated to ensure that the quantity values used to calculate a report value for a local sample id for a hit selection come from hits belonging to that specific hit selection.

comment:27 Changed 8 years ago by Fredrik Levander

(In [4265]) Refs #736. Now printing external ids for all peptides. Removed unused functions.

comment:28 Changed 7 years ago by olle

(In [4405]) Refs #790. Refs #736. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated:

  1. Inner class HitsComparisonData will no longer be used as a temporary copy of the data, in order to not require more memory than necessary, and to reduce the code size.
  2. Public method void doExport(DbControl dc, HitsComparisonData hcd, Directory outCoreDir, String filename, ProgressReporter progress) is removed, and the output file is now obtained by new public method File fetchOutCoreFile(DbControl dc, Directory outCoreDir, String filename).

comment:29 Changed 7 years ago by olle

(In [4406]) Refs #790. Refs #736. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated:

  1. Boolean variable modificationsIncluded is renamed includeModifications, to clarify that it represents a logical value, and not a collection like a list or a set.

comment:30 Changed 7 years ago by olle

(In [4407]) Refs #790. Refs #736. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated to have comparison report generation optimized for large data sets. Each hit selection list is now created by a single database query, where the results are sorted after external id for protein comparison and sequence values for peptide comparison. In the main report generation loop, an algorithm exploring the sorting is used to find the first list item (if any) with a specified value of the loop variable in the outer loop, instead of checking every item in the hit list. Since the list is sorted, all items with the specified value can be found by checking subsequent items in the list, until an item is found with a different value, or the end of the list is reached. Hopefully, this will reduce the report generation time for large data sets.

  1. Private method List<Hit> fetchHitSelectionHitList(...) updated with two new arguments, boolean gelBasedComparison and Boolean includeModifications. The hit list for each selection will now be created by a single database query obtained from updated private method ItemQuery<Hit> createBasicHitQuery(...).
  2. Private method ItemQuery<Hit> createBasicHitQuery(...) updated to take lists of gel external id, local sample id, and fraction id as arguments, instead of specific values for the variables. The lists are used directly to create the query.
  3. Private methods void createQuantitativeReportPeptideTable(...) and void createQuantitativeReportProteinTable(...) updated to call new private method List<Hit> updateHitList(...) to create the hit list used for the report.
  4. New private method List<Hit> updateHitList(List<Hit> hitList, List<Hit> sortedHitList, boolean gelBasedComparison, String comparisonType, Boolean includeModifications, String comparisonValue, Integer charge) added. It updates the hit list with hits from sorted hit list. The hits to process are found by calling new private method int firstSortItemIndexInSortedHitList(...) to find the first index for given value for sorted hit list.
  5. New private method int firstSortItemIndexInSortedHitList(List<Hit> sortedHitList, boolean gelBasedComparison, String comparisonType, Boolean includeModifications, String comparisonValue) added. It uses a binary search algorithm to find the first index in the hit list for an item having a given value.
  6. New private method void createHitDebugTable(PrintWriter writer, List<Hit> hitList, String comparisonType, String quantityVariable) added for debug purposes. It is not used in production code, but left in the code base for convenience.

comment:31 Changed 7 years ago by olle

(In [4408]) Refs #790. Refs #736. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated in public method void run(Request request, Response response, ProgressReporter progress) to set value of outfile string used in job completion comment. It was originally set in public method void doExport(DbControl dc, HitsComparisonData hcd, Directory outCoreDir, String filename, ProgressReporter progress), which was later removed.

comment:32 Changed 7 years ago by olle

(In [4409]) Refs #790. Refs #736. Class/file plugins/HitsComparisonQuantitativeReportPlugin.java in plugin/ updated to report progress percentage when generating the comparison report:

  1. Private methods void createQuantitativeReportPeptideTable(...) and void createQuantitativeReportProteinTable(...) updated with new argument ProgressReporter progress. Its display(int percent, String message) method is called to display an updated progress percentage whenever a new integer percentage value of the outer loop of the report generation occurs.
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