Feature table

[Fredrik Levander]

Try out if features should be in a table

[Fredrik Levander]

(In [3422]) Refs #614. Initial addition of feature table.

[Fredrik Levander]

(In [3423]) Refs #614. Cleaning of feature import plugin

[Fredrik Levander]

(In [3424]) Refs #614. Matching of features with hits and more.

[Fredrik Levander]

(In [3427]) Refs #614. Adjustments

[Fredrik Levander]

(In [3432]) Refs #614. Corrected proton mass

[Fredrik Levander]

(In [3445]) Merging test branch with trunk. Refs #585, Refs #614, Refs #621.

[Fredrik Levander]

It seems feasible to use a feature table, and initial implementations have been made already.

[Fredrik Levander]

(In [3560]) Refs #614. Updated for mzML support

[Fredrik Levander]

(In [3694]) Refs #614. Added time tolerance to feature matching and added batch import functionality

[Fredrik Levander]

(In [3731]) Refs #614. Support for agilent type scan ids

[Fredrik Levander]

(In [3764]) Refs #614. Updates in feature hit matching. Allowing matching with other files of same local sample id. Corrected retention time matching with tolerance. Added form for settings.

[Fredrik Levander]

(In [3765]) Refs #614. Updated default parameters for matching.

[Fredrik Levander]

(In [3766]) Refs #614. Added log file for matching features to hits.

[Fredrik Levander]

(In [3770]) Refs #614. Logging more parameters, and updating of hits when deleting features.

[Fredrik Levander]

(In [3777]) Refs #614. Adding link to feature peptide sequences, to find the matching hits.

[Fredrik Levander]

(In [3782]) Refs #614. reformatted

[Fredrik Levander]

(In [4121]) Refs #614. More informative decription of what is done.

[Fredrik Levander]

(In [4142]) Refs #614. Making several attempts to read mzML/mzXML file in case of IO problems.

[Fredrik Levander]

(In [4152]) Refs #614. Changing queries to allow matching with related hits also if there are no identified peptides in the feature file.

[Fredrik Levander]

(In [4156]) Refs #614. Added some more logged info.

[olle]

(In [4188]) Refs #752. Refs #668. Refs #614. Refs #287. Support for running msInspect feature detection from Proteios SE updated with option to import the created feature file directly:

1. Class/file action/file/UseSpectrumFileForMsInspectSearchExtension.java in client/servlet/ updated with new check box for option to import created feature file. The check box is coupled to new valid parameter VBoolean RunMsInspect.VMSINSPECTIMPORTRESULTS. Default is to not import the feature file directly.

2. Class/file action/msInspect/RunMsInspect.java in client/servlet/ updated:
   a. New valid parameter VBoolean VMSINSPECTIMPORTRESULTS added.
   b. Protected method void runMe() updated to retrieve the value of valid parameter VBoolean VMSINSPECTIMPORTRESULTS, and if the value is true create an import job after the feature detection job. The path of the feature file to be created is transferred to the import job as a string job parameter. Jobs are created by calling new private methods Job createMsInspectJob(...) and Job createMsInspectImportJob(...).
   c. New private method Job createMsInspectJob(DbControl dc, File spectrumFile, ... , Job blockerJob) added. It creates an msInspect job.
   d. New private method Job createMsInspectImportJob(DbControl dc, String featureFilePathStr, String featureFileName, Job blockerJob) added. It creates an msInspect import job.

3. Class/file plugins/MsInspectFeatureImporter.java in plugin/ updated:{{BR]]a. Public method void run(Request request, Response response, ProgressReporter progress) updated to retrieve value of feature file path from a string job parameter and obtain the feature file from this, in case the File value retrieved from a File job parameter is null.

4. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[olle]

(In [4206]) Refs #751. Refs #744. Refs #614. Refs #287. Support for running OpenMS feature detection from Proteios SE updated with option to import the created feature file directly:

1. Class/file action/file/UseSpectrumFileForOpenMsSearchExtension.java in client/servlet/ updated with new check box for option to import created feature file. The check box is coupled to new valid parameter VBoolean RunOpenMs.VOPENMSIMPORTRESULTS. Default is to not import the feature file directly.

2. Class/file action/openMs/RunOpenMs.java in client/servlet/ updated:
   a. New valid parameter VBoolean VOPENMSIMPORTRESULTS added.
   b. Protected method void runMe() updated to retrieve the value of valid parameter VBoolean VOPENMSIMPORTRESULTS, and if the value is true create an import job after the feature detection job. As import of features requires a preceding feature detection job, the code for running a single OpenMS job has been updated to clarify if the job instance is a PeakPicker or FeatureFinder job. The path of the feature file to be created is transferred to the import job as a string job parameter. Import jobs are created by calling new private method Job createOpenMsImportJob(...).
   c. New private method Job createOpenMsImportJob(DbControl dc, String featureFilePathStr, String featureFileName, Job blockerJob) added. It creates an OpenMS import job.

3. English dictionary file locale/en/dictionary in client/servlet/ updated with new string keys.

[Fredrik Levander]

(In [4257]) Refs #614. Allowing import of features in different projects.

[Fredrik Levander]

(In [4317]) Refs #614. Update to make sure that apex retention time will always be in minutes.

[Fredrik Levander]

(In [4355]) Refs #614. Adjusted parsing of scan ids in mzML for feature import.