Match between feature lists

[Fredrik Levander]

Allow propagating of identifications between feature lists from diffferent LC-MS runs

[Fredrik Levander]

(In [4276]) Refs #774. Added GUI classes for feature sequence propagation.

[marianne]

(In [4279]) Refs #774. Initial test ckeck-in.

[marianne]

(In [4280]) Refs #774. Committing complementary files.

[marianne]

(In [4282]) Refs #774. Alignment of charge states >1 and hits update.

[marianne]

(In [4283]) Refs #774. Charge states >1.

[marianne]

(In [4285]) Refs #774. Progress report and tolerance distribution calculation.

[marianne]

(In [4288]) Refs #774. Bug fix: Added two-way alignment. Skipping alignment if there are no matching sequences. Added: Recall and precision evaluation for features with sequences. Feature number coverage increase computation.

[marianne]

(In [4289]) Refs #774. Distribution tolerance update. ClusterID set only if features are aligned. Alignment if no common sequences.

[marianne]

(In [4290]) Refs #774. Conflict resolution for second file. Precision and recall evaluation moved to before matching.

[marianne]

(In [4292]) Refs #774. Bug fix for local sample id. Abortable interface implemented. Maximun RT difference used when sequences are matched for use as landmarks. Minimum pairwise recall set to 0.90.

[marianne]

(In [4296]) Refs #774. More efficient assignment of hits.

[marianne]

(In [4297]) Refs #774. Fraction information added.

[Fredrik Levander]

(In [4299]) Refs #745, #774. Correction of precursor quantity calculation for proteins.

[Fredrik Levander]

(In [4309]) Refs #774. Moved progress update to optimize performance.

[marianne]

(In [4313]) Refs #774. Printing math exception to alignment file. Will be deleted in later versions.

[marianne]

(In [4314]) Refs #774. More exception printouts.

[marianne]

(In [4315]) Refs #774. Updates: m/z tolerance for looping, database reconnect issue, pairwise matching order, only features in a cluster receive clusterID

[marianne]

(In [4316]) Refs #774. Bugfix, split clusterID database query, optimal recall and precision calculations.

[marianne]

(In [4318]) Refs #774. Feature and cluster counters. Updated precision and recall calculations, pairwise and global. Changed matching order. Automatic matching intervals and interest regions.

[marianne]

(In [4319]) Refs #774. Updated recall and precision computation. Updated removal of duplicate matches.

[marianne]

(In [4320]) Refs #774. Updated replaceOldHit

[marianne]

(In [4321]) Refs #774. Another update for replaceOldHit

[marianne]

(In [4322]) Refs #774. Tolerance update

[marianne]

(In [4324]) Refs #774. Added: Updated abort criteria for fraction alignment. Bugfix for clusterID-update. Adaptive bandwidth parameter. Feature based alignment and recall. Updated removal of duplicate features before database query. More extensive comments.

[marianne]

(In [4325]) Refs #774. clusterID fix

[marianne]

(In [4326]) Refs #774. Bugfix fractionmatch. Groundtruth computation based on fractions.

[marianne]

(In [4327]) Refs #774. Bugfix checking for duplicate matches and code cleanup.

[marianne]

(In [4329]) Refs #774. FeatureSequencePropagator?: Checking previous hits speed up, number of match times per file is set constant, ground truth based precision adjusted for number of mis-alignments. No tolerance for points sequence matches. Some GUI updates.

[marianne]

(In [4330]) Refs #774. Tweaked matching order. Improved handling of files with no sequence information. Global precision and recall calculations redone.

[marianne]

(In [4331]) Refs #774. Small fix.

[marianne]

(In [4333]) Refs #774. Increased nbr of matches per file.

[marianne]

(In [4341]) Refs #774. All features occurence based precision bug fix.

[marianne]

(In [4342]) Refs #774. Continued precision calculation bug fix and nMatches (similarity) cutoff added.

[marianne]

(In [4343]) Refs #774. Update of matching order to account for files with too few common id:s.

[marianne]

(In [4347]) Refs #774. Sequence propagation update.

[marianne]

(In [4353]) Refs #774. Bug fix during clusterID propagation and speed-up.

[marianne]

(In [4354]) Refs #774. Removal of debug print-out.

[marianne]

(In [4357]) Refs #774. Tiny ground truth size fix.

[marianne]

(In [4358]) Refs #774. Changed logger.

[marianne]

(In [4399]) Refs #774. Temporary no seq fix.

[marianne]

(In [4400]) Refs #774. Added tolerance based alignment if there are too few sequence matches.

[marianne]

(In [4401]) Refs #774. Bugfix in sequence coverage printout for files with no sequences.

[marianne]

(In [4402]) Refs #774. Continued printout fix.

[marianne]

(In [4441]) Refs #774. Added control to make sure that there are no unaligned subgroups of files before ending the alignment loop.

[marianne]

(In [4442]) Refs #774. Subgroup bugfix.

[marianne]

(In [4446]) Refs #774. Tolerances for extracting matching features are calculated from the set of matching sequences.

[marianne]

(In [4447]) Refs #774. Tolerance adjustment.

[marianne]

(In [4448]) Refs #774. Quartile factor adjustment.

[Fredrik Levander]

(In [4524]) Refs #774. Avoiding null pointer exception

[Fredrik Levander]

(In [4634]) Refs #774. Avoid db timeout when aligning large datasets.

[Fredrik Levander]

(In [4635]) Refs #774. Progress reporting update and avoiding db connection timeout when aligning large datasets.