Why is the same SQLite query being 30 times slower when fetching only twice as many results?

Question

I have been working on speeding up a query I\'m using for about a week now and asked several questions about it here ( How can I speed up fetching the results after running an s

Answer 1

Consider using covering indices on the tables involved in your query.

You are indeed fetching a limited amount of columns in your select statement and the corresponding inner join and where clauses. By using a covering index with the columns well ordered in it, you should get a very fast query, that is you will remove the scan table in favor of an search table using a covering index.

Try to use those indices on your tables:

CREATE INDEX `fk_covering_feature` ON `feature` (`msrun_msrun_id`,`mzMin`,`mzMax`,`rtMin`,`rtMax`,`feature_table_id`);
CREATE INDEX `fk_covering_spectrum` ON  `spectrum` (`msrun_msrun_id`,`scan_start_time`,`spectrum_id`);
CREATE INDEX `fk_covering_MSMS_precursor` ON  `MSMS_precursor` (`spectrum_spectrum_id`,`ion_mz`,`precursor_id`);

When going for speed, you should also hint the query planner to understand msrun_msrun_id is a constant to check for both feature and spectrum tables. Add the constant test in your query by putting this additional test at the end of the query (and pass spectrumFeature_InputValues twice):

"AND spectrum.msrun_msrun_id = ?"