Opened 9 years ago

Closed 9 years ago

#196 closed defect (fixed)

us_analyte - DNA entries lose MW from sequence

Reported by: demeler Owned by: bdubbs
Priority: normal Milestone: 1.0
Component: ultrascan3 Version:
Keywords: review Cc:

Description

When I enter a new DNA analyte, and then enter a sequence, it correctly calculates and displays the molecular weight. However, when I then double click on the analyte to select it, it resets the MW filed and other selections (double stranded, etc) to zero. This needs to be fixed.

Change History (6)

comment:1 follow-up: Changed 9 years ago by bdubbs

  • Status changed from new to assigned

I'm not sure if you are using the DB or the Disk, but there is one DNA example in the CAUMA3 DB:

     analyteID: 13
    analyteGUID: 3fe0f981-560c-45f0-9484-1e7e5568c1c9
           type: DNA
       sequence: 0001 tcggggaatt cggtattccc aggcggtctc ccatccaagt actaaccgag ccctatgctg
0061 cttgacttcg gtgatcggac gagaaccggt atattcagca tggtatggtc gtaggctctt
0121 gcttgatgaa agttaagcta tttaaagggt cagggatgtt atgacgtcat cggcttataa
0181 atccctggaa gttattcgtt ggaattcc
           vbar: 0.55
    description: 208bp DNA fragment
       spectrum:
molecularWeight: 0
 doubleStranded: 0
     complement: 0
        _3prime: 0
        _5prime: 0
         sodium: 0
      potassium: 0
        lithium: 0
      magnesium: 0
        calcium: 0

We don't actually save the MW, but calculate it. Note that the example above does not have any Counterion values or other components set. It looks like they may not be saved properly.

Clicking on 'Manage Sequence' and then accepting sets the MW so that logic is present, but not called properly.

These are two different, but related, problems.

comment:2 in reply to: ↑ 1 Changed 9 years ago by demeler

Replying to bdubbs:

I'm not sure if you are using the DB or the Disk, but there is one DNA example in the CAUMA3 DB:

We don't actually save the MW, but calculate it. Note that the example above does not have any Counterion values or other components set. It looks like they may not be saved properly.

Possibly, which is why I entered the ticket. The MW should be saved along with the other counter ion info if it is selected. If no counterions are selected, just save the plain MW from sequence.

Clicking on 'Manage Sequence' and then accepting sets the MW so that logic is present, but not called properly.

Yes, it does initially show up when I select the analyte, but double clicking resets this to zero. Either way, something is not working quite right with DNA. The MW needs to be available for the commonVbar calculation. Gary is right, these two tickets are related for that reason.

comment:3 follow-up: Changed 9 years ago by bdubbs

  • Keywords review added

OK, try the fixes in revision 1030.

The nucleotide info was not being saved or retrieved properly in the DB.

See if #197 is fixed by the same changes.

comment:4 in reply to: ↑ 3 Changed 9 years ago by demeler

  • Resolution set to fixed
  • Status changed from assigned to closed

Replying to bdubbs:

OK, try the fixes in revision 1030.

The nucleotide info was not being saved or retrieved properly in the DB.

See if #197 is fixed by the same changes.

Beutiful, this one is fixed! 197 unfortunately is not, sorry Gary/Dan?. Still need to look into why commonVbar is wrong.

Marking this one as fixed.

comment:5 Changed 9 years ago by demeler

  • Milestone changed from beta to 1.0
  • Resolution fixed deleted
  • Status changed from closed to reopened

Apparently the MW for DNA/RNA is still not saved in the database. If defined, or if sequence is entered, a MW should be saved in the DB so a commonVbar can be calculated.

comment:6 Changed 9 years ago by dzollars

  • Resolution set to fixed
  • Status changed from reopened to closed
Note: See TracTickets for help on using tickets.