Changes between Version 15 and Version 16 of FileOrganization


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Timestamp:
06/25/2018 10:54:37 PM (3 years ago)
Author:
dbrentw
Comment:

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  • FileOrganization

    v15 v16  
    1515
    1616== Writing the Project Files
    17 Through testing, we determined that it was most optimal in GELATO to first create temporary annotation files for each glycan that is annotated. For this reason the object ScansAnnotation.java was created. During annotation, ScansAnnotation objects are instantiated for all structures that match to a precursor MS/MS scan or any MSn scan that also has subscans. These files are written into a temp folder with the name of the glycan (or fragment) structure (the annotation string ID). Here is an example of the temporary GlycanScansAnnotation file for "GOG142":[[BR]]
    18 [[Image(glycan-centric-xml.jpg)]]
     17Through testing, we determined that it was most optimal in GELATO to first create temporary annotation files for each glycan that is annotated. For this reason the object ScansAnnotation.java was created. During annotation, Annotation objects are instantiated for all structures that match to a precursor MS/MS scan or any MSn scan that also has subscans and stored in a List in the Data object. Likewise, ScansAnnotation objects are instantiated for all annotated structures, as well. Files for each annotated structure are written into a temp folder with the name of the glycan (or fragment) structure (the annotation string ID). Here is an example of the temporary GlycanScansAnnotation file for "GOG142":[[BR]]
     18[[Image(glycan-centric-xml.jpg)]][[BR]]
     19Once all glycan-centric files are created, GELATO then creates the Scan-based files by iterating over all Glycan/Fragment annotations (List of Annotation objects in Data) and populating a ScanFeatures object for each scan. The ScanFeatures objects are added to the Data object. The final files are then written into the GRITS project folder.[[BR]]
     20 
    1921== Support for Different MS Types ==
    2022For non-LC-MS/MS data (direct infusion, MS Profile, and TIM) the data are organized as follows: