Changes between Version 16 and Version 17 of FileOrganization


Ignore:
Timestamp:
06/26/2018 04:34:04 PM (3 years ago)
Author:
dbrentw
Comment:

--

Legend:

Unmodified
Added
Removed
Modified
  • FileOrganization

    v16 v17  
    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, 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]]
     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). [[BR]]
     18Here is an example of the temporary GlycanScansAnnotation file for "GOG142":[[BR]]
    1819[[Image(glycan-centric-xml.jpg)]][[BR]]
     20In the image you can see that the outermost tag is specific for this particular glycan (GOG142) and within it are the scan(s) that match to the annotation (e.g. scanId="1").[[BR]][[BR]]
    1921Once 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  
     22Here is an example of the data.xml:[[BR]]
     23[[Image(data-xml.jpg​)]][[BR]]
     24In the image you can see that the outermost tag is the Data object and following are all of the annotated structures in the project (shown is the fragment structure "GOG428-2").[[BR]][[BR]]
     25Here is an example of the ScanFeatures xml file for a scan (scan 1):[[BR]]
     26[[Image(1-xml.jpg)]][[BR]]
     27In the image you can see that the outermost tag is the ScanFeatures object and following are first, the peak list of the scan and then the features that map to the annotated structures in the data.xml file (e.g. annId="1" corresponds to the GlycanAnnotation with annId="1" in the data.xml file).[[BR]][[BR]]
     28Please the attached xml fragments for more information.[[BR]][[BR]]
    2129== Support for Different MS Types ==
    2230For non-LC-MS/MS data (direct infusion, MS Profile, and TIM) the data are organized as follows: