wiki:GritsTutorial_MSMethodCreatoin
  1. Create a new MS method.
    1. Open class Method in package “edu.uga.ccrc.simiantools.ms.om.data”
      1. Add a new MS_TYPE_.... static String to name the MS method
        1. e.g. MS_TYPE_LC = “LC-MS/MS”
      2. Add this new MS_TYPE to the “String[] MS_TYPES” array
      3. Change version number if desired
  2. Compile jar “edu.uga.ccrc.simiantools.ms.om”
    1. Run “build.xml”
    2. Refresh the files list in the project
    3. You should see a new .jar file
      1. e.g. SimianTools.ms.om-01.b98.jar
  3. Copy new jar file into the project “edu.uga.ccrc.simiantools.ms.annotation”
    1. Put jar into the “lib” folder
    2. Remove previous jar for the “ms.om” from the Referenced Libraries Build Path
    3. From the lib folder, add the new jar to the project build path
    4. Remove old jar from the lib folder
  4. Modify class MzXMLReader.java
    1. Create a method “readMzXMLFile<ms_type>” method for your new method type
    2. Create a method “addAllScans<ms_type>”method for your new method type
  5. Create new StructureAnnotation class in edu.uga.ccrc.simiantools.ms.annotation.gelato
    1. Open package edu.uga.ccrc.simiantools.ms.annotation.gelato
    2. Create a new class “GlycanStructureAnnotation<ms_type>”
      1. Class must extend GlycanStructureAnnotation.java and implement the abstract methods
      2. In particular, the methods "getScans(...)" and "determineScanBounds(...)" should be overridden
  6. Create new GlycanMatcher class in edu.uga.ccrc.simiantools.ms.annotation.gelato
    1. Open package edu.uga.ccrc.simiantools.ms.annotation.gelato
    2. Create a new class “GlycanMatcher<ms_type>”
      1. Class must extend GlycanMatcher.java (or other sub-class of it) and implement the abstract methods
  7. Add the appropriate MS type to the new MS Wizard
    1. Open package "edu.uga.ccrc.simiantools.importer.ms"
    2. Open class "PageTwo.java"
    3. add a new Button for your MS Type
      1. e.g. "private Button msType<ms_type>Btn;"
    4. add the new button to the form w/ layout
      1. e.g. GridData msType<ms_type>BtnGridData = new GridData(); msType<ms_type>Btn = new Button(msTypeGroup, SWT.RADIO); msType<ms_type>Btn.setText(Method.MS_TYPE_<ms_type>); msType<ms_type>BtnGridData.horizontalAlignment = GridData.HORIZONTAL_ALIGN_CENTER; msType<ms_type>Btn.setLayoutData(msType<ms_type>BtnGridData);
  8. Add the appropriate Handler class in edu.uga.ccrc.simiantools.importer.ms.annotation.glycan.simiansearch
    1. Open package edu.uga.ccrc.simiantools.importer.ms.annotation.glycan.simiansearch.handler
    2. Create a new class "NewGelatoHandler<ms_type>"
      1. Class must extend NewGelatoHandler (or other sub-class of it) and implement any abstract methods
Last modified 7 years ago Last modified on 02/04/2015 01:09:19 PM