Changes between Version 6 and Version 7 of CreatingAnnotion


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Timestamp:
11/30/2016 08:21:09 PM (4 years ago)
Author:
dbrentw
Comment:

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  • CreatingAnnotion

    v6 v7  
    6363BuilderWorkspace bw = new BuilderWorkspace(new GlycanRendererAWT());
    6464}}}
     65
     66  b) Create a test GlycanStructure object and a corresponding Glycan object. I'm using a static GlycoWorkbench (GWB) formatted sequence
     67{{{
     68   private static String GLYCAN_SEQUENCE1 = "freeEnd--??1D-GlcNAc,p--??1D-GlcNAc,p--??1D-Man,p(--??1D-Man,p--??1D-Man,p--??1D-Man,p--??1D-Glc,p--??1D-Glc,p)--??1D-Man,p(--??1D-Man,p--??1D-Man,p)--??1D-Man,p--??1D-Man,p$MONO,perMe,0,0,freeEnd";
     69   private static String GLYCAN_ID1 = "TEST_GOG1";
     70   
     71   private void createTestGlycanObjects() {
     72      testGlycanStructure1 = new GlycanStructure();   // create the GlycanStructure object
     73      testGlycanStructure1.setGWBSequence(GLYCAN_SEQUENCE1); // set the sequence
     74      testGlycanStructure1.setId(GLYCAN_ID1);  // set its ID
     75
     76      testGlycan1 = Glycan.fromString(testGlycanStructure1.getGWBSequence());  // create the Glycan object using the "Glycan.fromString( <GWB Seq> )" method
     77      testGlycanStructure1.setSequence( testGlycan1.toGlycoCTCondensed() );   // set the alternative sequence (using GlycoCT Condensed)
     78      testGlycanStructure1.setSequenceFormat(GlycanAnnotation.SEQ_FORMAT_GLYCOCT_CONDENSED);  // set the type of sequence
     79   }
     80}}}