Changes between Version 9 and Version 10 of CreatingAnnotion

Timestamp:

01/11/2017 09:22:38 PM (6 years ago)

Author:

dbrentw

Comment:

--

CreatingAnnotion

@@ -211 +211 @@
                         if( ! glycanScanAnnotation.getScanAnnotations().isEmpty() ) {
                                 try {
-                                        writer.writeAnnotationsPerGlycan(glycanScanAnnotation, getTempOutputPath());
+                                        writer.writeAnnotationsPerGlycan(glycanScanAnnotation, getTempOutputPath());  // creates temp files that will be used to populate the archive in the next step
                                 } catch (IOException e) {
                                         // TODO Auto-generated catch block
@@ -222 +222 @@
         }
 }}}
+
+9) Create the archive that will be read by GRITS
+  a) Populate the Scan Feature object
+{{{
+        protected void populateScanFeatureData(String glycanFilesPath) {
+                //define objects to gather the MS1 annotation while processing MS2
+                AnnotationReader reader = new AnnotationReader(); // instantiate the reader, which will read the temp files created in Step 8
+                GlycanScansAnnotation glycanAnnotation = new GlycanScansAnnotation();
+                ScanFeatures scanFeatures = new ScanFeatures();  
+                for(Integer scanId : getTestData().getScans().keySet()){        
+                        if( isCanceled() )
+                                return;
+                        scanFeatures = new ScanFeatures(); // Create new ScanFeatures object to add features to the scan if it was annotated
+                        scanFeatures.setScanId(scanId);
+                        scanFeatures.setScanPeaks(new HashSet<Peak>(getTestData().getScans().get(scanId).getPeaklist()));
+                        getTestData().getScanFeatures().put(scanId, scanFeatures);
+                        if(getTestData().getAnnotatedScan().get(scanId) != null) { // this scan was annotated
+                                for(String glycanId : getTestData().getAnnotatedScan().get(scanId)){
+                                        glycanAnnotation = reader.readglycanAnnotation(glycanFilesPath, glycanId); // read the temp file for this particular glycan
+                                        if(glycanAnnotation != null && glycanAnnotation.getScanAnnotations().get(scanId) != null) {
+                                                for( GlycanFeature f : glycanAnnotation.getScanAnnotations().get(scanId) ) {
+                                                        if( ! scanFeatures.getFeatures().contains(f) ) {
+                                                                scanFeatures.getFeatures().add(f); // add each unique GlycanFeature (from ScanAnnotations) to the ScanFeatures list of features
+                                                        }
+                                                }
+                                        }
+                                }
+                        }
+                }
+        }
+}}}