Changes between Version 10 and Version 11 of CreatingAnnotion

Timestamp:

01/12/2017 08:20:06 PM (6 years ago)

Author:

dbrentw

Comment:

--

CreatingAnnotion

@@ -224 +224 @@
 
 9) Create the archive that will be read by GRITS
-  a) Populate the Scan Feature object
+  a) Populate the Scan Feature objects
 {{{
         protected void populateScanFeatureData(String glycanFilesPath) {
@@ -236 +236 @@
                         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);
+                        scanFeatures.setScanPeaks(new HashSet<Peak>(getTestData().getScans().get(scanId).getPeaklist())); // set the list of peaks to the ScanFeature that are in this Scan
+                        getTestData().getScanFeatures().put(scanId, scanFeatures); // add this new ScanFeatures object to list of ScanFeatures in the Data object (associated with this scan id)
                         if(getTestData().getAnnotatedScan().get(scanId) != null) { // this scan was annotated
                                 for(String glycanId : getTestData().getAnnotatedScan().get(scanId)){
@@ -253 +253 @@
         }
 }}}
+  b) Write the archive file(s)
+{{{
+        protected void populateScanFeatureData(String glycanFilesPath, Data data) {
+             AnnotationWriter writer = new AnnotationWriter();
+             writer.generateScansAnnotationFiles(glycanFilesPath, data)
+        }
+}}}
+
+    1) create ZipOutputStream
+{{{
+        FileOutputStream ms_final = new FileOutputStream(zipPath);
+        ZipOutputStream compressedFile = new ZipOutputStream(ms_final);
+}}}
+    2) Write DataHeader to compressed file
+{{{
+        public void writeDataHeaderToZip( DataHeader dHeader, ZipOutputStream compressedFile ) {
+                JAXBContext jaxbDataHeaderContext = null;
+                Marshaller jaxbDataHeaderMarshaller = null;
+                try {
+                        List<Class> contextList = new ArrayList<>(Arrays.asList(FilterUtils.filterClassContext));
+                        contextList.add(FilterSetting.class);
+                        contextList.add(DataHeader.class);
+                        jaxbDataHeaderContext = JAXBContext.newInstance(contextList.toArray(new Class[contextList.size()]));
+                        jaxbDataHeaderMarshaller = jaxbDataHeaderContext.createMarshaller();
+                } catch (JAXBException e1) {
+                        logger.error(e1.getMessage(), e1);
+                        return;
+                } catch ( Exception e2 ) {
+                        logger.error(e2.getMessage(), e2);
+                        return;
+                }
+                try {
+                        jaxbDataHeaderMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+                        compressedFile.putNextEntry(new ZipEntry(AnnotationWriter.DATA_HEADER));
+                        jaxbDataHeaderMarshaller.marshal(dHeader, compressedFile);
+                } catch (IOException e1) {
+                        logger.error(e1.getMessage(), e1);
+                } catch (JAXBException e2) {
+                        logger.error(e2.getMessage(), e2);
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }
+                try {
+                        compressedFile.closeEntry();
+                } catch (IOException e1) {
+                        logger.error(e1.getMessage(), e1);
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }
+        }
+}}}
+
+    3) Write Method object to compressed file
+{{{
+        public void writeMethodToZip( Method method, ZipOutputStream compressedFile ) {
+                JAXBContext jaxbMethodContext = null;
+                Marshaller jaxbMethodMarshaller = null;
+                try {
+                        List<Class> contextList = new ArrayList<>(Arrays.asList(FilterUtils.filterClassContext));
+                        contextList.add(FilterSetting.class);
+                        contextList.add(Method.class);
+                        jaxbMethodContext = JAXBContext.newInstance(contextList.toArray(new Class[contextList.size()]));
+                        jaxbMethodMarshaller = jaxbMethodContext.createMarshaller();
+                } catch (JAXBException e1) {
+                        logger.error(e1.getMessage(), e1);
+                        return;
+                } catch ( Exception e2 ) {
+                        logger.error(e2.getMessage(), e2);
+                        return;
+                }
+                try {
+                        jaxbMethodMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+                        compressedFile.putNextEntry(new ZipEntry(AnnotationWriter.SETTINGS_FILE));
+                        jaxbMethodMarshaller.marshal(method, compressedFile);
+                } catch (IOException e1) {
+                        logger.error(e1.getMessage(), e1);
+                } catch (JAXBException e2) {
+                        logger.error(e2.getMessage(), e2);
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }
+                try {
+                        compressedFile.closeEntry();
+                } catch (IOException e1) {
+                        logger.error(e1.getMessage(), e1);
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }               
+        }
+}}}
+
+    4) Write Data object WITHOUT ScanFeatures objects to compressed file
+{{{
+        public void writeDataToZip(Data data, ZipOutputStream compressedFile ) {
+                JAXBContext jaxbDataContext = null;
+                Marshaller jaxbDataMarshaller = null;
+                try {
+                        List<Class> contextList = new ArrayList<>(Arrays.asList(FilterUtils.filterClassContext));
+                        contextList.add(FilterSetting.class);
+                        contextList.add(Data.class);
+                        jaxbDataContext = JAXBContext.newInstance(contextList.toArray(new Class[contextList.size()]));
+                        jaxbDataMarshaller = jaxbDataContext.createMarshaller();
+                } catch (JAXBException e1) {
+                        logger.error(e1.getMessage(), e1);
+                        return;
+                } catch ( Exception e2 ) {
+                        logger.error(e2.getMessage(), e2);
+                        return;
+                }
+                try {
+                        jaxbDataMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+                        compressedFile.putNextEntry(new ZipEntry(AnnotationWriter.DATA_FILE));
+                        // testing not serializing the scanfeatures in the data object.
+                        HashMap<Integer, ScanFeatures> hm = data.getScanFeatures();
+                        data.setScanFeatures(null); // set scan features to null before writing data!
+                        jaxbDataMarshaller.marshal(data, compressedFile);
+                        data.setScanFeatures(hm);
+                } catch (IOException e1) {
+                        logger.error(e1.getMessage(), e1);
+                } catch (JAXBException e2) {
+                        logger.error(e2.getMessage(), e2);
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }
+                try {
+                        compressedFile.closeEntry();
+                } catch (IOException e1) {
+                        logger.error(e1.getMessage(), e1);
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }               
+        }
+}}}
+
+    5) Write ScanFeatures objects to compressed file
+{{{
+        public void writeScanFeaturesToZip(Data data, ZipOutputStream compressedFile, String glycanFilesPath ) throws Exception {
+                JAXBContext jaxbContextAnn = null;
+                Marshaller jaxbMarshallerAnn = null;
+                try {
+                        jaxbContextAnn = JAXBContext.newInstance(ScanFeatures.class);
+                        jaxbMarshallerAnn = jaxbContextAnn.createMarshaller();
+                } catch (JAXBException e1) {
+                        logger.error(e1.getMessage(), e1);
+                        return;
+                } catch ( Exception e2 ) {
+                        logger.error(e2.getMessage(), e2);
+                        return;
+                }
+                HashMap<String,String> gogCheckerForMS1 = new HashMap<String,String>();
+                try {
+                        if( data.getScans() != null ) {
+                                for(Integer scanId : data.getScans().keySet()){
+                                        try {
+                                                compressedFile.putNextEntry(new ZipEntry(scanId+".xml"));
+                                                jaxbMarshallerAnn.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+                                                jaxbMarshallerAnn.marshal(data.getScanFeatures().get(scanId),compressedFile);
+                                        } catch (IOException e1) {
+                                                logger.error(e1.getMessage(), e1);
+                                        } catch (JAXBException e2) {
+                                                logger.error(e2.getMessage(), e2);
+                                        } catch ( Exception ex ) {
+                                                logger.error(ex.getMessage(), ex);
+                                        }
+                                        try {
+                                                compressedFile.closeEntry();
+                                                if(data.getAnnotatedScan().get(scanId) != null){
+                                                        for(String gog : data.getAnnotatedScan().get(scanId)){
+                                                                gogCheckerForMS1.put(gog, "seen");
+                                                        }
+                                                }
+                                        } catch (IOException e1) {
+                                                logger.error(e1.getMessage(), e1);
+                                        } catch ( Exception ex ) {
+                                                logger.error(ex.getMessage(), ex);
+                                        }
+                                }
+                        }
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                        return;
+                }
+
+                try {
+                        deleteAnnotationsPerGlycan(glycanFilesPath,gogCheckerForMS1);  // clean up temporary folder of data
+                } catch ( Exception ex ) {
+                        logger.error(ex.getMessage(), ex);
+                }
+        }
+}}}
+
+    6) Close compressed file
+{{{
+                try {
+                        compressedFile.close();
+                }catch(Exception ex){
+                        logger.error("Error closing compressed file", ex);
+                }
+}}}