Package com.compomics.util.pride

Examples of com.compomics.util.pride.PrideObjectsFactory

232
233
234
235
236
237
238
239
240
241
        this.contactGroup = contactGroup;
        this.sample = sample;
        this.protocol = protocol;
        this.instrument = instrument;
        this.waitingHandler = waitingHandler;
        PrideObjectsFactory prideObjectsFactory = PrideObjectsFactory.getInstance();
        ptmToPrideMap = prideObjectsFactory.getPtmToPrideMap();
        r = new FileWriter(new File(outputFolder, fileName + ".xml"));
        br = new BufferedWriter(r);
    }
View Full Code Here
187
188
189
190
191
192
193
194
195
196
197
        this.spectrumCountingPreferences = spectrumCountingPreferences;
        this.identificationFeaturesGenerator = identificationFeaturesGenerator;
        this.annotationPreferences = annotationPreferences;
        this.sequenceMatchingPreferences = sequenceMatchingPreferences;
        this.waitingHandler = waitingHandler;
        PrideObjectsFactory prideObjectsFactory = PrideObjectsFactory.getInstance(); // @TODO: should be renamed!!!
        ptmToPrideMap = prideObjectsFactory.getPtmToPrideMap();
        this.peptideSpectrumAnnotator = new PeptideSpectrumAnnotator();
        r = new FileWriter(outputFile);
        br = new BufferedWriter(r);
    }
View Full Code Here
287
288
289
290
291
292
293
294
295
296
297
298
        }
        PTMFactory ptmFactory = PTMFactory.getInstance();
        PtmToPrideMap ptmToPrideMap = null;
        // get the psi-mod mappings
        try {
            PrideObjectsFactory prideObjectsFactory = PrideObjectsFactory.getInstance();
            ptmToPrideMap = prideObjectsFactory.getPtmToPrideMap();
        } catch (Exception e) {
            e.printStackTrace();
        }

        for (String accession : accessions) {
View Full Code Here
TOP

Related Classes of com.compomics.util.pride.PrideObjectsFactory

  • eu.isas.peptideshaker.export.MzIdentMLExport
  • eu.isas.peptideshaker.export.PrideXmlExport
  • eu.isas.peptideshaker.followup.SwathExport
    • Copyright © 2018 www.massapicom. All rights reserved.
    All source code are property of their respective owners. Java is a trademark of Sun Microsystems, Inc and owned by ORACLE Inc. Contact coftware#gmail.com.