Examples with SoliniaAlignment com.solinia.solinia.Models.SoliniaAlignment used on opensource projects

Example 1 with SoliniaAlignment

use of com.solinia.solinia.Models.SoliniaAlignment in project solinia3-core by mixxit.

the class JsonAlignmentRepository method commit.

@Override
public void commit() {
    // TODO Auto-generated method stub
    GsonBuilder gsonbuilder = new GsonBuilder();
    // gsonbuilder.setPrettyPrinting();
    Gson gson = gsonbuilder.create();
    String jsonOutput = gson.toJson(alignments.values(), new TypeToken<List<SoliniaAlignment>>() {
    }.getType());
    try {
        File file = new File(filePath);
        if (!file.exists())
            file.createNewFile();
        FileOutputStream fileOut = new FileOutputStream(file);
        OutputStreamWriter outWriter = new OutputStreamWriter(fileOut);
        outWriter.append(jsonOutput);
        outWriter.close();
        fileOut.close();
        System.out.println("Commited " + alignments.size() + " Alignments");
    } catch (FileNotFoundException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    } catch (IOException e) {
        // TODO Auto-generated catch block
        e.printStackTrace();
    }
}

Example 2 with SoliniaAlignment

use of com.solinia.solinia.Models.SoliniaAlignment in project solinia3-core by mixxit.

the class ConfigurationManager method addAlignment.

@Override
public void addAlignment(String alignmentname) throws Exception {
    for (ISoliniaAlignment alignment : getAlignments()) {
        if (alignment.getName().equals(alignmentname.toUpperCase()))
            throw new Exception("Alignment already exists");
    }
    SoliniaAlignment alignment = new SoliniaAlignment();
    alignment.setId(getNextAlignmentId());
    alignment.setName(alignmentname);
    alignmentsRepository.add(alignment);
}