Examples of pku.cbi.abcgrid.master.service.App

pku.cbi.abcgrid.master.service.App
The base interface for all bioinformatics applications. A application is a executable unit of a App. For example, "blastall" is a Application, "NCBI_BLAST" is a App. To add support to a new application, you should derived your class from this interface.


        String appName = commands[0];
        if(job_monitor.isJobFull(appName))
            throw new Exception("Job queue is full (Maximum:32)");


        App app = apps.get(appName);
        int priority = usermgr.getUserPriority(submitter);
        Job j = app.parse(submitter, commands, priority);
        j.setId(atomic_job_id.getAndIncrement());
        //partition this job into tasks
        List<Task> tasks = app.fragment(j);
        JobInfo ji = new JobInfo(j.getId(), j.getSubmitter(),commands);
        for (Task t : tasks)
        {
            ji.add(new TaskInfo(t));
        }

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    {
        createServiceQueue("NCBI_BLAST");
        createServiceQueue("HMMER");
        createServiceQueue("CE");
        //createServiceQueue("DALI");
        App s;


        s = new blastall();
        apps.put(s.getAppName(), s);


        s = new bl2seq();
        apps.put(s.getAppName(), s);


        s = new rpsblast();
        apps.put(s.getAppName(), s);


        s = new megablast();
        apps.put(s.getAppName(), s);


        s = new CE();
        apps.put(s.getAppName(), s);


        //s = new DaliLite();
        //services.put(s.getAppName(), s);


        s = new hmmpfam();
        apps.put(s.getAppName(), s);
    }

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    {
        List<String> buffer = new ArrayList<String>();
        for (Map.Entry<String, App> ss : apps.entrySet())
        {
            String name = ss.getKey();
            App serv = ss.getValue();
            String sa = serv.getServiceName() + "." + name + "\n";
            buffer.add(sa);
        }
        String[] ss = new String[buffer.size()];
        buffer.toArray(ss);
        return ss;

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Related Classes of pku.cbi.abcgrid.master.service.App

pku.cbi.abcgrid.master.JobScheduler

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