Package org.bioinfo.commons.log

Examples of org.bioinfo.commons.log.Logger

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  public RNASeqQCAnalysisThread(RNASeqQCDialog rnaSeqQCDialog,TabPageController resultManager) {

        super("RNASeqQCAnalysisThread");
    this.settingsDlg = rnaSeqQCDialog;
        this.resultManager = resultManager;
    logger = new Logger(this.getClass().getName());
  }
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    public void init() {

        // log
        logger = new Logger();

        // environment
    homePath = System.getenv("QUALIMAP_HOME");
        if (homePath == null) {
            homePath = new File("").getAbsolutePath() + File.separator;
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  StringBuffer stringValidation;
 
 
  public SavePanel() {
    super();
    logger = new Logger(this.getClass().getName());
  }
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        this.saveCoverage = false;
        this.nonZeroCoverageOnly = true;
        protocol = LibraryProtocol.NON_STRAND_SPECIFIC;
        pgProgram = "";
        pgCommandString = "";
    logger = new Logger();
        chromosomeWindowIndexes = new ArrayList<Integer>();
    }
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  public CountsQCAnalysisThread(CountsQcDialog countsQcDialog, TabPageController tabProperties) {
    super("MultisampleCountsQcThread");
    this.settingsDlg = countsQcDialog;
        this.tabProperties = tabProperties;
    logger = new Logger(this.getClass().getName());
  }
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    if(homeFolder == null){
            setQualimapFolder(new File("").getAbsolutePath()+File.separator);
        }  else {
            setQualimapFolder(homeFolder);
        }
        logger = new Logger(this.getClass().getName());
        logger.println("Qualimap home is " + getQualimapFolder());
        initGUI();
    this.setLocationRelativeTo(null);
    this.setVisible(true);
  }
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    public static String APP_VERSION = "debug";
    public static String APP_BUILT_DATE = "unknown";


  public static void main(String[] args) throws Exception {
    Logger logger = new Logger();
        NgsSmartTool tool = null;

        loadAppPropertiesFile();
        loadAppSettings();

    if(args.length == 0 || args[0].equals("--home")){
      launchGUI(args);
    } else {
           
      String toolName = args[0];

      // TODO: use factories map to create tools

            if(toolName.equalsIgnoreCase(Constants.TOOL_NAME_BAMQC)){
        tool = new BamQcTool();
      }

            if(toolName.equalsIgnoreCase(Constants.TOOL_NAME_RNASEQ_QC)){
                tool = new RnaSeqQcTool();
            }

            if(toolName.equalsIgnoreCase(Constants.TOOL_NAME_COUNTS_QC)){
                tool = new CountsQcTool();
            }

            if (toolName.equals(Constants.TOOL_NAME_COMPUTE_COUNTS)) {
                tool = new ComputeCountsTool();
            }

            if (toolName.equals(Constants.TOOL_NAME_CLUSTERING)) {
                tool = new EpiTool();
            }

            if (toolName.equals(Constants.TOOL_NAME_GC_CONTENT)) {
                tool = new GCContentTool();
            }

            if (toolName.equals(Constants.TOOL_NAME_INDEL_COUNT)) {
                tool = new IndelCountTool();
            }

            if (toolName.equals(Constants.TOOL_NAME_MULTISAMPLE_BAM_QC)) {
                tool = new MultisampleBamQcTool();
            }

            if (toolName.equalsIgnoreCase("run-tests")) {
                System.out.println("Supposed to run tests... Needs testing");
                //runTests();
            } else if(toolName.equalsIgnoreCase("-h") || toolName.equalsIgnoreCase("-help")
                    || toolName.equalsIgnoreCase("--h") || toolName.equalsIgnoreCase("--help")){
        logger.println("");
        logger.println(getHelp());
      } else {
        logger.println("");
        logger.println("Selected tool: " + toolName);
        if(tool==null){
                    logger.println("No proper tool name is provided.\n");
                    logger.println(getHelp());
                } else {
          try {         
            tool.run(args);
          } catch(ParseException pe){         
            logger.println("");
            logger.println("ERROR: " + pe.getMessage());
            logger.println("");
            tool.printHelp();
          } catch(Exception e){
            e.printStackTrace();
          }
        }
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  public BamAnalysisThread(String str, BamAnalysisDialog bamDialog, TabPageController tabProperties) {
    super(str);
    this.bamDialog = bamDialog;
        this.resultManager = tabProperties;
    logger = new Logger(this.getClass().getName());
  }
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        }
    }

  public AboutDialog(HomeFrame frame) {
    super(frame, "About");
    logger = new Logger(this.getClass().getName());
    this.homeFrame = frame;
    initGUI();
        pack();
        setResizable(false);
  }
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Related Classes of org.bioinfo.commons.log.Logger

  • org.bioinfo.ngs.qc.qualimap.gui.dialogs.AboutDialog
  • org.bioinfo.ngs.qc.qualimap.gui.frames.HomeFrame
  • org.bioinfo.ngs.qc.qualimap.gui.panels.SavePanel
  • org.bioinfo.ngs.qc.qualimap.gui.threads.BamAnalysisThread
  • org.bioinfo.ngs.qc.qualimap.gui.threads.CountsQCAnalysisThread
  • org.bioinfo.ngs.qc.qualimap.gui.threads.RNASeqQCAnalysisThread
  • org.bioinfo.ngs.qc.qualimap.main.NgsSmartMain
  • org.bioinfo.ngs.qc.qualimap.main.NgsSmartTool
  • org.bioinfo.ngs.qc.qualimap.process.BamStatsAnalysis
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