Examples with TraceException dr.inference.trace.TraceException used on opensource projects

Example 6 with TraceException

use of dr.inference.trace.TraceException in project beast-mcmc by beast-dev.

the class GPSkytrackAnalysisParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    System.err.println("The Summary Statistics are being created...");
    try {
        // 10% is brun-in default
        final double burnin = xo.getAttribute(BURN_IN, 0.1);
        if (burnin < 0) {
            throw new XMLParseException("burnIn should be either between 0 and 1 or a positive number");
        }
        Parameter numGridPoints = new Parameter.Default(0, 1);
        if (xo.getChild(N_GRID) != null) {
            XMLObject cxo = xo.getChild(N_GRID);
            numGridPoints = (Parameter) cxo.getChild(Parameter.class);
        }
        final File log = FileHelpers.getFile(getElementText(xo, LOG_FILE_NAME));
        return new dr.evomodel.coalescent.GPSkytrackAnalysis(log, burnin, numGridPoints);
    } catch (java.io.IOException ioe) {
        throw new XMLParseException(ioe.getMessage());
    } catch (Importer.ImportException e) {
        throw new XMLParseException(e.toString());
    } catch (TraceException e) {
        throw new XMLParseException(e.toString());
    }
}

Example 7 with TraceException

use of dr.inference.trace.TraceException in project beast-mcmc by beast-dev.

the class MapperFrame method processTraces.

protected void processTraces(final LogFileTraces[] tracesArray) {
    final JFrame frame = this;
    if (tracesArray.length == 1) {
        try {
            final LogFileTraces traces = tracesArray[0];
            final String fileName = traces.getName();
            final ProgressMonitorInputStream in = new ProgressMonitorInputStream(this, "Reading " + fileName, new FileInputStream(traces.getFile()));
            in.getProgressMonitor().setMillisToDecideToPopup(0);
            in.getProgressMonitor().setMillisToPopup(0);
            //                final Reader reader = new InputStreamReader(in);
            Thread readThread = new Thread() {

                public void run() {
                    try {
                        traces.loadTraces(in);
                        EventQueue.invokeLater(new Runnable() {

                            public void run() {
                            //                                            analyseTraceList(traces);
                            //                                            addTraceList(traces);
                            }
                        });
                    } catch (final TraceException te) {
                        EventQueue.invokeLater(new Runnable() {

                            public void run() {
                                JOptionPane.showMessageDialog(frame, "Problem with trace file: " + te.getMessage(), "Problem with tree file", JOptionPane.ERROR_MESSAGE);
                            }
                        });
                    } catch (final InterruptedIOException iioex) {
                    // The cancel dialog button was pressed - do nothing
                    } catch (final IOException ioex) {
                        EventQueue.invokeLater(new Runnable() {

                            public void run() {
                                JOptionPane.showMessageDialog(frame, "File I/O Error: " + ioex.getMessage(), "File I/O Error", JOptionPane.ERROR_MESSAGE);
                            }
                        });
                    //                    } catch (final Exception ex) {
                    //                        EventQueue.invokeLater (
                    //                                new Runnable () {
                    //                                    public void run () {
                    //                                        JOptionPane.showMessageDialog(frame, "Fatal exception: " + ex.getMessage(),
                    //                                                "Error reading file",
                    //                                                JOptionPane.ERROR_MESSAGE);
                    //                                    }
                    //                                });
                    }
                }
            };
            readThread.start();
        } catch (FileNotFoundException fnfe) {
            JOptionPane.showMessageDialog(this, "Unable to open file: File not found", "Unable to open file", JOptionPane.ERROR_MESSAGE);
        } catch (IOException ioex) {
            JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
        } catch (Exception ex) {
            JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        }
    } else {
        Thread readThread = new Thread() {

            public void run() {
                try {
                    for (final LogFileTraces traces : tracesArray) {
                        //                            final Reader reader = new FileReader(traces.getFile());
                        traces.loadTraces();
                        EventQueue.invokeLater(new Runnable() {

                            public void run() {
                            //                                            analyseTraceList(traces);
                            //                                            addTraceList(traces);
                            }
                        });
                    }
                } catch (final TraceException te) {
                    EventQueue.invokeLater(new Runnable() {

                        public void run() {
                            JOptionPane.showMessageDialog(frame, "Problem with trace file: " + te.getMessage(), "Problem with tree file", JOptionPane.ERROR_MESSAGE);
                        }
                    });
                } catch (final InterruptedIOException iioex) {
                // The cancel dialog button was pressed - do nothing
                } catch (final IOException ioex) {
                    EventQueue.invokeLater(new Runnable() {

                        public void run() {
                            JOptionPane.showMessageDialog(frame, "File I/O Error: " + ioex.getMessage(), "File I/O Error", JOptionPane.ERROR_MESSAGE);
                        }
                    });
                //                    } catch (final Exception ex) {
                //                        EventQueue.invokeLater (
                //                                new Runnable () {
                //                                    public void run () {
                //                                        JOptionPane.showMessageDialog(frame, "Fatal exception: " + ex.getMessage(),
                //                                                "Error reading file",
                //                                                JOptionPane.ERROR_MESSAGE);
                //                                    }
                //                                });
                }
            }
        };
        readThread.start();
    }
}

Example 8 with TraceException

use of dr.inference.trace.TraceException in project beast-mcmc by beast-dev.

the class SkylineReconstructor method main.

public static void main(String[] argv) {
    Variate x = null;
    List<Variate> plots = new ArrayList<Variate>();
    for (int i = 1; i <= 200; i++) {
        String stem = "sim" + (i < 10 ? "00" : (i < 100 ? "0" : "")) + i;
        try {
            SkylineReconstructor skyline = new SkylineReconstructor(new File(stem + ".log"), new File(stem + ".trees"), 1000000, 200, 0.0, 150000, 0.0);
            if (x == null) {
                x = skyline.getXData();
            }
            plots.add(skyline.getYDataMean());
        } catch (IOException e) {
            e.printStackTrace();
        } catch (ImportException e) {
            e.printStackTrace();
        } catch (TraceException e) {
            e.printStackTrace();
        }
        if (i % 10 == 0) {
            System.err.println("Read " + i);
        }
    }
    for (int i = 0; i < x.getCount(); i++) {
        System.out.print(x.get(i));
        for (Variate y : plots) {
            System.out.print("\t" + y.get(i));
        }
        System.out.println();
    }
}

Example 9 with TraceException

use of dr.inference.trace.TraceException in project beast-mcmc by beast-dev.

the class MarginalLikelihoodAnalysisParser method parseXMLObject.

public Object parseXMLObject(XMLObject xo) throws XMLParseException {
    String fileName = xo.getStringAttribute(FILE_NAME);
    try {
        File file = new File(fileName);
        String name = file.getName();
        String parent = file.getParent();
        if (!file.isAbsolute()) {
            parent = System.getProperty("user.dir");
        }
        file = new File(parent, name);
        fileName = file.getAbsolutePath();
        XMLObject cxo = xo.getChild(COLUMN_NAME);
        String likelihoodName = cxo.getStringAttribute(Attribute.NAME);
        LogFileTraces traces = new LogFileTraces(fileName, file);
        traces.loadTraces();
        long maxState = traces.getMaxState();
        // leaving the burnin attribute off will result in 10% being used
        long burnin = xo.getAttribute(BURN_IN, maxState / 10);
        if (burnin < 0 || burnin >= maxState) {
            burnin = maxState / 10;
            System.out.println("WARNING: Burn-in larger than total number of states - using to 10%");
        }
        traces.setBurnIn(burnin);
        int traceIndex = -1;
        for (int i = 0; i < traces.getTraceCount(); i++) {
            String traceName = traces.getTraceName(i);
            if (traceName.equals(likelihoodName)) {
                traceIndex = i;
                break;
            }
        }
        if (traceIndex == -1) {
            throw new XMLParseException("Column '" + likelihoodName + "' can not be found for " + getParserName() + " element.");
        }
        // Set analysisType
        String analysisType = "smoothed";
        boolean harmonicOnly = false;
        if (xo.hasAttribute(ONLY_HARMONIC))
            harmonicOnly = xo.getBooleanAttribute(ONLY_HARMONIC);
        if (harmonicOnly)
            analysisType = "harmonic";
        int bootstrapLength = cxo.getAttribute(BOOTSTRAP_LENGTH, 1000);
        List<Double> sample = traces.getValues(traceIndex);
        MarginalLikelihoodAnalysis analysis = new MarginalLikelihoodAnalysis(sample, traces.getTraceName(traceIndex), (int) burnin, analysisType, bootstrapLength);
        System.out.println(analysis.toString());
        return analysis;
    } catch (FileNotFoundException fnfe) {
        throw new XMLParseException("File '" + fileName + "' can not be opened for " + getParserName() + " element.");
    } catch (java.io.IOException ioe) {
        throw new XMLParseException(ioe.getMessage());
    } catch (TraceException e) {
        throw new XMLParseException(e.getMessage());
    }
}

Example 10 with TraceException

use of dr.inference.trace.TraceException in project beast-mcmc by beast-dev.

the class CoalGenFrame method readFromFile.

protected boolean readFromFile(final File file) throws IOException {
    try {
        final String fileName = file.getName();
        final ProgressMonitorInputStream in = new ProgressMonitorInputStream(this, "Reading " + fileName, new FileInputStream(file));
        //            final Reader reader = new InputStreamReader(in);
        final JFrame frame = this;
        // the monitored activity must be in a new thread.
        Thread readThread = new Thread() {

            public void run() {
                try {
                    final File file1 = new File(fileName);
                    final LogFileTraces traces = new LogFileTraces(fileName, file1);
                    traces.loadTraces(in);
                    EventQueue.invokeLater(new Runnable() {

                        public void run() {
                            data.logFile = file;
                            data.traces = traces;
                            fireTracesChanged();
                        }
                    });
                } catch (final TraceException tex) {
                    EventQueue.invokeLater(new Runnable() {

                        public void run() {
                            JOptionPane.showMessageDialog(frame, "Error reading trace file: " + tex, "Error reading trace file", JOptionPane.ERROR_MESSAGE);
                        }
                    });
                } catch (final InterruptedIOException iioex) {
                // The cancel dialog button was pressed - do nothing
                } catch (final IOException ioex) {
                    EventQueue.invokeLater(new Runnable() {

                        public void run() {
                            JOptionPane.showMessageDialog(frame, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
                        }
                    });
                } catch (final Exception ex) {
                    EventQueue.invokeLater(new Runnable() {

                        public void run() {
                            JOptionPane.showMessageDialog(frame, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
                        }
                    });
                }
            }
        };
        readThread.start();
    } catch (IOException ioex) {
        JOptionPane.showMessageDialog(this, "File I/O Error: " + ioex, "File I/O Error", JOptionPane.ERROR_MESSAGE);
        return false;
    } catch (Exception ex) {
        JOptionPane.showMessageDialog(this, "Fatal exception: " + ex, "Error reading file", JOptionPane.ERROR_MESSAGE);
        return false;
    }
    return true;
}