Example usage for com.google.common.io LittleEndianDataInputStream readDouble

Introduction

In this page you can find the example usage for com.google.common.io LittleEndianDataInputStream readDouble.

Prototype

@Override
public double readDouble() throws IOException 

Source Link

Document

Reads a double as specified by DataInputStream#readDouble() , except using little-endian byte order.

Usage

From source file:xyz.kuori.timeseries.TimeSeries.java

public int load(File archive) {
    FileInputStream fin = null;/*  w w w.  j  a  v  a 2  s . com*/

    try {
        fin = new FileInputStream(archive);
    } catch (Exception e) {
        init(0);
        return (-1);
    }

    int record_count = (int) (archive.length() / 16);
    init(record_count);

    LittleEndianDataInputStream in = new LittleEndianDataInputStream(fin);

    try {
        for (int i = 0; i < record_count; i++) {
            timestamps[i] = in.readLong();
            values[i] = in.readDouble();
        }
    } catch (Exception e) {
        init(0);
        return (-1);
    }

    return (record_count);
}

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From source file:net.sf.mzmine.modules.rawdatamethods.rawdataimport.fileformats.XcaliburRawFileReadTask.java

/**
 * This method reads the dump of the RAW data file produced by RAWdump.exe
 * utility (see RAWdump.cpp source for details).
 *//*from ww w. j a va2  s .co  m*/
private void readRAWDump(InputStream dumpStream) throws IOException {

    String line;
    while ((line = TextUtils.readLineFromStream(dumpStream)) != null) {

        if (isCanceled()) {
            return;
        }

        if (line.startsWith("ERROR: ")) {
            throw (new IOException(line.substring("ERROR: ".length())));
        }

        if (line.startsWith("NUMBER OF SCANS: ")) {
            totalScans = Integer.parseInt(line.substring("NUMBER OF SCANS: ".length()));
        }

        if (line.startsWith("SCAN NUMBER: ")) {
            scanNumber = Integer.parseInt(line.substring("SCAN NUMBER: ".length()));
        }

        if (line.startsWith("SCAN FILTER: ")) {

            /*
             * A typical filter line for MS/MS scan looks like this:
             * 
             * ITMS - c ESI d Full ms3 587.03@cid35.00 323.00@cid35.00
             */
            Pattern p = Pattern.compile("ms(\\d).* (\\d+\\.\\d+)@");
            Matcher m = p.matcher(line);
            if (m.find()) {
                msLevel = Integer.parseInt(m.group(1));

                // Initially we obtain precursor m/z from this filter line,
                // even though the precision is not good. Later more precise
                // precursor m/z may be reported using PRECURSOR: line, but
                // sometimes it is missing (equal to 0)
                precursorMZ = Double.parseDouble(m.group(2));
            } else {
                msLevel = 1;
            }

        }

        if (line.startsWith("RETENTION TIME: ")) {
            // Retention time in the RAW file is reported in minutes.
            retentionTime = Double.parseDouble(line.substring("RETENTION TIME: ".length()));
        }

        if (line.startsWith("PRECURSOR: ")) {
            String tokens[] = line.split(" ");
            double token2 = Double.parseDouble(tokens[1]);
            int token3 = Integer.parseInt(tokens[2]);
            if (token2 > 0) {
                precursorMZ = token2;
                precursorCharge = token3;
            }
        }

        if (line.startsWith("DATA POINTS: ")) {
            int numOfDataPoints = Integer.parseInt(line.substring("DATA POINTS: ".length()));

            DataPoint completeDataPoints[] = new DataPoint[numOfDataPoints];

            // Because Intel CPU is using little endian natively, we
            // need to use LittleEndianDataInputStream instead of normal
            // Java DataInputStream, which is big-endian.
            LittleEndianDataInputStream dis = new LittleEndianDataInputStream(dumpStream);
            for (int i = 0; i < numOfDataPoints; i++) {
                double mz = dis.readDouble();
                double intensity = dis.readDouble();
                completeDataPoints[i] = new SimpleDataPoint(mz, intensity);
            }
            dis.close();

            boolean centroided = ScanUtils.isCentroided(completeDataPoints);

            DataPoint optimizedDataPoints[] = ScanUtils.removeZeroDataPoints(completeDataPoints, centroided);

            /*
             * If this scan is a full scan (ms level = 1), it means that the
             * previous scans stored in the stack, are complete and ready to
             * be written to the raw data file.
             */
            if (msLevel == 1) {
                while (!parentStack.isEmpty()) {
                    SimpleScan currentScan = parentStack.removeFirst();
                    newMZmineFile.addScan(currentScan);
                }
            }

            // Setting the current parentScan
            int parentScan = -1;
            if (msLevel > 1) {
                parentScan = parentTreeValue[msLevel - 1];

                if (!parentStack.isEmpty()) {
                    for (SimpleScan s : parentStack) {
                        if (s.getScanNumber() == parentScan) {
                            s.addFragmentScan(scanNumber);
                        }
                    }
                }
            }

            // Setting the parent scan number for this level of fragments
            parentTreeValue[msLevel] = scanNumber;

            SimpleScan newScan = new SimpleScan(null, scanNumber, msLevel, retentionTime, parentScan,
                    precursorMZ, precursorCharge, null, optimizedDataPoints, centroided);

            parentStack.add(newScan);
            parsedScans++;

            // Clean the variables for next scan
            scanNumber = 0;
            msLevel = 0;
            retentionTime = 0;
            precursorMZ = 0;
            precursorCharge = 0;

        }

    }

    // Add remaining scans in the parentStack
    while (!parentStack.isEmpty()) {
        SimpleScan currentScan = parentStack.removeFirst();
        newMZmineFile.addScan(currentScan);
    }

}

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