The simplest method to parse the whole MsmsPipelineAnalysis from a file.

@param path Path to the file
@return MsmsPipelineAnalysis
328402
public static MsmsPipelineAnalysis parse(Path path) throws FileParsingException {

    try {
      XMLStreamReader xsr = JaxbUtils.createXmlStreamReader(path, false);
      MsmsPipelineAnalysis msmsPipelineAnalysis = JaxbUtils
          .unmarshal(MsmsPipelineAnalysis.class, xsr);
      return msmsPipelineAnalysis;
    } catch (JAXBException e) {
      throw new FileParsingException(
          String
              .format("JAXB parsing of PepXML file failed (%s)", path.toAbsolutePath().toString()),
          e);
    }
  }
759569
public static String readAsString( String path ) {
		InputStream stream = openStream(path);
		if( stream == null ) {
			System.err.println("Failed to open "+path);
			return null;
		}
		return readAsString(stream);
	}
271872
private static String fileAsString(String path) throws Exception {
        StringBuffer buffer = new StringBuffer();
        InputStream fis = new FileInputStream(path);
        InputStreamReader isr = new InputStreamReader(fis, "UTF-8");
        Reader in = new BufferedReader(isr);
        int ch;
        while ((ch = in.read()) > -1) {
            buffer.append((char) ch);
        }
        in.close();
        return buffer.toString();
    }
1173005
public static PrototypeMeasurementFilter loadFromPath(String path) throws IOException {
    PrototypeMeasurementFilterSpecification spec =
        PrototypeMeasurementFilterSpecification.loadFromPath(path);
    return new PrototypeMeasurementFilter(spec);
  }
147510
public String getFullPath(String path) {

		if (StringUtils.isEmpty(pathPrefix)) {
			return path;
		}

		return PathNormalizer.asPath(pathPrefix + path);
	}
149160
public static String[] getPathComponents(String path) throws InvalidPathException {
    path = cleanPath(path);
    if (isRoot(path)) {
      return new String[]{""};
    }
    return path.split(AlluxioURI.SEPARATOR);
  }
1369623
public Certificate []getCertificates(String path)
  {
    if (! isSigned())
      return null;
    
    if (path.length() > 0 && path.charAt(0) == '/')
      path = path.substring(1);

    try {
      if (! getBacking().canRead())
        return null;
      
      JarFile jarFile = getJarFile();
      JarEntry entry;
      InputStream is = null;

      try {
        entry = jarFile.getJarEntry(path);

        if (entry != null) {
          is = jarFile.getInputStream(entry);

          while (is.skip(65536) > 0) {
          }

          is.close();

          return entry.getCertificates();
        }
      } finally {
        closeJarFile(jarFile);
      }
    } catch (IOException e) {
      log.log(Level.FINE, e.toString(), e);

      return null;
    }

    return null;
  }
1337677
public static String separatorsToSystem(final String path) {
        if (path == null) {
            return null;
        }
        if (IOUtil.IS_OS_WINDOWS) {
            return separatorsToWindows(path);
        } else {
            return separatorsToUnix(path);
        }
    }
46090
public PropertyPath parse(final String path) {
        
        ArgUtils.notEmpty(path, "path");
        
        final PropertyPath tokenStore = new PropertyPath(path);
        splitToken(tokenStore, path);
        return tokenStore;
    }
1268118
public static WorkspacePath parsePathInWorkspace( String path ) {
        // Extract the workspace name and absPath from the supplied path ...
        java.util.regex.Matcher pathMatcher = WORKSPACE_AND_PATH_PATTERN.matcher(path);
        if (!pathMatcher.matches()) {
            // No match ...
            return null;
        }
        String workspaceName = pathMatcher.group(2);
        String absolutePath = pathMatcher.group(3);
        if (workspaceName == null || workspaceName.length() == 0 || workspaceName.trim().length() == 0) workspaceName = null;
        return new WorkspacePath(workspaceName, absolutePath);
    }
1190589
public static long[] parseMetafileName(String path) {
    String[] groundSeparated = StringUtils.split(path, '_');
    if (groundSeparated.length != 3) { // blk, blkid, genstamp.meta
      throw new IllegalArgumentException("Not a valid meta file name");
    }
    String[] dotSeparated = StringUtils.split(groundSeparated[2], '.');
    if (dotSeparated.length != 2) {
      throw new IllegalArgumentException("Not a valid meta file name");
    }
    return new long[] { Long.parseLong(groundSeparated[1]),
        Long.parseLong(dotSeparated[0]) };
  }
1214319
public static String dirpart(final String path) {
        int s = path.lastIndexOf(File.separatorChar);
        if (s != -1) {
            return path.substring(0, s);
        } else {
            return null;
        } 
    }
1093136
public InputStream getResourceAsStream( String path ) {
        Object in = null;
        if ( externalClassLoader != null )
            // classloader wants no leading slash
            in = externalClassLoader.getResourceAsStream( path.substring(1) );
        if ( in == null )
            return Interpreter.class.getResourceAsStream( path );

        return (InputStream) in;
    }
1187728
public static Map<String, String> read(final String path) {

        Map<String, String> map = new HashMap<String, String>();

        if (path != null) {
            try {
                Properties p = loadProperties(path);

                for (Object key : p.keySet()) {

                    String value = p.getProperty(String.valueOf(key));

                    // remove single/double quotes
                    if ((value.startsWith("\"") && value.endsWith("\"")) ||
                            (value.startsWith("\'") && value.endsWith("\'"))) {
                        value = value.substring(1, value.length() - 1);
                    }

                    value = value.trim();

                    if (!value.equals("")) {
                        map.put(String.valueOf(key), value);
                    }
                }

            } catch (Exception e) {
                log.error(e.getMessage(), e);
            }
        }

        return map;
    }
896636
private String getSlaveIdFromCurrentUsagePath(String path) {
    return path.substring(path.indexOf(SLAVE_PATH) + SLAVE_PATH.length() + 1, path.lastIndexOf("/"));
  }
1243955
public void readData(String path) {
        jTextFieldResultsPath.setText(path);
        cleanTables();
        rf = new ReadFile(path);
        String str = rf.processFiles();
        if (str.equals("")) {
             algotithmID = rf.getAlgShortNames();
             algorithmNames = rf.getAlgNames();
             streamNames = rf.getStream();
            this.measures = rf.getMeasures();
            //Set algorithms an streams
            for (int i = 0; i < algotithmID.size(); i++) {
                this.algoritmModel.addRow(new Object[]{algorithmNames.get(i), algotithmID.get(i)});
            }
            streamNames.stream().forEach((streamName) -> {
                this.streamModel.addRow(new Object[]{streamName, streamName});
            });

            // set the measures into the combobox
            String measuresNames[] = measures.getFirst().split(",");
            jComboBoxMeasure.removeAllItems();
            for (String measuresName : measuresNames) {
                jComboBoxMeasure.addItem(measuresName);
            }

        }
55968
public void readData(String path) {
        reset();
        resetP();
        this.jTextFieldResultPath.setText(path);
        this.path = path;
        rf = new ReadFile(path);
        String str = rf.processFiles();
        if (str.equals("")) {

            int algSize = rf.getAlgShortNames().size();
            int streamSize = rf.getStream().size();
            this.measures = rf.getMeasures();
            for (int i = 0; i < algSize; i++) {
                this.algoritmModel.addRow(new Object[]{rf.getAlgNames().get(i), rf.getAlgShortNames().get(i)});
            }
            for (int i = 0; i < streamSize; i++) {
                this.streamModel.addRow(new Object[]{rf.getStream().get(i), rf.getStream().get(i)});
            }
            String measuresNames[] = measures.getFirst().split(",");
            for (String measuresName : measuresNames) {
                jComboBoxXColumn.addItem(measuresName);
                jComboBoxYColumn.addItem(measuresName);
                jComboBoxXColumnGnuP.addItem(measuresName);
                jComboBoxYColumnGnuP.addItem(measuresName);
                if (measuresName.equals("learning evaluation instances") == true) {
                    jComboBoxXColumn.setSelectedItem(measuresName);
                    jComboBoxXColumnGnuP.setSelectedItem(measuresName);
                }
                if (measuresName.equals("classifications correct (percent)") == true || measuresName.equals("[avg] classifications correct (percent)")) {
                    jComboBoxYColumn.setSelectedItem(measuresName);
                    jComboBoxYColumnGnuP.setSelectedItem(measuresName);
                }

            }
        } else {

            JOptionPane.showMessageDialog(this, str,
                    "Error", JOptionPane.ERROR_MESSAGE);
        }

    }