net.maizegenetics.util

Class Utils

net.maizegenetics.util.Utils

public class Utils

Method Detail

getBasename

public static java.lang.String getBasename(java.lang.String str)

Returns the base name of a string delimited with periods (i.e. Java Class).

Parameters:

str - string to parse

Returns:

org.jetbrains.dokka.NodeRenderContent@2bd45f25: base name

getFilename

public static java.lang.String getFilename(java.lang.String str)

This returns the filename only. Preceding directories are removed and everything after last . is removed.

Parameters:

str - original filename

Returns:

org.jetbrains.dokka.NodeRenderContent@6bf0332e: trimmed filename

getFilename

public static java.lang.String getFilename(java.lang.String str,
                                           java.lang.String suffix)

This returns the filename only. Preceding directories are removed and suffix. If suffix not found, then everything after last . is removed.

Parameters:

str - original filename

suffix - suffix

Returns:

org.jetbrains.dokka.NodeRenderContent@503db2d4: trimmed filename

getDirectory

public static java.lang.String getDirectory(java.lang.String str)

Returns just the directory with the filename removed.

Parameters:

str - original filename

Returns:

org.jetbrains.dokka.NodeRenderContent@3c788dbb: directory

getFullyQualifiedResourceNames

public static java.util.Set<java.lang.String> getFullyQualifiedResourceNames(java.lang.String filename)

This returns a set of fully qualified resource names that match the specified filename.

Parameters:

filename - filename

Returns:

org.jetbrains.dokka.NodeRenderContent@355cd066: set of resource names

getFullyQualifiedClassNames

public static java.util.List<java.lang.String> getFullyQualifiedClassNames(java.lang.String simpleName)

getJavaPackages

public static java.util.Collection<java.lang.String> getJavaPackages()

getPackagesFromClassPath

public static java.util.Set<java.lang.String> getPackagesFromClassPath(java.lang.String classpath)

getTasselClasses

public static java.util.Set<java.lang.String> getTasselClasses()

readDirectory

public static java.util.Set<java.lang.String> readDirectory(java.lang.String path)

recursiveRead

public static void recursiveRead(java.io.File file,
                                 int startIndex,
                                 java.util.Set<java.lang.String> packages)

readZipFile

public static java.util.Set<java.lang.String> readZipFile(java.lang.String path)

shortenStrLineLen

public static java.lang.String shortenStrLineLen(java.lang.String str,
                                                 int preferredLen)

shortenStrLineLen

public static java.lang.String shortenStrLineLen(java.lang.String str,
                                                 int preferredLen,
                                                 int preferredLines)

addSuffixIfNeeded

public static java.lang.String addSuffixIfNeeded(java.lang.String filename,
                                                 java.lang.String suffix)

Adds suffix (i.e. .txt) to end of filename if it's not already there.

Parameters:

filename - filename

suffix - suffix

Returns:

org.jetbrains.dokka.NodeRenderContent@5f5ffca0: filename with suffix

addGzSuffixIfNeeded

public static java.lang.String addGzSuffixIfNeeded(java.lang.String filename,
                                                   java.lang.String suffix)

addSuffixIfNeeded

public static java.lang.String addSuffixIfNeeded(java.lang.String filename,
                                                 java.lang.String defaultSuffix,
                                                 java.lang.String[] possible)

Adds default suffix if not already one of the possible suffixes.

Parameters:

filename - filename

defaultSuffix - default suffix

possible - possible suffixes

Returns:

org.jetbrains.dokka.NodeRenderContent@62494e8d: filename with suffix

getBufferedReader

public static java.io.BufferedReader getBufferedReader(java.lang.String inSourceName)

getBufferedReader

public static java.io.BufferedReader getBufferedReader(java.lang.String inSourceName,
                                                       int bufSize)

getBufferedReader

public static java.io.BufferedReader getBufferedReader(java.io.File file,
                                                       int bufSize)

lines

public static java.util.stream.Stream<java.lang.String> lines(java.nio.file.Path path,
                                                              int bufSize)

Read all lines from a file as a Stream. Unlike Path.readAllLines, this method does not read all lines into a List, but instead populates lazily as the stream is consumed.

Bytes from the file are decoded into characters using the specified charset and the same line terminators as specified by readAllLines are supported.

After this method returns, then any subsequent I/O exception that occurs while reading from the file or when a malformed or unmappable byte sequence is read, is wrapped in an java.io.UncheckedIOException that will be thrown from the java.util.stream.Stream method that caused the read to take place. In case an IOException is thrown when closing the file, it is also wrapped as an UncheckedIOException.

The returned stream encapsulates a java.io.Reader. If timely disposal of file system resources is required, the try-with-resources construct should be used to ensure that the stream's close method is invoked after the stream operations are completed.

Parameters:

path - the path to the file

Returns:

org.jetbrains.dokka.NodeRenderContent@1aa4122a: the lines from the file as a Stream

Throws:

IOException - if an I/O error occurs opening the file

SecurityException - In the case of the default provider, and a security manager is installed, the checkRead method is invoked to check read access to the file

getBufferedWriter

public static java.io.BufferedWriter getBufferedWriter(java.lang.String filename)

getBufferedWriter

public static java.io.BufferedWriter getBufferedWriter(java.lang.String filename,
                                                       boolean append)

getBufferedWriter

public static java.io.BufferedWriter getBufferedWriter(java.io.File file)

getBufferedWriter

public static java.io.BufferedWriter getBufferedWriter(java.io.File file,
                                                       boolean append)

getDataOutputStream

public static java.io.DataOutputStream getDataOutputStream(java.lang.String filename,
                                                           int bufSize)

findNthOccurrenceInString

public static int findNthOccurrenceInString(java.lang.String str,
                                            char match,
                                            int n)

Finds index of Nth occurrence of character in string.

Parameters:

str - string

match - character to match

n - Nth occurrence

Returns:

org.jetbrains.dokka.NodeRenderContent@49a82ef8: index

getMaxHeapSizeMB

public static long getMaxHeapSizeMB()

Returns max heap size in MB.

Returns:

org.jetbrains.dokka.NodeRenderContent@69b27191: max heap size

getInputStream

public static java.io.InputStream getInputStream(java.lang.String filename)

Gets input stream for given file.

Parameters:

filename - file name

Returns:

org.jetbrains.dokka.NodeRenderContent@4127670c: input stream

getBufferedOutputStream

public static java.io.BufferedOutputStream getBufferedOutputStream(java.lang.String filename)

getNumberLines

public static int getNumberLines(java.lang.String filename)

Return number of lines in given file.

Parameters:

filename - file name

Returns:

org.jetbrains.dokka.NodeRenderContent@7b280840: number of lines

getNumberLinesNotHashOrBlank

public static int getNumberLinesNotHashOrBlank(java.lang.String filename)

Return number of lines in given file that doesn't begin with Hash (#) and isn't blank.

Parameters:

filename - file name

Returns:

org.jetbrains.dokka.NodeRenderContent@737f2633: number of lines

readLineSkipComments

public static java.lang.String readLineSkipComments(java.io.BufferedReader br)