Package com.biomatters.geneious.publicapi.utilities

Class FileUtilities

  • public class FileUtilities
extends java.lang.Object
    Provides utility methods for dealing with files.

    • Nested Class Summary

      Nested Classes 
      Modifier and Type Class Description
      static class  FileUtilities.RetryPolicy
      Specifies a policy about what to do if a file action (e.g.
      static class  FileUtilities.TargetExistsAction
      The action to take when moving/copying files and the target already exists

    • Field Summary

      Fields 
      Modifier and Type Field Description
      static int MAX_FILENAME_LENGTH
      Maximum allowed filename (just name, excluding path) length on the operating systems supported by Geneious.

    • Method Summary

      All Methods Static Methods Concrete Methods Deprecated Methods 
      Modifier and Type Method Description
      static void copyDirectory​(java.io.File sourceDirectory, java.io.File destinationDirectory, boolean overwrite, jebl.util.ProgressListener progressListener)
      Recursively copies the entire contents of one directory to another.
      static void copyFile​(java.io.File sourceFile, java.io.File destinationFile, FileUtilities.TargetExistsAction targetExistsAction, jebl.util.ProgressListener progressListener)
      Copies the contents of a file to another file If canceled in the middle of the copy (so that the destination file is partially written), the destination file will be deleted.
      static boolean createHardLink​(java.io.File existingFile, java.io.File newFile)
      Creates a file system hard link.
      static java.io.File createTempDir​(boolean deleteDirectoryOnceItIsNoLongerReferenced)
      Creates a temporary directory.
      static java.io.File createTempFile​(java.lang.String fileName, boolean deleteFileAndParentFolderWhenFileIsNoLongerReferenced)
      Returns a temporary file with the given name.
      static java.io.File createTempFile​(java.lang.String prefix, java.lang.String suffix)
      Deprecated.
      use createTempFile(String, String, boolean) instead.
      static java.io.File createTempFile​(java.lang.String prefix, java.lang.String suffix, boolean deleteFileOnceItIsNoLongerReferenced)
      Creates a temporary file as specified by File.createTempFile(String, String, java.io.File).
      static boolean deleteDirectory​(java.io.File path, jebl.util.ProgressListener progressListener)
      Recursively deletes a directory.
      static boolean deleteFileOrDirectory​(java.io.File file, boolean retryIfNecessary)
      Deletes the given file or directory.
      static boolean deleteFileOrDirectory​(java.io.File file, FileUtilities.RetryPolicy retryPolicy)
      Deletes the given file or directory.
      static java.lang.String getCanonicalOrAbsolutePath​(java.io.File file)
      Returns the result of calling File.getCanonicalPath(), or if that fails, returns the result of calling File.getAbsolutePath() .
      static java.lang.String getFileNameExtension​(java.io.File file)
      Get the extension of a file name.
      static java.lang.String getFileNameWithoutExtension​(java.io.File file)
      Get the name of a file, excluding its path, excluding its extension and excluding the '.' prior to its extension.
      static long getFileOrFolderSize​(java.io.File file, jebl.util.ProgressListener progressListener)
      If file is not a directory this returns File.length(), if file is a directory this recurses through all files in the directory and sub directories to return the sum of File.length()s.
      static java.lang.String getLegalFileName​(java.lang.String fileName, java.lang.String illegalCharacterReplacement)
      Get a file name that is guaranteed to be legal by replacing all characters in the given string that are not allowed in a file name with the given replacement.
      static java.io.File getResourceForClass​(java.lang.Class cl, java.lang.String resourceName)
      for grabbing resources based on a directory hirarchy identical to the one that the class cl is found in.
      static java.lang.String getTextFromFile​(java.io.File file)
      Reads the entire contents of a file into a string.
      static java.lang.String getTextFromFile​(java.io.File file, int maxCharactersToRead)
      Reads the contents of a file into a string, but at most maxCharactersToRead.
      static java.io.File getUserSelectedFile​(java.lang.String title, java.io.FilenameFilter filter, int fileSelectionType)
      Displays a file open dialog to the user (a Java dialog on windows and unix, a Mac dialog on MacOS), and returns the file that the user selected (or null if they cancelled)
      static java.io.File getUserSelectedSaveFile​(java.lang.String approveButtonText, java.lang.String title, java.lang.String defaultFileName, java.lang.String defaultFilterExtension)
      Displays a file save dialog to the user (a Java dialog on windows and unix, a Mac dialog on MacOS), and returns the file that the user selected (or null if they cancelled)
      static java.lang.String isFileNameAllowed​(java.lang.String fileName)
      Will check a filename for validity on all platforms supported by Geneious.
      static java.io.FileInputStream newFileInputStreamWithRetry​(java.io.File file)
      Attempts to create a new FileInputStream, but if it fails, retries a few times until it succeeds.
      static java.io.FileOutputStream newFileOutputStreamWithRetry​(java.io.File file)
      Attempts to create a new FileOutputStream, but if it fails with a FileNotFoundException, retries a few times until it succeeds.
      static java.io.RandomAccessFile newRandomAccessFileWithRetry​(java.io.File file, java.lang.String mode)
      Attempts to create a new RandomAccessFile, but if it fails, retries a few times until it succeeds.
      static boolean renameToWithRetry​(java.io.File source, java.io.File destination)
      Similar to File.renameTo(java.io.File) except that if the rename fails, we retry a few times (performing garbage collections and sleeping briefly between attempts) if necessary until it succeeds, potentially waiting for up to approximately 1 second.
      static void setExecutableFlags​(java.io.File file)
      Set the executable flag on a file, or do nothing if the OS does not support this behaviour Since Geneious 5.1.2 will accept a directory as argument to world execute on the entire directory tree A symlink pointing to a file that is not already executable will cause an IOException to be thrown All other symlinks are ignored after attempting to resolve them
      static void unzip​(java.io.File zipFile, java.io.File destinationDirectory, jebl.util.ProgressListener progressListener)
      Extract a zip file.
      static void writeTextToFile​(java.io.File file, java.lang.String text)
      Writes the given text to a file, overwriting any existing contents of the file.
      static void zip​(java.io.File fileOrDirectory, java.io.File zipFile, boolean includeRootDirectory, jebl.util.ProgressListener progressListener)
      Create a compressed zip containing a file or directory.
      static void zipWithoutCompression​(java.io.File fileOrDirectory, java.io.File zipFile, boolean includeRootDirectory, jebl.util.ProgressListener progressListener)
      Create a zip containing a file or directory without any compression.

      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    • Field Detail

      • MAX_FILENAME_LENGTH

        public static final int MAX_FILENAME_LENGTH
        Maximum allowed filename (just name, excluding path) length on the operating systems supported by Geneious.
        Since:
        API 4.202010 (Geneious Prime 2020.1.0)
        See Also:
        Constant Field Values

    • Method Detail

      • isFileNameAllowed

        public static java.lang.String isFileNameAllowed​(java.lang.String fileName)
        Will check a filename for validity on all platforms supported by Geneious. eg. checks for illegal filename characters and length.
        Parameters:
        fileName - the name of a file excluding the path. must not be null
        Returns:
        null if filename is valid or a message describing why it is invalid if it is not valid.

      • getLegalFileName

        public static java.lang.String getLegalFileName​(java.lang.String fileName,
                                                java.lang.String illegalCharacterReplacement)
        Get a file name that is guaranteed to be legal by replacing all characters in the given string that are not allowed in a file name with the given replacement. If the name has an illegal extension or if the name itself is illegal then '1' will be appended to the name to make it legal.
        Parameters:
        fileName - file name to make legal
        illegalCharacterReplacement - string to replace every occurrence of an illegal character with
        Returns:
        a guaranteed legal version of the file name or the unmodified fileName if the name was already legal.

      • getFileNameWithoutExtension

        public static java.lang.String getFileNameWithoutExtension​(java.io.File file)
        Get the name of a file, excluding its path, excluding its extension and excluding the '.' prior to its extension. If the file has no extension, the file name (excluding its path) is returned.
        Parameters:
        file - the file to get the name for
        Returns:
        the name of a file, excluding its path, excluding its extension and excluding the '.' prior to its extension.

      • getFileNameExtension

        public static java.lang.String getFileNameExtension​(java.io.File file)
        Get the extension of a file name. This is the suffix of the file name after the last '.'
        Parameters:
        file - the file to get the extension for
        Returns:
        the extension of the file name excluding the '.'. If the file has no extension returns an empty string.

      • writeTextToFile

        public static void writeTextToFile​(java.io.File file,
                                   java.lang.String text)
                            throws java.io.IOException
        Writes the given text to a file, overwriting any existing contents of the file.
        Parameters:
        file - the file to write to.
        text - the text to write to the file
        Throws:
        java.io.IOException - if any method calls to the File throw an IOException
        See Also:
        getTextFromFile(java.io.File)

      • copyFile

        public static void copyFile​(java.io.File sourceFile,
                            java.io.File destinationFile,
                            FileUtilities.TargetExistsAction targetExistsAction,
                            jebl.util.ProgressListener progressListener)
                     throws java.io.IOException
        Copies the contents of a file to another file If canceled in the middle of the copy (so that the destination file is partially written), the destination file will be deleted. Note that in this case, a previously existing destinationFile will be erased if targetExistsAction == Overwrite.
        Parameters:
        sourceFile - the file to copy the contents from
        destinationFile - the file to copy the contents to
        targetExistsAction - action to take when the destination file already exists: Fail (throw an IOException), skip (silently keep the destination file), overwrite (silently copy anyway, overwriting the destination file)
        progressListener - a progress listener to notify about progress during the copy and also provide the ability to cancel the copy. If the copy is cancelled, any partially written destination file will be removed. Must not be null, but may be ProgressListener.EMPTY.
        Throws:
        java.io.IOException - if the file cannot be copied for any reason.

      • copyDirectory

        public static void copyDirectory​(java.io.File sourceDirectory,
                                 java.io.File destinationDirectory,
                                 boolean overwrite,
                                 jebl.util.ProgressListener progressListener)
                          throws java.io.IOException
        Recursively copies the entire contents of one directory to another. Note: ignores .cvs and .svn directories. If canceled, this method does not restore the destination to its original state.
        Parameters:
        sourceDirectory - the directory to copy the contents of
        destinationDirectory - the directly to copy the contents to
        overwrite - true to overwrite files of the same name that exist in the desitination directory.
        progressListener - ProgressListener to report progress of the copying to. If the progressListener is canceled, this method does not restore the destination to its original state. Must not be null, but may be ProgressListener.EMPTY.
        Throws:
        java.io.IOException - if the directory cannot be copied for any reason.
        java.lang.IllegalArgumentException - if sourceDirectory is not a directory.

      • getFileOrFolderSize

        public static long getFileOrFolderSize​(java.io.File file,
                                       jebl.util.ProgressListener progressListener)
        If file is not a directory this returns File.length(), if file is a directory this recurses through all files in the directory and sub directories to return the sum of File.length()s.
        Parameters:
        file - a directory or file to calculate the size of
        progressListener - since this method may potentially take a long time, this may be used to abort this method in which case it returns the total size calculated so far. This method does not report any progress (rather it only reports to the progressListeners message the size calculated so far and uses it for determining whether to cancel). progressListener may be null.
        Returns:
        total size of file or all contained files for a directory.

      • zip

        public static void zip​(java.io.File fileOrDirectory,
                       java.io.File zipFile,
                       boolean includeRootDirectory,
                       jebl.util.ProgressListener progressListener)
                throws java.io.IOException
        Create a compressed zip containing a file or directory.
        Parameters:
        fileOrDirectory - a file or directory to be compressed
        zipFile - the target zip file. will be created if doesn't exist, will be replaced if already exists
        includeRootDirectory - true to include fileOrDirectory in the zip file, false to only include the contents of fileOrDirectory. Only applicable when a directory is passed in, ignored otherwise.
        progressListener - allows canceling and progress reporting
        Throws:
        java.io.IOException - if the zip file couldn't be written for any reason
        Since:
        API 4.14 (Geneious 5.1)

      • zipWithoutCompression

        public static void zipWithoutCompression​(java.io.File fileOrDirectory,
                                         java.io.File zipFile,
                                         boolean includeRootDirectory,
                                         jebl.util.ProgressListener progressListener)
                                  throws java.io.IOException
        Create a zip containing a file or directory without any compression. Same as zip(java.io.File, java.io.File, boolean, jebl.util.ProgressListener) except much faster and zip file will be larger.
        Parameters:
        fileOrDirectory - a file or directory to be compressed
        zipFile - the target zip file. will be created if doesn't exist, will be replaced if already exists
        includeRootDirectory - true to include fileOrDirectory in the zip file, false to only include the contents of fileOrDirectory. Only applicable when a directory is passed in, ignored otherwise.
        progressListener - allows canceling and progress reporting
        Throws:
        java.io.IOException - if the zip file couldn't be written for any reason
        Since:
        API 4.51 (Geneious 5.5.1)

      • unzip

        public static void unzip​(java.io.File zipFile,
                         java.io.File destinationDirectory,
                         jebl.util.ProgressListener progressListener)
                  throws java.io.IOException
        Extract a zip file.
        Parameters:
        zipFile - the zip file to be extracted
        destinationDirectory - the directory to extract the contents of the zip file to
        progressListener - allows canceling and progress reporting
        Throws:
        java.io.IOException - if extracted files couldn't be written for any reason
        Since:
        API 4.14 (Geneious 5.1)

      • deleteDirectory

        public static boolean deleteDirectory​(java.io.File path,
                                      jebl.util.ProgressListener progressListener)
        Recursively deletes a directory. Unlike File.delete() this method will remove non-empty directories.
        Parameters:
        path - the directory to delete
        progressListener - ProgressListener to report progress of the deletion to. If the progressListener is canceled, this method does not restore any already deleted files or sub-directories. Must not be null, but may be ProgressListener.EMPTY.
        Returns:
        true if and only if the directory was successfully deleted. In keeping with the File.delete() contract, this means this method will return false if the directory did not previously exist.

      • renameToWithRetry

        public static boolean renameToWithRetry​(java.io.File source,
                                        java.io.File destination)
        Similar to File.renameTo(java.io.File) except that if the rename fails, we retry a few times (performing garbage collections and sleeping briefly between attempts) if necessary until it succeeds, potentially waiting for up to approximately 1 second. This is a workaround for Java bug 6213298 at http://bugs.sun.com/view_bug.do?bug_id=6213298
        Parameters:
        source - the file or directory to rename
        destination - the new name for the source file.
        Returns:
        true if and only if the renaming succeeded; false otherwise (just like File.renameTo(java.io.File) )

      • setExecutableFlags

        public static void setExecutableFlags​(java.io.File file)
                               throws java.io.IOException,
                                      java.lang.InterruptedException
        Set the executable flag on a file, or do nothing if the OS does not support this behaviour Since Geneious 5.1.2 will accept a directory as argument to world execute on the entire directory tree A symlink pointing to a file that is not already executable will cause an IOException to be thrown All other symlinks are ignored after attempting to resolve them
        Parameters:
        file - file or directory to set permissions for
        Throws:
        java.lang.InterruptedException - if something interrupts the process setting the permissions
        java.io.IOException - if something else goes wrong

      • getCanonicalOrAbsolutePath

        public static java.lang.String getCanonicalOrAbsolutePath​(java.io.File file)
        Returns the result of calling File.getCanonicalPath(), or if that fails, returns the result of calling File.getAbsolutePath() .
        Parameters:
        file - the file to get the canonical or absolute path of.
        Returns:
        the result of calling File.getCanonicalPath(), or if that fails, returns the result of calling File.getAbsolutePath() .

      • deleteFileOrDirectory

        public static boolean deleteFileOrDirectory​(java.io.File file,
                                            boolean retryIfNecessary)
        Deletes the given file or directory.
        Parameters:
        file - the file or directory to delete.
        retryIfNecessary - true to retry a few times for up to approximately a second to delete the file if it can't be deleted the first time, performing garbage collection and sleeping briefly between attempts
        Returns:
        true if the file exists and was deleted. true if the file did not exist. false if the file or directory exists and we cannot delete it.

      • deleteFileOrDirectory

        public static boolean deleteFileOrDirectory​(java.io.File file,
                                            FileUtilities.RetryPolicy retryPolicy)
        Deletes the given file or directory.
        Parameters:
        file - the file or directory to delete.
        retryPolicy - if the file can't be deleted, indicates what to do. If it is RetryPolicy.Never returns false. If it is RetryPolicy.Now a few attempts are immediately made to delete the file. If it is RetryPolicy.Later, this method returns false, the file will be queued, and it will attempts to delete it will be made periodically until successful.
        Returns:
        true if the file exists and was deleted. true if the file did not exist. false if the file or directory exists and we cannot delete it.
        Since:
        API 4.40 (Geneious 5.4.0)

      • getUserSelectedFile

        public static java.io.File getUserSelectedFile​(java.lang.String title,
                                               java.io.FilenameFilter filter,
                                               int fileSelectionType)
        Displays a file open dialog to the user (a Java dialog on windows and unix, a Mac dialog on MacOS), and returns the file that the user selected (or null if they cancelled)
        Parameters:
        title - the title of the file dialog
        filter - to filter the files displayed in the dialog
        fileSelectionType - either JFileChooser.FILES_AND_DIRECTORIES, JFileChooser.FILES_ONLY, or JFileChooser.DIRECTORIES_ONLY
        Returns:
        the file that the user selected (or null if they cancelled)

      • getUserSelectedSaveFile

        public static java.io.File getUserSelectedSaveFile​(java.lang.String approveButtonText,
                                                   java.lang.String title,
                                                   java.lang.String defaultFileName,
                                                   java.lang.String defaultFilterExtension)
        Displays a file save dialog to the user (a Java dialog on windows and unix, a Mac dialog on MacOS), and returns the file that the user selected (or null if they cancelled)
        Parameters:
        title - the title of the file dialog
        defaultFileName - the default name for the file (this will be entered into the file dialog when it first opens)
        defaultFilterExtension - the default extension for the file filter
        Returns:
        the file that the user selected (or null if they cancelled)
        Since:
        API 4.14 (Geneious 5.1)

      • createTempFile

        public static java.io.File createTempFile​(java.lang.String prefix,
                                          java.lang.String suffix,
                                          boolean deleteFileOnceItIsNoLongerReferenced)
                                   throws java.io.IOException
        Creates a temporary file as specified by File.createTempFile(String, String, java.io.File). If Geneious is running when this method is invoked, Geneious will supply a temporary directory in the user's data directory which will have its contents deleted when Geneious is next started. If Geneious is not running when this method is invoked, the standard system temporary directory is used.

        It is preferable to use this method rather than File.createTempFile(String, String, java.io.File) because

        • If the machine or Geneious terminates before the code deletes the temporary file, with File.createTempFile the temporary file may never get deleted. With Geneious the temporary file will be deleted on the next start up of Geneious.
        • We have had reports of very slow performance when Geneious uses File.createTempFile. This occurs when the user has 100,000+ files in their system temp folder.
        • File.createTempFile may create files readable by any user in the system temp folder which is not desirable for sensitive data.

        If deleteFileOnceItIsNoLongerReferenced is true, then the returned file will be automatically deleted once the returned File or the String obtained from File.getPath() or File.toString() are no longer referenced in this JVM. The returned file will already have had its path canonicalized (via File.getCanonicalPath()) so there is no need to call that method on the returned file and doing so will not hold a reference to the given file potentially causing it to be deleted early. No matter what the value of deleteFileOnceItIsNoLongerReferenced, the file will be deleted if it still exists when the user next starts Geneious. Do not set this to true for files passed to external command line programs or the file may end up getting deleted before the external command line program accesses it.

        The user may change their data directory from preferences while Geneious is running, so plugins should not assume the path of the returned file to necessarily be the same from separate calls to this method.

        Parameters:
        prefix - - The prefix string to be used in generating the file's name; must be at least three characters long
        suffix - - The suffix string to be used in generating the file's name; may be null, in which case the suffix ".tmp" will be used
        deleteFileOnceItIsNoLongerReferenced - - see above. use false to make this method behave like File.createTempFile(String, String, java.io.File). WARNING: do not set this to true for files passed to external command line programs or the file may end up getting deleted before the external command line program accesses it.
        Returns:
        a file that will be automatically deleted when the given file object (or it's path) are no longer referenced.
        Throws:
        java.io.IOException - If a file could not be created
        Since:
        API 4.14 (Geneious 5.1)

      • createTempFile

        public static java.io.File createTempFile​(java.lang.String fileName,
                                          boolean deleteFileAndParentFolderWhenFileIsNoLongerReferenced)
                                   throws java.io.IOException
        Returns a temporary file with the given name. This file will be created in a newly created sub-folder of the temp folder and the file is guaranteed to have the given name unlike createTempFile(String, String, boolean) which only allows specifying the prefix or suffix
        Parameters:
        fileName - the name of the file to return
        deleteFileAndParentFolderWhenFileIsNoLongerReferenced - true to delete the parent sub-folder and everything in it once this file is no longer referenced.
        Returns:
        a temporary file
        Throws:
        java.io.IOException - If a file or directory could not be created
        Since:
        API 4.700 (Geneious 7.0.0)

      • createTempDir

        public static java.io.File createTempDir​(boolean deleteDirectoryOnceItIsNoLongerReferenced)
                                  throws java.io.IOException
        Creates a temporary directory. If Geneious is running when this method is invoked, the parent directory of the returned temp directory will be the user's data directory which will have its contents deleted when Geneious is next started. If Geneious is not running when this method is invoked, the temp directory is created inside the standard system temporary directory.

        If deleteDirectoryOnceItIsNoLongerReferenced is true, then the returned directory will be automatically deleted once the returned File or the String obtained from File.getPath() or File.toString() are no longer referenced, even if there are still referenced files within that directory. The returned directory will already have had its path made canonical (via File.getCanonicalPath()) so there is no need to call that method on the returned file and doing so will not hold a reference to the given directory potentially causing it to be deleted early. No matter what the value of deleteDirectoryOnceItIsNoLongerReferenced, the directory will be deleted if it still exists when the user next starts Geneious.

        The user may change their data directory from preferences while Geneious is running, so plugins should not assume the path of the returned directory to necessarily be the same from separate calls to this method.

        Parameters:
        deleteDirectoryOnceItIsNoLongerReferenced - - see above.
        Returns:
        a File that will be automatically deleted when the given File object (or it's path) are no longer referenced.
        Throws:
        java.io.IOException - If a file could not be created
        Since:
        API 4.60 (Geneious 5.6.0)

      • createHardLink

        public static boolean createHardLink​(java.io.File existingFile,
                                     java.io.File newFile)
        Creates a file system hard link. Not all file systems support hard links. For example on a Windows platform, NTFS does support hard links, but FAT32 doesn't.

        A hard link has the effect of creating multiple names for the same file, causing an aliasing effect: if the file is opened by one of its names, and changes are made to its content, then these changes will also be visible when the file is opened by an alternative name. A file is not removed from the file system until all names it is known by are deleted.

        Windows has unusual and very annoying behaviour when dealing with hard links. Consider a file called file1.txt with a hard link called file2.txt to it. Then while anything has file2.txt open, attempts to delete file1.txt will fail. More annoyingly, if 1 thread is in the process of deleting file1, another thread that tries to open file2 for reading may fail with a "The process cannot access the file because it is being used by another process" error. Waiting a fraction of a second and trying again generally fixes this, so it is recommended that any code that tries to open a file that has been hard linked to, or has had a hard link to it created, it should use newRandomAccessFileWithRetry(java.io.File, String) or newFileInputStreamWithRetry(java.io.File)

        Parameters:
        existingFile - a currently existing file to link to
        newFile - the new file to create which should link to the existing file
        Returns:
        true if the link is successfully created. false if not or if this thread is interrupted while attempting to create the hard link or if there is a timout creating the hard link
        Since:
        API 4.40 (Geneious 5.4.0)

      • newRandomAccessFileWithRetry

        public static java.io.RandomAccessFile newRandomAccessFileWithRetry​(java.io.File file,
                                                                    java.lang.String mode)
                                                             throws java.io.FileNotFoundException
        Attempts to create a new RandomAccessFile, but if it fails, retries a few times until it succeeds. This is recommended if you attempt to open files that have been created as hard links or have had hard links to them created. See createHardLink(java.io.File, java.io.File)
        Parameters:
        file - the file to open
        mode - the access mode. See RandomAccessFile(java.io.File, String)
        Returns:
        a new RandomAccessFile
        Throws:
        java.io.FileNotFoundException - if RandomAccessFile(java.io.File, String) still throws a FileNotFoundException after a few attempts
        Since:
        API 4.40 (Geneious 5.4.0)

      • newFileInputStreamWithRetry

        public static java.io.FileInputStream newFileInputStreamWithRetry​(java.io.File file)
                                                           throws java.io.FileNotFoundException
        Attempts to create a new FileInputStream, but if it fails, retries a few times until it succeeds. This is recommended if you attempt to open files that have been created as hard links or have had hard links to them created. See createHardLink(java.io.File, java.io.File)
        Parameters:
        file - the file to open
        Returns:
        a new FileInputStream
        Throws:
        java.io.FileNotFoundException - if FileInputStream(java.io.File) still throws a FileNotFoundException after a few attempts
        Since:
        API 4.40 (Geneious 5.4.0)
        See Also:
        newFileOutputStreamWithRetry(java.io.File)

      • newFileOutputStreamWithRetry

        public static java.io.FileOutputStream newFileOutputStreamWithRetry​(java.io.File file)
                                                             throws java.io.FileNotFoundException
        Attempts to create a new FileOutputStream, but if it fails with a FileNotFoundException, retries a few times until it succeeds. This is recommended if you attempt to open files that have been created as hard links or have had hard links to them created. See createHardLink(java.io.File, java.io.File). This is also useful when trying to write to a file of the same name that was recently deleted on systems with virus scanners. The virus scanner may still have the original file open, preventing it from being deleted immediately and causing Windows to deny access to writing to a new file with the same name. See comments at http://stackoverflow.com/questions/8670317/why-cant-i-create-a-txt-file-after-having-just-deleted-it
        Parameters:
        file - the file to open
        Returns:
        a new FileOutputStream
        Throws:
        java.io.FileNotFoundException - if FileOutputStream(java.io.File) still throws a FileNotFoundException after a few attempts
        Since:
        API 4.701 (Geneious 7.0.1)
        See Also:
        newFileInputStreamWithRetry(java.io.File)

      • getResourceForClass

        public static java.io.File getResourceForClass​(java.lang.Class cl,
                                               java.lang.String resourceName)
        for grabbing resources based on a directory hirarchy identical to the one that the class cl is found in.
        Parameters:
        cl - for example a GeneiousPlugin subclass
        resourceName - for example a file needed by the plugin
        Returns:
        The needed file
        Throws:
        java.lang.IllegalStateException - if the resource is not found.
        Since:
        API 4.58 (Geneious 5.5.50)