Package org.cytoscape.io

Class BasicCyFileFilter

java.lang.Object
org.cytoscape.io.BasicCyFileFilter
All Implemented Interfaces:
CyFileFilter
public class BasicCyFileFilter extends Object implements CyFileFilter
This is meant to be an basic implementation of CyFileFilter that can either be used directly or extended to provide different acceptance criteria. Only the accepts() methods may be overridden.

Cytoscape Backwards Compatibility (Abstract Class): This class is abstract and meant to be extended by users. This means that we may add methods for minor version updates. Methods will only be removed for major version updates.

Module: io-api

To use this in your app, include the following dependency in your POM:

<dependency>
    <groupId>org.cytoscape</groupId>
    <artifactId>io-api</artifactId>
</dependency>

  • Field Details

    • extensions

      protected final Set<String> extensions

    • contentTypes

      protected final Set<String> contentTypes

    • description

      protected final String description

    • streamUtil

      protected final StreamUtil streamUtil

    • category

      protected final DataCategory category
      Type of data that this filter applies to.

  • Constructor Details

    • BasicCyFileFilter

      public BasicCyFileFilter​(Set<String> extensions, Set<String> contentTypes, String description, DataCategory category, StreamUtil streamUtil)
      Creates a file filter from the specified arguments. Note that a "." before the extension is not needed and will be ignored.
      Parameters:
      extensions - The set of valid extensions for this filter.
      contentTypes - The set of valid MIME content types that this filter should recognize.
      description - A human readable description of the filter.
      category - The type of data this filter is meant to support.
      streamUtil - An instance of the StreamUtil service.

    • BasicCyFileFilter

      public BasicCyFileFilter​(String[] extensions, String[] contentTypes, String description, DataCategory category, StreamUtil streamUtil)
      Creates a file filter from the specified arguments. Note that a "." before the extension is not needed and will be ignored.
      Parameters:
      extensions - The set of valid extensions for this filter.
      contentTypes - The set of valid MIME content types that this filter should recognize.
      description - A human readable description of the filter.
      category - The type of data this filter is meant to support.
      streamUtil - An instance of the StreamUtil service.

  • Method Details

    • accepts

      public boolean accepts​(URI uri, DataCategory category)
      Description copied from interface: CyFileFilter
      A method that attempts to determine whether the specified URI can be read by the Reader using this filter.
      Specified by:
      accepts in interface CyFileFilter
      Parameters:
      uri - The URI to be checked.
      category - The data category of URI.
      Returns:
      True if we believe the URI can be read, false otherwise.

    • accepts

      public boolean accepts​(InputStream stream, DataCategory category)
      This method always returns false in this particular implementation. You must extend this class and override this method to get alternative behavior. Ideally this method would return true if this class is capable of processing the specified InputStream.
      Specified by:
      accepts in interface CyFileFilter
      Parameters:
      stream - The stream that references the file we'd like to read.
      category - The type of input that we're considering.
      Returns:
      Always returns false in this particular implementation.

    • getExtensions

      public final Set<String> getExtensions()
      Description copied from interface: CyFileFilter
      Returns a list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.
      Specified by:
      getExtensions in interface CyFileFilter
      Returns:
      A list of file extensions (xml, xgmml, sif) suitable for for use in FileChoosers.

    • getContentTypes

      public final Set<String> getContentTypes()
      Description copied from interface: CyFileFilter
      The MIME content types supported by this filter.
      Specified by:
      getContentTypes in interface CyFileFilter
      Returns:
      A set of strings the describe the different MIME types supported by this filter.

    • getDescription

      public final String getDescription()
      Description copied from interface: CyFileFilter
      A short, human readable description of the file extensions suitable for display in FileChoosers.
      Specified by:
      getDescription in interface CyFileFilter
      Returns:
      A string describing this file type.

    • getDataCategory

      public final DataCategory getDataCategory()
      Description copied from interface: CyFileFilter
      The DataCategory supported by this filter.
      Specified by:
      getDataCategory in interface CyFileFilter
      Returns:
      The DataCategory supported by this filter.

    • toString

      public String toString()
      Returns a human readable description of this class.
      Overrides:
      toString in class Object
      Returns:
      a human readable description of this class.

    • getExtension

      protected final String getExtension​(String filename)
      Returns a string of the characters following the last '.' in the input string, which is to say the file extension assuming that the input string represents a file name. Will return null if no '.' is found.
      Parameters:
      filename - the file name as a string.
      Returns:
      a string representing the file extension of the input string.

    • getHeader

      protected final String getHeader​(InputStream stream, int numLines)
      Returns a string containing the specified number of lines from the beginning of the file. This is useful for testing input streams.
      Parameters:
      stream - the input stream from which to read the header.
      numLines - the number of lines from the beginning of the file.
      Returns:
      a string containing the specified number of lines from the beginning of the file.