Package org.biojava3.core.sequence.io.util

Class IOUtils

java.lang.Object
org.biojava3.core.sequence.io.util.IOUtils
public class IOUtils extends Object

  • Constructor Details

    • IOUtils

      public IOUtils()

  • Method Details

    • close

      public static void close(Closeable c)
      Closes any Object which implements the interface Closeable and sending any error to the logger but not forcing any explicit catching of stream errors.
      Parameters:
      c - The stream to close

    • copy

      public static void copy(InputStream input, OutputStream output) throws IOException
      Moves the bytes from input to output using a 4KB byte array.
      Parameters:
      input - Input stream of bytes
      output - Output stream of bytes
      Throws:
      IOException - If anything occurs in the case of the reads and writes

    • processReader

      public static void processReader(BufferedReader br, IOUtils.ReaderProcessor processor) throws ParserException
      Takes in a reader and a processor, reads every line from the given file and then invokes the processor. What you do with the lines is dependent on your processor. The code will automatically close the given BufferedReader.
      Parameters:
      br - The reader to process
      processor - The processor to invoke on all lines
      Throws:
      ParserException - Can throw this if we cannot parse the given reader

    • getList

      public static List<String> getList(BufferedReader br) throws ParserException
      Returns the contents of a buffered reader as a list of strings
      Parameters:
      br - BufferedReader to read from; will be closed
      Returns:
      List of Strings
      Throws:
      ParserException - Can throw this if we cannot parse the given reader

    • getList

      public static List<String> getList(InputStream is) throws ParserException
      Delegates to getList(BufferedReader) by wrapping the InputStream in a valid reader. No encoding is mentioned so if you need anything more advanced then use the other version of this method.
      Parameters:
      is - InputStream which is a text file
      Returns:
      List of Strings representing the lines of the files
      Throws:
      ParserException - Can throw this if the file is not a file or we cannot parse it

    • getList

      public static List<String> getList(File file) throws ParserException
      Delegates to getList(InputStream) by wrapping the File in a valid stream. No encoding is mentioned so if you need anything more advanced then use the other version of this method. Since this uses openFile(File) this code can support GZipped and plain files.
      Parameters:
      file - File which is a text file
      Returns:
      List of Strings representing the lines of the files
      Throws:
      ParserException - Can throw this if the file is not a file or we cannot parse it

    • openFile

      public static InputStream openFile(File file) throws ParserException
      For a filename this code will check the extension of the file for a .gz extension. If it finds one then the InputStream given back is a GZIPInputStream. Otherwise we return a normal FileInputStream.
      Parameters:
      file - File which may or may not be GZipped
      Returns:
      The final stream
      Throws:
      ParserException - Can throw this if the file is not a file or we cannot open it for processing

    • getGCGChecksum

      public static <S extends Sequence<C>, C extends Compound> int getGCGChecksum(List<S> sequences)
      Calculates GCG checksum for entire list of sequences
      Parameters:
      sequences - list of sequences
      Returns:
      GCG checksum

    • getGCGChecksum

      public static <S extends Sequence<C>, C extends Compound> int getGCGChecksum(S sequence)
      Calculates GCG checksum for a given sequence
      Parameters:
      sequence - given sequence
      Returns:
      GCG checksum

    • getGCGHeader

      public static <S extends Sequence<C>, C extends Compound> String getGCGHeader(List<S> sequences)
      Assembles a GCG file header
      Parameters:
      sequences - list of sequences
      Returns:
      GCG header

    • getGCGType

      public static <C extends Compound> String getGCGType(CompoundSet<C> cs)
      Determines GCG type
      Parameters:
      cs - compound set of sequences
      Returns:
      GCG type

    • getIDFormat

      public static <S extends Sequence<C>, C extends Compound> String getIDFormat(List<S> sequences)
      Creates format String for accession IDs
      Parameters:
      sequences - list of sequences
      Returns:
      format String for accession IDs

    • getPDBCharacter

      public static String getPDBCharacter(boolean web, char c1, char c2, boolean similar, char c)
      Creates formatted String for a single character of PDB output
      Parameters:
      web - true for HTML display
      c1 - character in first sequence
      c2 - character in second sequence
      similar - true if c1 and c2 are considered similar compounds
      c - character to display
      Returns:
      formatted String

    • getPDBConservation

      public static String getPDBConservation(boolean web, char c1, char c2, boolean similar)
      Creates formatted String for displaying conservation in PDB output
      Parameters:
      web - true for HTML display
      c1 - character in first sequence
      c2 - character in second sequence
      similar - true if c1 and c2 are considered similar compounds
      Returns:
      formatted String

    • getPDBLegend

      public static String getPDBLegend()
      Creates formatted String for displaying conservation legend in PDB output
      Returns:
      legend String