Class ImportHelper

Method Details

• setExpectedInputLength

  public void setExpectedInputLength(long l)

• getProgress

  public double getProgress()

  Returns:

  If the length of the input is known (because a file was passed to the constructor), this reports a value between 0.0 and 1.0 indicating the relative read position in the file. Otherwise, this always returns 0.0. This method assumes that all characters in the input are one byte long (to get its estimate, it divides the number of *characters* read by the number of *bytes* in the file). If there is an efficient way to fix this, we should do so :)

• closeReader

  public void closeReader() throws IOException

  Throws:

  IOException

• setCommentDelimiters

  public void setCommentDelimiters(char line)

• setCommentDelimiters

  public void setCommentDelimiters(char start, char stop)

• setCommentDelimiters

  public void setCommentDelimiters(char start, char stop, char line)

• setCommentDelimiters

  public void setCommentDelimiters(char start, char stop, char line, char write, char meta)

• setCommentWriter

  public void setCommentWriter(Writer commentWriter)

• getLineNumber

  public int getLineNumber()

• getLastDelimiter

  public int getLastDelimiter()

• nextCharacter

  public char nextCharacter() throws IOException

  Throws:

  IOException

• readCharacter

  public char readCharacter() throws IOException

  Throws:

  IOException

• unreadCharacter

  public void unreadCharacter(char ch)

• next

  public char next() throws IOException

  Throws:

  IOException

• read

  public char read() throws IOException

  All read attempts pass through this function.

  Returns:

  Throws:

  IOException

• readLine

  public String readLine() throws IOException

  Reads a line, skipping over any comments.

  Returns:

  one line of text

  Throws:

  IOException

• readSequence

  public void readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence) throws IOException, ImportException

  Throws:

  IOException

  ImportException

• readSequence

  public void readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, boolean stopAtDoubleNewLine) throws IOException, ImportException

  Throws:

  IOException

  ImportException

• readSequence

  public void readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress) throws IOException, ImportException

  Throws:

  IOException

  ImportException

• readSequence

  public void readSequence(StringBuilder sequence, SequenceType sequenceType, String delimiters, int maxSites, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence, ProgressListener progress, boolean stopAtDoubleNewLine) throws IOException, ImportException

  Reads sequence, skipping over any comments and filtering using sequenceType.

  Parameters:

  sequence - a StringBuilder into which the sequence is put

  sequenceType - the sequenceType of the sequence

  delimiters - list of characters that will stop the reading

  maxSites - maximum number of sites to read

  gapCharacters - list of characters that will be read as gaps

  missingCharacters - list of characters that will be read as missing

  matchCharacters - list of characters that will be read as matching the matchSequence

  matchSequence - the sequence string to match match characters to

  progress - optional ProgressListener. Must not be null.

  stopAtDoubleNewLine - if true will stop reading if it encounters two consectutive new line characters.

  Throws:

  IOException

  ImportException

• readSequenceLine

  public void readSequenceLine(StringBuffer sequence, SequenceType sequenceType, String delimiters, String gapCharacters, String missingCharacters, String matchCharacters, String matchSequence) throws IOException, ImportException

  Reads a line of sequence, skipping over any comments and filtering using sequenceType.

  Parameters:

  sequence - a StringBuffer into which the sequence is put

  sequenceType - the sequenceType of the sequence

  delimiters - list of characters that will stop the reading

  gapCharacters - list of characters that will be read as gaps

  missingCharacters - list of characters that will be read as missing

  matchCharacters - list of characters that will be read as matching the matchSequence

  matchSequence - the sequence string to match match characters to

  Throws:

  IOException

  ImportException

• readInteger

  public int readInteger() throws IOException, ImportException

  Attempts to read and parse an integer delimited by whitespace.

  Throws:

  IOException

  ImportException

• readInteger

  public int readInteger(String delimiters) throws IOException, ImportException

  Attempts to read and parse an integer delimited by whitespace or by any character in delimiters.

  Throws:

  IOException

  ImportException

• readDouble

  public double readDouble() throws IOException, ImportException

  Attempts to read and parse a double delimited by whitespace.

  Throws:

  IOException

  ImportException

• readDouble

  public double readDouble(String delimiters) throws IOException, ImportException

  Attempts to read and parse a double delimited by whitespace or by any character in delimiters.

  Throws:

  IOException

  ImportException

• readToken

  public String readToken() throws IOException

  Reads a token stopping when any whitespace or a comment is found. If the token begins with a quote char then all characters will be included in token until a matching quote is found (including whitespace or comments).

  Throws:

  IOException

• readToken

  public String readToken(String delimiters) throws IOException

  Reads a token stopping when any whitespace, a comment or when any character in delimiters is found. If the token begins with a quote char then all characters will be included in token until a matching quote is found (including whitespace or comments).

  Throws:

  IOException

• skipToEndOfLine

  public void skipToEndOfLine() throws IOException

  Skips to the end of the line. If a comment is found then this is read.

  Throws:

  IOException

• skipWhile

  public void skipWhile(String skip) throws IOException

  Skips char any contiguous characters in skip. Will also skip comments.

  Throws:

  IOException

• skipSpace

  public void skipSpace() throws IOException

  Skips over any space (plus tabs and returns) in the file. Will also skip comments.

  Throws:

  IOException

• skipCharacters

  public void skipCharacters(String skip) throws IOException

  Skips over any contiguous characters in skip. Will also skip comments and space.

  Throws:

  IOException

• skipUntil

  public char skipUntil(String skip) throws IOException

  Skips over the file until a character from delimiters is found. Returns the delimiter found. Will skip comments and will ignore delimiters within comments.

  Throws:

  IOException

• getMetaComments

  public List<String> getMetaComments()

  This method has been introduced because this class previously skipped over consecutive comments and discarded all but the last. This method returns all comments that have been read over since clearLastMetaComment() was last called.

  Returns:

  List of previously read comments (since clearLastMetaComment was called), never null but may be empty.

  See Also:

  • clearLastMetaComment()

• getLastMetaComment

  @Deprecated public String getLastMetaComment()

  Deprecated.

  use getMetaComments() instead

• clearLastMetaComment

  public void clearLastMetaComment()