/* Generated By:JavaCC: Do not edit this line. SimpleCharStream.java Version 5.0 */
/* JavaCCOptions:STATIC=false,SUPPORT_CLASS_VISIBILITY_PUBLIC=true */
/*
The MIT License (MIT)
Copyright (c) 2017 Pierre Lindenbaum
Permission is hereby granted, free of charge, to any person obtaining a copy
of this software and associated documentation files (the "Software"), to deal
in the Software without restriction, including without limitation the rights
to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
copies of the Software, and to permit persons to whom the Software is
furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all
copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
SOFTWARE.
*/
package com.github.lindenb.jvarkit.util.bio.samfilter;
/**
* An implementation of interface CharStream, where the stream is assumed to
* contain only ASCII characters (without unicode processing).
*/
public class SimpleCharStream
{
/** Whether parser is static. */
public static final boolean staticFlag = false;
int bufsize;
int available;
int tokenBegin;
/** Position in buffer. */
public int bufpos = -1;
protected int bufline[];
protected int bufcolumn[];
protected int column = 0;
protected int line = 1;
protected boolean prevCharIsCR = false;
protected boolean prevCharIsLF = false;
protected java.io.Reader inputStream;
protected char[] buffer;
protected int maxNextCharInd = 0;
protected int inBuf = 0;
protected int tabSize = 8;
protected void setTabSize(int i) { tabSize = i; }
protected int getTabSize(int i) { return tabSize; }
protected void ExpandBuff(boolean wrapAround)
{
char[] newbuffer = new char[bufsize + 2048];
int newbufline[] = new int[bufsize + 2048];
int newbufcolumn[] = new int[bufsize + 2048];
try
{
if (wrapAround)
{
System.arraycopy(buffer, tokenBegin, newbuffer, 0, bufsize - tokenBegin);
System.arraycopy(buffer, 0, newbuffer, bufsize - tokenBegin, bufpos);
buffer = newbuffer;
System.arraycopy(bufline, tokenBegin, newbufline, 0, bufsize - tokenBegin);
System.arraycopy(bufline, 0, newbufline, bufsize - tokenBegin, bufpos);
bufline = newbufline;
System.arraycopy(bufcolumn, tokenBegin, newbufcolumn, 0, bufsize - tokenBegin);
System.arraycopy(bufcolumn, 0, newbufcolumn, bufsize - tokenBegin, bufpos);
bufcolumn = newbufcolumn;
maxNextCharInd = (bufpos += (bufsize - tokenBegin));
}
else
{
System.arraycopy(buffer, tokenBegin, newbuffer, 0, bufsize - tokenBegin);
buffer = newbuffer;
System.arraycopy(bufline, tokenBegin, newbufline, 0, bufsize - tokenBegin);
bufline = newbufline;
System.arraycopy(bufcolumn, tokenBegin, newbufcolumn, 0, bufsize - tokenBegin);
bufcolumn = newbufcolumn;
maxNextCharInd = (bufpos -= tokenBegin);
}
}
catch (Throwable t)
{
throw new Error(t.getMessage());
}
bufsize += 2048;
available = bufsize;
tokenBegin = 0;
}
protected void FillBuff() throws java.io.IOException
{
if (maxNextCharInd == available)
{
if (available == bufsize)
{
if (tokenBegin > 2048)
{
bufpos = maxNextCharInd = 0;
available = tokenBegin;
}
else if (tokenBegin < 0)
bufpos = maxNextCharInd = 0;
else
ExpandBuff(false);
}
else if (available > tokenBegin)
available = bufsize;
else if ((tokenBegin - available) < 2048)
ExpandBuff(true);
else
available = tokenBegin;
}
int i;
try {
if ((i = inputStream.read(buffer, maxNextCharInd, available - maxNextCharInd)) == -1)
{
inputStream.close();
throw new java.io.IOException();
}
else
maxNextCharInd += i;
return;
}
catch(java.io.IOException e) {
--bufpos;
backup(0);
if (tokenBegin == -1)
tokenBegin = bufpos;
throw e;
}
}
/** Start. */
public char BeginToken() throws java.io.IOException
{
tokenBegin = -1;
char c = readChar();
tokenBegin = bufpos;
return c;
}
protected void UpdateLineColumn(char c)
{
column++;
if (prevCharIsLF)
{
prevCharIsLF = false;
line += (column = 1);
}
else if (prevCharIsCR)
{
prevCharIsCR = false;
if (c == '\n')
{
prevCharIsLF = true;
}
else
line += (column = 1);
}
switch (c)
{
case '\r' :
prevCharIsCR = true;
break;
case '\n' :
prevCharIsLF = true;
break;
case '\t' :
column--;
column += (tabSize - (column % tabSize));
break;
default :
break;
}
bufline[bufpos] = line;
bufcolumn[bufpos] = column;
}
/** Read a character. */
public char readChar() throws java.io.IOException
{
if (inBuf > 0)
{
--inBuf;
if (++bufpos == bufsize)
bufpos = 0;
return buffer[bufpos];
}
if (++bufpos >= maxNextCharInd)
FillBuff();
char c = buffer[bufpos];
UpdateLineColumn(c);
return c;
}
@Deprecated
/**
* @deprecated
* @see #getEndColumn
*/
public int getColumn() {
return bufcolumn[bufpos];
}
@Deprecated
/**
* @deprecated
* @see #getEndLine
*/
public int getLine() {
return bufline[bufpos];
}
/** Get token end column number. */
public int getEndColumn() {
return bufcolumn[bufpos];
}
/** Get token end line number. */
public int getEndLine() {
return bufline[bufpos];
}
/** Get token beginning column number. */
public int getBeginColumn() {
return bufcolumn[tokenBegin];
}
/** Get token beginning line number. */
public int getBeginLine() {
return bufline[tokenBegin];
}
/** Backup a number of characters. */
public void backup(int amount) {
inBuf += amount;
if ((bufpos -= amount) < 0)
bufpos += bufsize;
}
/** Constructor. */
public SimpleCharStream(java.io.Reader dstream, int startline,
int startcolumn, int buffersize)
{
inputStream = dstream;
line = startline;
column = startcolumn - 1;
available = bufsize = buffersize;
buffer = new char[buffersize];
bufline = new int[buffersize];
bufcolumn = new int[buffersize];
}
/** Constructor. */
public SimpleCharStream(java.io.Reader dstream, int startline,
int startcolumn)
{
this(dstream, startline, startcolumn, 4096);
}
/** Constructor. */
public SimpleCharStream(java.io.Reader dstream)
{
this(dstream, 1, 1, 4096);
}
/** Reinitialise. */
public void ReInit(java.io.Reader dstream, int startline,
int startcolumn, int buffersize)
{
inputStream = dstream;
line = startline;
column = startcolumn - 1;
if (buffer == null || buffersize != buffer.length)
{
available = bufsize = buffersize;
buffer = new char[buffersize];
bufline = new int[buffersize];
bufcolumn = new int[buffersize];
}
prevCharIsLF = prevCharIsCR = false;
tokenBegin = inBuf = maxNextCharInd = 0;
bufpos = -1;
}
/** Reinitialise. */
public void ReInit(java.io.Reader dstream, int startline,
int startcolumn)
{
ReInit(dstream, startline, startcolumn, 4096);
}
/** Reinitialise. */
public void ReInit(java.io.Reader dstream)
{
ReInit(dstream, 1, 1, 4096);
}
/** Constructor. */
public SimpleCharStream(java.io.InputStream dstream, String encoding, int startline,
int startcolumn, int buffersize) throws java.io.UnsupportedEncodingException
{
this(encoding == null ? new java.io.InputStreamReader(dstream) : new java.io.InputStreamReader(dstream, encoding), startline, startcolumn, buffersize);
}
/** Constructor. */
public SimpleCharStream(java.io.InputStream dstream, int startline,
int startcolumn, int buffersize)
{
this(new java.io.InputStreamReader(dstream), startline, startcolumn, buffersize);
}
/** Constructor. */
public SimpleCharStream(java.io.InputStream dstream, String encoding, int startline,
int startcolumn) throws java.io.UnsupportedEncodingException
{
this(dstream, encoding, startline, startcolumn, 4096);
}
/** Constructor. */
public SimpleCharStream(java.io.InputStream dstream, int startline,
int startcolumn)
{
this(dstream, startline, startcolumn, 4096);
}
/** Constructor. */
public SimpleCharStream(java.io.InputStream dstream, String encoding) throws java.io.UnsupportedEncodingException
{
this(dstream, encoding, 1, 1, 4096);
}
/** Constructor. */
public SimpleCharStream(java.io.InputStream dstream)
{
this(dstream, 1, 1, 4096);
}
/** Reinitialise. */
public void ReInit(java.io.InputStream dstream, String encoding, int startline,
int startcolumn, int buffersize) throws java.io.UnsupportedEncodingException
{
ReInit(encoding == null ? new java.io.InputStreamReader(dstream) : new java.io.InputStreamReader(dstream, encoding), startline, startcolumn, buffersize);
}
/** Reinitialise. */
public void ReInit(java.io.InputStream dstream, int startline,
int startcolumn, int buffersize)
{
ReInit(new java.io.InputStreamReader(dstream), startline, startcolumn, buffersize);
}
/** Reinitialise. */
public void ReInit(java.io.InputStream dstream, String encoding) throws java.io.UnsupportedEncodingException
{
ReInit(dstream, encoding, 1, 1, 4096);
}
/** Reinitialise. */
public void ReInit(java.io.InputStream dstream)
{
ReInit(dstream, 1, 1, 4096);
}
/** Reinitialise. */
public void ReInit(java.io.InputStream dstream, String encoding, int startline,
int startcolumn) throws java.io.UnsupportedEncodingException
{
ReInit(dstream, encoding, startline, startcolumn, 4096);
}
/** Reinitialise. */
public void ReInit(java.io.InputStream dstream, int startline,
int startcolumn)
{
ReInit(dstream, startline, startcolumn, 4096);
}
/** Get token literal value. */
public String GetImage()
{
if (bufpos >= tokenBegin)
return new String(buffer, tokenBegin, bufpos - tokenBegin + 1);
else
return new String(buffer, tokenBegin, bufsize - tokenBegin) +
new String(buffer, 0, bufpos + 1);
}
/** Get the suffix. */
public char[] GetSuffix(int len)
{
char[] ret = new char[len];
if ((bufpos + 1) >= len)
System.arraycopy(buffer, bufpos - len + 1, ret, 0, len);
else
{
System.arraycopy(buffer, bufsize - (len - bufpos - 1), ret, 0,
len - bufpos - 1);
System.arraycopy(buffer, 0, ret, len - bufpos - 1, bufpos + 1);
}
return ret;
}
/** Reset buffer when finished. */
public void Done()
{
buffer = null;
bufline = null;
bufcolumn = null;
}
/**
* Method to adjust line and column numbers for the start of a token.
*/
public void adjustBeginLineColumn(int newLine, int newCol)
{
int start = tokenBegin;
int len;
if (bufpos >= tokenBegin)
{
len = bufpos - tokenBegin + inBuf + 1;
}
else
{
len = bufsize - tokenBegin + bufpos + 1 + inBuf;
}
int i = 0, j = 0, k = 0;
int nextColDiff = 0, columnDiff = 0;
while (i < len && bufline[j = start % bufsize] == bufline[k = ++start % bufsize])
{
bufline[j] = newLine;
nextColDiff = columnDiff + bufcolumn[k] - bufcolumn[j];
bufcolumn[j] = newCol + columnDiff;
columnDiff = nextColDiff;
i++;
}
if (i < len)
{
bufline[j] = newLine++;
bufcolumn[j] = newCol + columnDiff;
while (i++ < len)
{
if (bufline[j = start % bufsize] != bufline[++start % bufsize])
bufline[j] = newLine++;
else
bufline[j] = newLine;
}
}
line = bufline[j];
column = bufcolumn[j];
}
}
/* JavaCC - OriginalChecksum=e623f56108a6e684bfd277d3cdc28161 (do not edit this line) */