protected void readAlignments(BufferedReader stdInput, InputStream errorStream)
throws IOException {
String outLine;
SAMAlignmentReader alignmentReader = new SAMAlignmentReader();
while ((outLine = stdInput.readLine()) != null) {
if (logger.isDebugEnabled()) {
logger.debug("LINE: " + outLine);
}
if (outLine.startsWith("@")) {
logger.debug("SAM HEADER LINE: " + outLine);
continue;
}
String readPairId = outLine.substring(0, outLine.indexOf('\t'));
if (readPairId.endsWith("/1") || readPairId.endsWith("/2")) {
readPairId = readPairId.substring(0, readPairId.length() - 2);
}
AlignmentRecord alignment = alignmentReader.parseRecord(outLine);
if (!alignment.isMapped()) {
continue;
}
getOutput().collect(new Text(readPairId), new Text(outLine));
}
String errLine;
BufferedReader errorReader = new BufferedReader(new InputStreamReader(errorStream));
while ((errLine = errorReader.readLine()) != null) {
logger.error("ERROR: " + errLine);
}
}
public final void writeASCII(String s) throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
OutputStream os = getOutputStream();
synchronized (os) {
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + s);
os.write(s.getBytes("ASCII"));
os.write((byte) 13);
os.write((byte) 10);
os.flush();
}
}
public final String readCommand(byte[] b)
throws IOException, InterruptedException, MessagingNetworkException {
InputStream is = getInputStream();
synchronized (is) {
long abortTime =
System.currentTimeMillis() + 1000 * MSNMessagingNetwork.REQPARAM_SOCKET_TIMEOUT_SECONDS;
int ofs = 0;
boolean d = false;
for (; ; ) {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
int by = is.read();
if (by == -1) throw new IOException("unexpected EOF");
if (by == 10 && d) break;
d = (by == 13);
if (ofs < b.length) {
b[ofs++] = (byte) by;
}
if (System.currentTimeMillis() > abortTime) throw new IOException("connection timed out");
/*
if (len >= buffer.length)
{
...
return ...;
}
int pos = findCRLF();
if (pos != -1) break;
fill(is, abortTime);
*/
}
if (b[ofs - 1] == 13) --ofs;
String line = new String(b, 0, ofs, "ASCII");
if (StringUtil.startsWith(line, "MSG")) {
StringTokenizer st = new StringTokenizer(line);
String len_s = null;
while (st.hasMoreTokens()) {
len_s = st.nextToken();
}
if (len_s == null) throw new AssertException("len_s is null");
int len;
try {
len = Integer.parseInt(len_s);
} catch (NumberFormatException ex) {
ServerConnection.throwProtocolViolated("MSG length must be int");
len = 0;
}
String msg = readMSG(len);
line = line + "\r\n" + msg;
}
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("S: " + line);
return line;
}
}
/**
* UTF byte count is appended to the asciiPrefix, then UTF bytes are appended to the result; the
* final result is sent.
*/
public final void writeMSG(String asciiPrefix, String msgBody) throws IOException {
if (Thread.currentThread().isInterrupted()) throw new InterruptedIOException();
OutputStream os = getOutputStream();
synchronized (os) {
byte[] utfBytes = msgBody.getBytes("UTF-8");
asciiPrefix = asciiPrefix + ' ' + utfBytes.length;
if (Defines.DEBUG && CAT.isDebugEnabled()) CAT.debug("C: " + asciiPrefix + "\r\n" + msgBody);
os.write(asciiPrefix.getBytes("ASCII"));
os.write((byte) 13);
os.write((byte) 10);
os.write(utfBytes);
os.flush();
}
}