Program: 16527
Project: 16527
Buggy source:
/** 
 * Tries to determine the source and pdbId without fully realizing the identifier, which could require I/O depending on the source
 * @throws IllegalArgumentException if the source is recognizable but invalid
 */
private void init(){
  Matcher matcher=scopPattern.matcher(name);
  if (matcher.matches()) {
    mySource=Source.SCOP;
    pdbId=matcher.group(1);
    chainId=matcher.group(2);
    return;
  }
  if (name.startsWith(AtomCache.PDP_DOMAIN_IDENTIFIER)) {
    mySource=Source.PDP;
    matcher=PDPDomain.PDP_NAME_PATTERN.matcher(name);
    if (!matcher.matches()) {
      throw new IllegalArgumentException("String_Node_Str");
    }
    pdbId=matcher.group(1);
    chainId=matcher.group(2);
    return;
  }
  matcher=cathPattern.matcher(name);
  if (matcher.matches()) {
    mySource=Source.CATH;
    pdbId=matcher.group(1);
    chainId=matcher.group(2);
    return;
  }
  try {
    new URL(name);
    mySource=Source.URL;
    pdbId=null;
    chainId=null;
    return;
  }
 catch (  MalformedURLException e) {
  }
  File file=new File(FileDownloadUtils.expandUserHome(name));
  if (file.exists()) {
    mySource=Source.FILE;
    pdbId=null;
    chainId=null;
    return;
  }
  mySource=Source.PDB;
  SubstructureIdentifier si=new SubstructureIdentifier(getIdentifier());
  realized=si;
  pdbId=si.getPdbId();
  Set<String> chains=getChainIds(si);
  if (chains.size() == 1) {
    this.chainId=chains.iterator().next();
  }
 else   if (chains.size() > 1) {
    this.chainId="String_Node_Str";
  }
 else {
    this.chainId=null;
  }
}

Fixed version (ground truth):
/** 
 * Tries to determine the source and pdbId without fully realizing the identifier, which could require I/O depending on the source
 * @throws IllegalArgumentException if the source is recognizable but invalid
 */
private void init(){
  Matcher matcher=scopPattern.matcher(name);
  if (matcher.matches()) {
    mySource=Source.SCOP;
    pdbId=matcher.group(1);
    chainId=matcher.group(2);
    return;
  }
  if (name.startsWith(AtomCache.PDP_DOMAIN_IDENTIFIER)) {
    mySource=Source.PDP;
    matcher=PDPDomain.PDP_NAME_PATTERN.matcher(name);
    if (!matcher.matches()) {
      throw new IllegalArgumentException("String_Node_Str");
    }
    pdbId=matcher.group(1);
    chainId=matcher.group(2);
    return;
  }
  matcher=cathPattern.matcher(name);
  if (matcher.matches()) {
    mySource=Source.CATH;
    pdbId=matcher.group(1);
    chainId=matcher.group(2);
    return;
  }
  try {
    new URL(name);
    mySource=Source.URL;
    pdbId=null;
    chainId=null;
    return;
  }
 catch (  MalformedURLException e) {
  }
  File file=new File(FileDownloadUtils.expandUserHome(name));
  if (file.exists() || (file.getParentFile() != null && file.getParentFile().exists())) {
    mySource=Source.FILE;
    pdbId=null;
    chainId=null;
    return;
  }
  mySource=Source.PDB;
  SubstructureIdentifier si=new SubstructureIdentifier(getIdentifier());
  realized=si;
  pdbId=si.getPdbId();
  Set<String> chains=getChainIds(si);
  if (chains.size() == 1) {
    this.chainId=chains.iterator().next();
  }
 else   if (chains.size() > 1) {
    this.chainId="String_Node_Str";
  }
 else {
    this.chainId=null;
  }
}