private void relabelToFront() {
assert (!V.isEmpty()) : "No vertices";
ListIterator<Vertex> iter = V.listIterator();
while (iter.hasNext()) {
Vertex v = iter.next();
// System.out.println("Considering vertex: " + v);
int oldHeight = v.getHeight();
discharge(v);
if (v.getHeight() > oldHeight) {
iter.remove();
V.addFirst(v);
iter = V.listIterator(1);
}
}
}
public String hasSameContent(JarFile2 file, JarEntry entry) throws IOException {
String thisName = null;
Long crcL = new Long(entry.getCrc());
// check if this jar contains files with the passed in entry's crc
if (_crcToEntryMap.containsKey(crcL)) {
// get the Linked List with files with the crc
LinkedList ll = (LinkedList) _crcToEntryMap.get(crcL);
// go through the list and check for content match
ListIterator li = ll.listIterator(0);
if (li != null) {
while (li.hasNext()) {
JarEntry thisEntry = (JarEntry) li.next();
// check for content match
InputStream oldIS = getJarFile().getInputStream(thisEntry);
InputStream newIS = file.getJarFile().getInputStream(entry);
if (!differs(oldIS, newIS)) {
thisName = thisEntry.getName();
return thisName;
}
}
}
}
return thisName;
}
public static void maxFlow(ListGraph g) {
ListGraph residualG = g.residualGraph();
LinkedList<DirEdge> path = residualG.getFlowPath();
while (path != null) {
// System.out.println("Got path");
int minCapacity = ListGraph.minCapacityInPath(path);
assert minCapacity > 0;
// augment every edge on the path in the original graph
int head = g.getSource();
ListIterator it = path.listIterator();
while (it.hasNext()) {
DirEdge rEdge = (DirEdge) it.next();
int tail = rEdge.end;
DirEdge e = g.getEdge(head, tail);
e.flow += minCapacity;
// System.out.println("Augmenting (" + head + "," + tail + ") to be " + e.flow);
head = tail;
}
residualG = g.residualGraph();
// System.out.println("g:");
// g.print();
// System.out.println("Residual graph:");
// residualG.print();
path = residualG.getFlowPath();
}
}
/** Sorts the static LinkedList mainlineLinks in the order they appear on the freeway */
private LinkedList<Link> recursiveLinkSort(LinkedList<Link> links2) {
if (links2.size() == 1) {
return links2;
} else {
boolean swapMade = false;
ListIterator<Link> itr1 = links2.listIterator();
while (itr1.hasNext()) {
Link temp = itr1.next();
int tempindex = itr1.nextIndex();
// if this loop makes any switches, set the flag to true
if (links2.getFirst().getUpNode().getNodeID() == temp.getDownNode().getNodeID()) {
swapMade = true;
links2.addFirst(temp);
links2.remove(tempindex);
return this.recursiveLinkSort(links2);
}
}
if (!swapMade) {
// assign last n-1 links to links3
LinkedList<Link> links3 = new LinkedList<Link>();
Link temp = links2.getFirst();
links2.removeFirst();
links3 = this.recursiveLinkSort(links2);
links3.addFirst(temp);
return links3;
} else {
return links2;
}
}
}
public static int minCapacityInPath(LinkedList<DirEdge> path) {
int minCapacity = Integer.MAX_VALUE;
ListIterator it = path.listIterator();
while (it.hasNext()) {
DirEdge e = (DirEdge) it.next();
if (e.capacity < minCapacity) {
minCapacity = e.capacity;
}
}
return minCapacity;
}
/**
* Perform this job - start compilation.
*
* @param compiler The compiler to use.
* @param arguments The compiler arguments to use.
* @return The result.
*/
public CompileResult perform(String compiler, ArrayList<String> arguments) {
Debug.trace("starting job " + this.name);
// we have some maximum command line length - need to count
int cmdline_len = 0;
// used to collect the arguments for executing the compiler
LinkedList<String> args = new LinkedList<String>(arguments);
{
for (String arg : args) {
cmdline_len += (arg).length() + 1;
}
}
boolean isEclipseCompiler = compiler.equalsIgnoreCase(ECLIPSE_COMPILER_NAME);
// add compiler in front of arguments
args.add(0, compiler);
cmdline_len += compiler.length() + 1;
// construct classpath argument for compiler
// - collect all classpaths
StringBuffer classpath_sb = new StringBuffer();
for (String cp : this.classpath) {
if (classpath_sb.length() > 0) {
classpath_sb.append(File.pathSeparatorChar);
}
classpath_sb.append(new File(cp).getAbsolutePath());
}
String classpath_str = classpath_sb.toString();
// - add classpath argument to command line
if (classpath_str.length() > 0) {
args.add("-classpath");
cmdline_len += 11;
args.add(classpath_str);
cmdline_len += classpath_str.length() + 1;
}
// remember how many arguments we have which don't change for the
// job
int common_args_no = args.size();
// remember how long the common command line is
int common_args_len = cmdline_len;
// used for execution
FileExecutor executor = new FileExecutor();
String output[] = new String[2];
// used for displaying the progress bar
String jobfiles = "";
int fileno = 0;
int last_fileno = 0;
// now iterate over all files of this job
for (File file : this.files) {
String fpath = file.getAbsolutePath();
Debug.trace("processing " + fpath);
// we add the file _first_ to the arguments to have a better
// chance to get something done if the command line is almost
// MAX_CMDLINE_SIZE or even above
fileno++;
jobfiles += file.getName() + " ";
args.add(fpath);
cmdline_len += fpath.length();
// start compilation if maximum command line length reached
if (!isEclipseCompiler && cmdline_len >= MAX_CMDLINE_SIZE) {
Debug.trace("compiling " + jobfiles);
// display useful progress bar (avoid showing 100% while
// still compiling a lot)
this.listener.progress(last_fileno, jobfiles);
last_fileno = fileno;
int retval = runCompiler(executor, output, args);
// update progress bar: compilation of fileno files done
this.listener.progress(fileno, jobfiles);
if (retval != 0) {
CompileResult result =
new CompileResult(
this.langpack.getString("CompilePanel.error"), args, output[0], output[1]);
this.listener.handleCompileError(result);
if (!result.isContinue()) {
return result;
}
} else {
// verify that all files have been compiled successfully
// I found that sometimes, no error code is returned
// although compilation failed.
Iterator<String> arg_it = args.listIterator(common_args_no);
while (arg_it.hasNext()) {
File java_file = new File(arg_it.next());
String basename = java_file.getName();
int dotpos = basename.lastIndexOf('.');
basename = basename.substring(0, dotpos) + ".class";
File class_file = new File(java_file.getParentFile(), basename);
if (!class_file.exists()) {
CompileResult result =
new CompileResult(
this.langpack.getString("CompilePanel.error.noclassfile")
+ java_file.getAbsolutePath(),
args,
output[0],
output[1]);
this.listener.handleCompileError(result);
if (!result.isContinue()) {
return result;
}
// don't continue any further
break;
}
}
}
// clean command line: remove files we just compiled
for (int i = args.size() - 1; i >= common_args_no; i--) {
args.removeLast();
}
cmdline_len = common_args_len;
jobfiles = "";
}
}
if (cmdline_len > common_args_len) {
this.listener.progress(last_fileno, jobfiles);
int retval = runCompiler(executor, output, args);
if (!isEclipseCompiler) {
this.listener.progress(fileno, jobfiles);
}
if (retval != 0) {
CompileResult result =
new CompileResult(
this.langpack.getString("CompilePanel.error"), args, output[0], output[1]);
this.listener.handleCompileError(result);
if (!result.isContinue()) {
return result;
}
} else {
// verify that all files have been compiled successfully
// I found that sometimes, no error code is returned
// although compilation failed.
Iterator<String> arg_it = args.listIterator(common_args_no);
while (arg_it.hasNext()) {
File java_file = new File(arg_it.next());
String basename = java_file.getName();
int dotpos = basename.lastIndexOf('.');
basename = basename.substring(0, dotpos) + ".class";
File class_file = new File(java_file.getParentFile(), basename);
if (!class_file.exists()) {
CompileResult result =
new CompileResult(
this.langpack.getString("CompilePanel.error.noclassfile")
+ java_file.getAbsolutePath(),
args,
output[0],
output[1]);
this.listener.handleCompileError(result);
if (!result.isContinue()) {
return result;
}
// don't continue any further
break;
}
}
}
}
Debug.trace("job " + this.name + " done (" + fileno + " files compiled)");
return new CompileResult();
}
public void run() {
System.err.println();
Date now = new Date();
if (!done) flout("INTERRUPTED\n");
flout("START: " + start + "\n");
flout("FINISH: " + now + "\n");
flout("N: " + n_files + "\n");
flout("Subject id: " + subject_id + "\n");
flout("Sample id: " + sample_id + "\n");
flout("total files: " + total_files + "\n");
flout("total bytes: " + total_bytes + "\n");
flout("retrieve failures: " + retrieve_failures + "\n");
flout("metadata retrieve failures: " + md_retrieve_failures + "\n");
flout("bad files retrieved: " + bad_file_errors + "\n");
flout("bad metadata retrieved: " + bad_md_errors + "\n");
reportExceptions();
flout("store retries: " + store_retries + "\n");
flout("retrieve retries: " + retrieve_retries + "\n");
flout("md retrieve retries: " + md_retrieve_retries + "\n");
if (md_retrieve_time > 0)
flout("md retrieve rate (ms/record): " + (md_retrieve_time / md_retrieves) + "\n");
if (total_store_time > 0)
flout("total store rate (bytes/sec): " + ((total_bytes * 1000) / total_store_time) + "\n");
if (total_retrieve_time > 0)
flout(
"total retrieve rate (bytes/sec): "
+ ((total_bytes * 1000) / total_retrieve_time)
+ "\n");
if (time_store_30M > 0)
flout("30 MB store (bytes/sec): " + (1000 * bytes_30M / time_store_30M) + "\n");
if (time_retrv_30M > 0)
flout("30 MB retrieve (bytes/sec): " + (1000 * bytes_30M / time_retrv_30M) + "\n");
if (time_store_3M > 0)
flout("3 MB store (bytes/sec): " + (1000 * bytes_30M / time_store_3M) + "\n");
if (time_retrv_3M > 0)
flout("3 MB retrieve (bytes/sec): " + (1000 * bytes_3M / time_retrv_3M) + "\n");
if (time_store_300K > 0)
flout("300 KB store (bytes/sec): " + (1000 * bytes_300K / time_store_300K) + "\n");
if (time_retrv_300K > 0)
flout("300 KB retrieve (bytes/sec): " + (1000 * bytes_300K / time_retrv_300K) + "\n");
if (update) {
flout("update oid query retries: " + query_retries + "\n");
flout("update retries: " + update_retries + "\n");
if (oid_query_time > 0) flout("query-oid's time (ms): " + oid_query_time + "\n");
if (update_time > 0) flout("update time (ms/record): " + (update_time / updates) + "\n");
if (updating && updates != n_files * 3)
flout("files saved: " + (n_files * 3) + " updates: " + updates + "\n");
}
if (failed_rtrv.size() > 0) {
ListIterator li = failed_rtrv.listIterator(0);
while (li.hasNext()) flout("lost data: " + (String) li.next() + "\n");
}
if (failed_md_rtrv.size() > 0) {
ListIterator li = failed_md_rtrv.listIterator(0);
while (li.hasNext()) flout("lost mdata: " + (String) li.next() + "\n");
}
// long deltat = now.getTime() - start.getTime();
// if (deltat > 0)
// flout("total thruput (bytes/sec rdwr): " +
// (2000 * total_bytes / deltat) + "\n");
try {
new File(lastfile).delete();
} catch (Exception e) {
}
}