public static void randomToolActions(int numStrokes, boolean brushOnly) {
Composition comp = ImageComponents.getActiveComp().get();
Random random = new Random();
if (comp != null) {
int canvasWidth = comp.getCanvasWidth();
int canvasHeight = comp.getCanvasHeight();
ProgressMonitor progressMonitor = Utils.createPercentageProgressMonitor("1001 Tool Actions");
// So far we are on the EDT
Runnable notEDTThreadTask =
() -> {
assert !SwingUtilities.isEventDispatchThread();
for (int i = 0; i < numStrokes; i++) {
int progressPercentage = (int) ((float) i * 100 / numStrokes);
progressMonitor.setProgress(progressPercentage);
progressMonitor.setNote(progressPercentage + "%");
Runnable edtRunnable =
() -> testToolAction(comp, random, canvasWidth, canvasHeight, brushOnly);
try {
SwingUtilities.invokeAndWait(edtRunnable);
} catch (InterruptedException | InvocationTargetException e) {
e.printStackTrace();
}
comp.repaint();
}
progressMonitor.close();
};
new Thread(notEDTThreadTask).start();
}
}
private void commandLoad(Options options) {
LoadResult result;
Project project = codeAssist.getProject(options);
try {
progressMonitor.attach(project);
if (options.isFileStdin()) {
result = codeAssist.load(project, new File("(stdin)"), options.getHereDocReader(inReader));
} else {
result = codeAssist.load(project, options.getFile(), options.getEncoding());
}
if (options.isPrintAST()) {
Logger.debug("AST:\n%s", result.getAST());
}
if (options.isEmacsFormat()) {
out.print("(");
codeAssistError(result, options);
out.println(")");
} else {
codeAssistError(result, options);
}
} catch (Exception e) {
commandException(e, options);
} finally {
progressMonitor.detach(project);
}
}
public static SubMonitor convert(
ProgressMonitor paramProgressMonitor, String paramString, int paramInt) {
if ((paramProgressMonitor instanceof SubMonitor)) {
paramProgressMonitor.beginTask(paramString, paramInt, paramProgressMonitor.isCancelable());
return (SubMonitor) paramProgressMonitor;
}
paramProgressMonitor.beginTask(paramString, 1000, paramProgressMonitor.isCancelable());
return new SubMonitor(paramProgressMonitor, 1000, paramInt);
}
private void commandTypeInference(Options options) {
TypeInferenceResult result;
Project project = codeAssist.getProject(options);
try {
progressMonitor.attach(project);
if (options.isFileStdin()) {
result =
codeAssist.typeInference(
project,
new File("(stdin)"),
options.getHereDocReader(inReader),
options.getLocation());
} else {
result =
codeAssist.typeInference(
project, options.getFile(), options.getEncoding(), options.getLocation());
}
if (options.isPrintAST()) {
Logger.debug("AST:\n%s", result.getAST());
}
if (options.isTest()) {
Set<String> data = new HashSet<String>();
for (IRubyObject klass : result.getTypeSet()) {
data.add(klass.toString());
}
test(options, data);
} else {
if (options.isEmacsFormat()) {
out.print("(");
out.print("(type");
for (IRubyObject klass : result.getTypeSet()) {
out.print(" \"");
out.print(klass);
out.print("\"");
}
out.println(")");
codeAssistError(result, options);
out.println(")");
} else {
for (IRubyObject klass : result.getTypeSet()) {
out.print("type: ");
out.println(klass);
}
codeAssistError(result, options);
}
}
} catch (Exception e) {
if (options.isTest()) {
testError(options);
}
commandException(e, options);
} finally {
progressMonitor.detach(project);
}
}
/**
* Overrides <code>FilterInputStream.read</code> to update the progress monitor after the read.
*/
public int read(byte b[], int off, int len) throws IOException {
int nr = in.read(b, off, len);
if (nr > 0) monitor.setProgress(nread += nr);
if (monitor.isCanceled()) {
InterruptedIOException exc = new InterruptedIOException("progress");
exc.bytesTransferred = nread;
throw exc;
}
return nr;
}
/**
* Overrides <code>FilterInputStream.read</code> to update the progress monitor after the read.
*/
public int read() throws IOException {
int c = in.read();
if (c >= 0) monitor.setProgress(++nread);
if (monitor.isCanceled()) {
InterruptedIOException exc = new InterruptedIOException("progress");
exc.bytesTransferred = nread;
throw exc;
}
return c;
}
private ProgressMonitorInputStream getMonitorableStream(InputStream stream, String message) {
final ProgressMonitorInputStream pmis = new ProgressMonitorInputStream(this, message, stream);
ProgressMonitor progress = pmis.getProgressMonitor();
progress.setMillisToDecideToPopup(1);
progress.setMillisToPopup(1);
return pmis;
}
/** Construct progress source object. */
public ProgressSource(URL url, String method, int expected) {
this.url = url;
this.method = method;
this.contentType = "content/unknown";
this.progress = 0;
this.lastProgress = 0;
this.expected = expected;
this.state = State.NEW;
this.progressMonitor = ProgressMonitor.getDefault();
this.threshold = progressMonitor.getProgressUpdateThreshold();
}
private void commandFindDefinition(Options options) {
FindDefinitionResult result;
Project project = codeAssist.getProject(options);
try {
progressMonitor.attach(project);
if (options.isFileStdin()) {
result =
codeAssist.findDefinition(
project,
new File("(stdin)"),
options.getHereDocReader(inReader),
options.getLocation());
} else {
result =
codeAssist.findDefinition(
project, options.getFile(), options.getEncoding(), options.getLocation());
}
if (options.isPrintAST()) {
Logger.debug("AST:\n%s", result.getAST());
}
if (options.isTest()) {
Set<String> data = new HashSet<String>();
for (SourceLocation location : result.getLocations()) {
data.add(location.toString());
}
test(options, data);
} else {
if (options.isEmacsFormat()) {
out.print("(");
out.print("(location");
for (SourceLocation location : result.getLocations()) {
if (location.getFile() != null)
out.printf(" (%s . %d)", emacsStringLiteral(location.getFile()), location.getLine());
}
out.println(")");
codeAssistError(result, options);
out.println(")");
} else {
for (SourceLocation location : result.getLocations()) {
out.printf("location: %d %s\n", location.getLine(), location.getFile());
}
codeAssistError(result, options);
}
}
} catch (Exception e) {
if (options.isTest()) testError(options);
commandException(e, options);
} finally {
progressMonitor.detach(project);
}
}
private void init(Options options) {
codeAssist = new CodeAssist(options);
Integer interval = options.getProgress();
progressMonitor = new ProgressMonitor(out, interval != null ? interval * 1000 : -1);
progressMonitor.setDaemon(true);
}
@Before
public void setUp() throws DaoException {
DaoCancerStudy.reCacheAll();
DaoGeneOptimized.getInstance().reCache();
ProgressMonitor.resetWarnings();
studyId = DaoCancerStudy.getCancerStudyByStableId("study_tcga_pub").getInternalId();
GeneticProfile newGeneticProfile = new GeneticProfile();
newGeneticProfile.setCancerStudyId(studyId);
newGeneticProfile.setGeneticAlterationType(GeneticAlterationType.COPY_NUMBER_ALTERATION);
newGeneticProfile.setStableId("study_tcga_pub_test");
newGeneticProfile.setProfileName("Barry CNA Results");
newGeneticProfile.setDatatype("test");
DaoGeneticProfile.addGeneticProfile(newGeneticProfile);
geneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("study_tcga_pub_test").getGeneticProfileId();
sample1 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SB-01").getInternalId();
sample2 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SD-01").getInternalId();
sample3 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SE-01").getInternalId();
sample4 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SF-01").getInternalId();
sample5 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SG-01").getInternalId();
}
/**
* Read word list from file with name WORDLISTFILENAME, and pass a Set containing those words to
* the computer player to intialize its lexicon.
*/
private void initLexicon(InputStream stream) {
ProgressMonitorInputStream pmis;
ProgressMonitor progress = null;
pmis = new ProgressMonitorInputStream(this, "reading words", stream);
progress = pmis.getProgressMonitor();
progress.setMillisToDecideToPopup(10);
Scanner s = new Scanner(pmis);
myLexicon.load(s);
try {
pmis.close();
} catch (IOException e) {
JOptionPane.showMessageDialog(
null, "Error Closing Stream", "Error", JOptionPane.ERROR_MESSAGE);
}
}
// command line utility
public static void main(String[] args) throws IOException, DaoException {
if (args.length != 2) {
System.out.printf(
"command line usage: importGistic.pl <gistic-data-file.txt> <cancer-study-id>\n"
+ "\t <gistic-data-file.txt> Note that gistic-data-file.txt must be a massaged file, it does not come straight from the Broad\n"
+ "\t <cancer-study-id> e.g. 'tcga_gbm'");
return;
}
SpringUtil.initDataSource();
GisticReader gisticReader = new GisticReader();
File gistic_f = new File(args[0]);
int cancerStudyInternalId = gisticReader.getCancerStudyInternalId(args[1]);
ProgressMonitor.setConsoleMode(false);
System.out.println("Reading data from: " + gistic_f.getAbsolutePath());
System.out.println("CancerStudyId: " + cancerStudyInternalId);
int lines = FileUtil.getNumLines(gistic_f);
System.out.println(" --> total number of lines: " + lines);
ProgressMonitor.setMaxValue(lines);
ArrayList<Gistic> gistics = null;
gistics = gisticReader.parse(gistic_f, cancerStudyInternalId);
if (gistics == null) {
System.out.println("Error: didn't get any data");
return;
}
// add to CGDS database
for (Gistic g : gistics) {
try {
DaoGistic.addGistic(g);
} catch (validationException e) {
// only catching validationException, not DaoException
logger.debug(e);
} catch (DaoException e) {
System.err.println(e);
}
}
ConsoleUtil.showWarnings();
}
private void commandWhere(Options options) {
WhereResult result;
Project project = codeAssist.getProject(options);
try {
progressMonitor.attach(project);
if (options.isFileStdin()) {
result =
codeAssist.where(
project,
new File("(stdin)"),
options.getHereDocReader(inReader),
options.getLine());
} else {
result =
codeAssist.where(project, options.getFile(), options.getEncoding(), options.getLine());
}
if (options.isPrintAST()) {
Logger.debug("AST:\n%s", result.getAST());
}
if (options.isTest()) {
Set<String> data = new HashSet<String>();
if (result.getName() != null) data.add(result.getName());
test(options, data);
} else {
if (options.isEmacsFormat()) {
out.print("(");
if (result.getName() != null) out.printf("(name . \"%s\")", result.getName());
codeAssistError(result, options);
out.println(")");
} else {
if (result.getName() != null) {
out.print("name: ");
out.println(result.getName());
}
codeAssistError(result, options);
}
}
} catch (Exception e) {
if (options.isTest()) testError(options);
commandException(e, options);
} finally {
progressMonitor.detach(project);
}
}
@Override
public void setActiveAlgorithm(int indexFamily, String name, Object cookie) {
if (input == null) {
return;
}
GeneralFeatureIntensity<T, D> intensity = (GeneralFeatureIntensity<T, D>) cookie;
gui.reset();
BufferedImage b = VisualizeImageData.grayMagnitude(workImage, null, 255);
gui.addImage(b, "Gray Image");
final ProgressMonitor progressMonitor =
new ProgressMonitor(
this, "Computing Scale Space Pyramid Response", "", 0, pyramid.getNumLayers());
for (int i = 0; i < pyramid.getNumLayers() && !progressMonitor.isCanceled(); i++) {
double scale = pyramid.getScale(i);
T scaledImage = pyramid.getLayer(i);
anyDerivative.setInput(scaledImage);
D derivX = anyDerivative.getDerivative(true);
D derivY = anyDerivative.getDerivative(false);
D derivXX = anyDerivative.getDerivative(true, true);
D derivYY = anyDerivative.getDerivative(false, false);
D derivXY = anyDerivative.getDerivative(true, false);
intensity.process(scaledImage, derivX, derivY, derivXX, derivYY, derivXY);
ImageFloat32 featureImg = intensity.getIntensity();
// scale it up to full resolution
DistortImageOps.scale(featureImg, scaledIntensity, TypeInterpolate.NEAREST_NEIGHBOR);
// visualize the rescaled intensity
b = VisualizeImageData.colorizeSign(scaledIntensity, null, PixelMath.maxAbs(scaledIntensity));
gui.addImage(b, String.format("Scale %6.2f", scale));
final int progressStatus = i + 1;
SwingUtilities.invokeLater(
new Runnable() {
public void run() {
progressMonitor.setProgress(progressStatus);
}
});
}
gui.requestFocusInWindow();
}
private ProgressMonitorInputStream getMonitorableStream(File file, String message) {
try {
FileInputStream stream = new FileInputStream(file);
if (stream == null) {
System.out.println("null on " + file.getCanonicalPath());
}
final ProgressMonitorInputStream pmis = new ProgressMonitorInputStream(this, message, stream);
ProgressMonitor progress = pmis.getProgressMonitor();
progress.setMillisToDecideToPopup(1);
progress.setMillisToPopup(1);
return pmis;
} catch (IOException e) {
showError("could not open " + file.getName());
e.printStackTrace();
return null;
}
}
private void runImportCnaData() throws DaoException, IOException {
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
// the largest current true Entrez gene ID counts 8 digits
daoGene.addGene(new CanonicalGene(999999207, "TESTAKT1"));
daoGene.addGene(new CanonicalGene(999999208, "TESTAKT2"));
daoGene.addGene(new CanonicalGene(999910000, "TESTAKT3"));
daoGene.addGene(new CanonicalGene(999999369, "TESTARAF"));
daoGene.addGene(new CanonicalGene(999999472, "TESTATM"));
daoGene.addGene(new CanonicalGene(999999673, "TESTBRAF"));
daoGene.addGene(new CanonicalGene(999999672, "TESTBRCA1"));
daoGene.addGene(new CanonicalGene(999999675, "TESTBRCA2"));
ProgressMonitor.setConsoleMode(false);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/cna_test.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, "Barry", geneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
String value = dao.getGeneticAlteration(geneticProfileId, sample1, 999999207);
assertEquals("0", value);
value = dao.getGeneticAlteration(geneticProfileId, sample4, 999999207);
assertEquals("-1", value);
value = dao.getGeneticAlteration(geneticProfileId, sample2, 999999207);
assertEquals("0", value);
value = dao.getGeneticAlteration(geneticProfileId, sample2, 999910000);
assertEquals("2", value);
value = dao.getGeneticAlteration(geneticProfileId, sample3, 999910000);
assertEquals("2", value);
int cnaStatus =
Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 999910000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 999910000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 999999207));
assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus);
Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB");
Sample sample =
DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ");
sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
ArrayList caseIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId);
assertEquals(14, caseIds.size());
}
public void test_checkAllConditions_isCancelled() throws Exception {
Refactoring refactoring = mock(RefactoringImpl.class);
when(refactoring.checkAllConditions(any(ProgressMonitor.class))).thenCallRealMethod();
// make monitor as cancelled
when(pm.isCanceled()).thenReturn(true);
// check all conditions
try {
refactoring.checkAllConditions(pm);
fail();
} catch (OperationCanceledException e) {
}
verify(refactoring).checkInitialConditions(any(ProgressMonitor.class));
verify(refactoring, times(0)).checkFinalConditions(any(ProgressMonitor.class));
}
@Override
public void compile(
final CCTask task,
final File outputDir,
final String[] sourceFiles,
final boolean relentless,
final ProgressMonitor monitor)
throws BuildException {
if (monitor != null) {
monitor.start(this);
}
try {
this.compiler.compile(
task, outputDir, sourceFiles, this.args, this.endArgs, relentless, this, monitor);
if (monitor != null) {
monitor.finish(this, true);
}
} catch (final BuildException ex) {
if (monitor != null) {
monitor.finish(this, false);
}
throw ex;
}
}
private void runImportRnaData1() throws DaoException, IOException {
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
daoGene.addGene(new CanonicalGene(999999780, "A"));
daoGene.addGene(new CanonicalGene(999995982, "B"));
daoGene.addGene(new CanonicalGene(999993310, "C"));
daoGene.addGene(new CanonicalGene(999997849, "D"));
daoGene.addGene(new CanonicalGene(999992978, "E"));
daoGene.addGene(new CanonicalGene(999997067, "F"));
daoGene.addGene(new CanonicalGene(999911099, "G"));
daoGene.addGene(new CanonicalGene(999999675, "6352"));
GeneticProfile geneticProfile = new GeneticProfile();
geneticProfile.setCancerStudyId(studyId);
geneticProfile.setStableId("gbm_mrna");
geneticProfile.setGeneticAlterationType(GeneticAlterationType.MRNA_EXPRESSION);
geneticProfile.setDatatype("CONTINUOUS");
geneticProfile.setProfileName("MRNA Data");
geneticProfile.setProfileDescription("mRNA Data");
DaoGeneticProfile.addGeneticProfile(geneticProfile);
int newGeneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("gbm_mrna").getGeneticProfileId();
ProgressMonitor.setConsoleMode(true);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/mrna_test.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, newGeneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
ConsoleUtil.showMessages();
int sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "DD639").getInternalId();
String value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999992978);
assertEquals("2.01", value);
sampleId = DaoSample.getSampleByCancerStudyAndSampleId(studyId, "DD638").getInternalId();
value = dao.getGeneticAlteration(newGeneticProfileId, sampleId, 999997849);
assertEquals("0.55", value);
}
private void runImportCnaData2() throws DaoException, IOException {
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
ProgressMonitor.setConsoleMode(false);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/cna_test2.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, geneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
String value = dao.getGeneticAlteration(geneticProfileId, sample1, 207);
assertEquals(value, "0");
value = dao.getGeneticAlteration(geneticProfileId, sample4, 207);
assertEquals(value, "-1");
value = dao.getGeneticAlteration(geneticProfileId, sample2, 207);
assertEquals(value, "0");
value = dao.getGeneticAlteration(geneticProfileId, sample2, 10000);
assertEquals(value, "2");
value = dao.getGeneticAlteration(geneticProfileId, sample3, 10000);
assertEquals(value, "2");
int cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 10000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 10000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 207));
assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus);
Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB");
Sample sample =
DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ");
sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
ArrayList sampleIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId);
assertEquals(14, sampleIds.size());
}
public EntryDialog(Activity context) {
super(context, android.R.style.Theme_Light);
mMenuInflater = context.getMenuInflater();
// Request a progress bar to display while the HTML content is loading.
Window window = getWindow();
ProgressMonitor.requestWindowFeatures(window);
setContentView(R.layout.atom_entry);
// Find the ScrollView
mScrollView = (ScrollView) findViewById(android.R.id.tabcontent);
// Find the title view, and make it a clickable link
mTitleView = (TextView) findViewById(android.R.id.text1);
addLinkMovementMethod(mTitleView);
// Find the content view, and configure the progress monitor.
mContentView = (WebView) findViewById(android.R.id.text2);
WebChromeClient monitor = new ProgressMonitor(window);
mContentView.setWebChromeClient(monitor);
}
/** Update progress. */
public void updateProgress(int latestProgress, int expectedProgress) {
lastProgress = progress;
progress = latestProgress;
expected = expectedProgress;
if (connected() == false) state = State.CONNECTED;
else state = State.UPDATE;
// The threshold effectively divides the progress into
// different set of ranges:
//
// Range 0: 0..threshold-1,
// Range 1: threshold .. 2*threshold-1
// ....
// Range n: n*threshold .. (n+1)*threshold-1
//
// To determine which range the progress belongs to, it
// would be calculated as follow:
//
// range number = progress / threshold
//
// Notification should only be triggered when the current
// progress and the last progress are in different ranges,
// i.e. they have different range numbers.
//
// Using this range scheme, notification will be generated
// only once when the progress reaches each range.
//
if (lastProgress / threshold != progress / threshold) {
progressMonitor.updateProgress(this);
}
// Detect read overrun
if (expected != -1) {
if (progress >= expected && progress != 0) close();
}
}
public void run() {
WindowBlocker blocker = new WindowBlocker(NearInfinity.getInstance());
blocker.setBlocked(true);
List<ResourceEntry> creFiles = ResourceFactory.getInstance().getResources("CRE");
creFiles.addAll(ResourceFactory.getInstance().getResources("CHR"));
ProgressMonitor progress =
new ProgressMonitor(
NearInfinity.getInstance(), "Checking inventories...", null, 0, creFiles.size());
table =
new SortableTable(
new String[] {"File", "Name", "Item", "Message"},
new Class[] {Object.class, Object.class, Object.class, Object.class},
new int[] {100, 100, 200, 200});
for (int i = 0; i < creFiles.size(); i++) {
ResourceEntry entry = creFiles.get(i);
try {
if (typeButtons[0].isSelected())
checkCreatureInventory((CreResource) ResourceFactory.getResource(entry));
if (typeButtons[1].isSelected())
checkItemAttribute((CreResource) ResourceFactory.getResource(entry));
} catch (Exception e) {
e.printStackTrace();
}
progress.setProgress(i + 1);
if (progress.isCanceled()) {
JOptionPane.showMessageDialog(
NearInfinity.getInstance(),
"Operation canceled",
"Info",
JOptionPane.INFORMATION_MESSAGE);
blocker.setBlocked(false);
return;
}
}
if (table.getRowCount() == 0)
JOptionPane.showMessageDialog(
NearInfinity.getInstance(), "No hits found", "Info", JOptionPane.INFORMATION_MESSAGE);
else {
resultFrame = new ChildFrame("Result of CRE inventory check", true);
resultFrame.setIconImage(Icons.getIcon("Refresh16.gif").getImage());
bopen = new JButton("Open", Icons.getIcon("Open16.gif"));
bopennew = new JButton("Open in new window", Icons.getIcon("Open16.gif"));
JLabel count = new JLabel(table.getRowCount() + " hit(s) found", JLabel.CENTER);
count.setFont(count.getFont().deriveFont((float) count.getFont().getSize() + 2.0f));
bopen.setMnemonic('o');
bopennew.setMnemonic('n');
resultFrame.getRootPane().setDefaultButton(bopennew);
JPanel panel = new JPanel(new FlowLayout(FlowLayout.CENTER));
panel.add(bopen);
panel.add(bopennew);
JScrollPane scrollTable = new JScrollPane(table);
scrollTable.getViewport().setBackground(table.getBackground());
JPanel pane = (JPanel) resultFrame.getContentPane();
pane.setLayout(new BorderLayout(0, 3));
pane.add(count, BorderLayout.NORTH);
pane.add(scrollTable, BorderLayout.CENTER);
pane.add(panel, BorderLayout.SOUTH);
bopen.setEnabled(false);
bopennew.setEnabled(false);
table.setFont(BrowserMenuBar.getInstance().getScriptFont());
table.getSelectionModel().addListSelectionListener(this);
table.addMouseListener(
new MouseAdapter() {
public void mouseReleased(MouseEvent event) {
if (event.getClickCount() == 2) {
int row = table.getSelectedRow();
if (row != -1) {
ResourceEntry resourceEntry = (ResourceEntry) table.getValueAt(row, 0);
Resource resource = ResourceFactory.getResource(resourceEntry);
new ViewFrame(resultFrame, resource);
((AbstractStruct) resource)
.getViewer()
.selectEntry(((Item) table.getValueAt(row, 2)).getName());
}
}
}
});
bopen.addActionListener(this);
bopennew.addActionListener(this);
pane.setBorder(BorderFactory.createEmptyBorder(3, 3, 3, 3));
resultFrame.pack();
Center.center(resultFrame, NearInfinity.getInstance().getBounds());
resultFrame.setVisible(true);
}
blocker.setBlocked(false);
// for (int i = 0; i < table.getRowCount(); i++) {
// CreInvError error = (CreInvError)table.getTableItemAt(i);
// System.out.println(error.resourceEntry + " (" + error.resourceEntry.getSearchString() +
// ") -> " + error.itemRef.getAttribute("Item"));
// }
}
/**
* Overrides <code>FilterInputStream.reset</code> to reset the progress monitor as well as the
* stream.
*/
public synchronized void reset() throws IOException {
in.reset();
nread = size - in.available();
monitor.setProgress(nread);
}
/**
* Overrides <code>FilterInputStream.close</code> to close the progress monitor as well as the
* stream.
*/
public void close() throws IOException {
in.close();
monitor.close();
}
/**
* Overrides <code>FilterInputStream.skip</code> to update the progress monitor after the skip.
*/
public long skip(long n) throws IOException {
long nr = in.skip(n);
if (nr > 0) monitor.setProgress(nread += nr);
return nr;
}
public void run() {
WindowBlocker blocker = new WindowBlocker(NearInfinity.getInstance());
blocker.setBlocked(true);
List<ResourceEntry> files = new ArrayList<ResourceEntry>();
for (final String fileType : FILETYPES)
files.addAll(ResourceFactory.getInstance().getResources(fileType));
ProgressMonitor progress =
new ProgressMonitor(NearInfinity.getInstance(), "Searching...", null, 0, files.size());
table =
new SortableTable(
new String[] {"String", "StrRef"},
new Class[] {Object.class, Integer.class},
new int[] {450, 20});
StringResource.getStringRef(0);
strUsed = new boolean[StringResource.getMaxIndex() + 1];
for (int i = 0; i < files.size(); i++) {
ResourceEntry entry = files.get(i);
Resource resource = ResourceFactory.getResource(entry);
if (resource instanceof DlgResource) checkDialog((DlgResource) resource);
else if (resource instanceof BcsResource) checkScript((BcsResource) resource);
else if (resource instanceof PlainTextResource) checkTextfile((PlainTextResource) resource);
else if (resource != null) checkStruct((AbstractStruct) resource);
progress.setProgress(i + 1);
if (progress.isCanceled()) {
JOptionPane.showMessageDialog(
NearInfinity.getInstance(),
"Operation canceled",
"Info",
JOptionPane.INFORMATION_MESSAGE);
blocker.setBlocked(false);
return;
}
}
for (int i = 0; i < strUsed.length; i++)
if (!strUsed[i]) table.addTableItem(new UnusedStringTableItem(new Integer(i)));
if (table.getRowCount() == 0)
JOptionPane.showMessageDialog(
NearInfinity.getInstance(),
"No unused strings found",
"Info",
JOptionPane.INFORMATION_MESSAGE);
else {
table.tableComplete(1);
textArea = new JTextArea(10, 40);
textArea.setEditable(false);
textArea.setWrapStyleWord(true);
textArea.setLineWrap(true);
JScrollPane scrollText = new JScrollPane(textArea);
resultFrame = new ChildFrame("Result", true);
save = new JMenuItem("Save");
save.addActionListener(this);
JMenu fileMenu = new JMenu("File");
fileMenu.add(save);
JMenuBar menuBar = new JMenuBar();
menuBar.add(fileMenu);
resultFrame.setJMenuBar(menuBar);
resultFrame.setIconImage(Icons.getIcon("Find16.gif").getImage());
JLabel count = new JLabel(table.getRowCount() + " unused string(s) found", JLabel.CENTER);
count.setFont(count.getFont().deriveFont((float) count.getFont().getSize() + 2.0f));
JScrollPane scrollTable = new JScrollPane(table);
scrollTable.getViewport().setBackground(table.getBackground());
JPanel pane = (JPanel) resultFrame.getContentPane();
pane.setLayout(new BorderLayout(0, 3));
pane.add(count, BorderLayout.NORTH);
pane.add(scrollTable, BorderLayout.CENTER);
JPanel bottomPanel = new JPanel(new BorderLayout());
JPanel searchPanel = SearchMaster.createAsPanel(this, resultFrame);
bottomPanel.add(scrollText, BorderLayout.CENTER);
bottomPanel.add(searchPanel, BorderLayout.EAST);
pane.add(bottomPanel, BorderLayout.SOUTH);
table.setFont(BrowserMenuBar.getInstance().getScriptFont());
pane.setBorder(BorderFactory.createEmptyBorder(3, 3, 3, 3));
table.getSelectionModel().addListSelectionListener(this);
resultFrame.pack();
Center.center(resultFrame, NearInfinity.getInstance().getBounds());
resultFrame.setVisible(true);
}
blocker.setBlocked(false);
}
/**
* Creates a new request wrapper to handle multi-part data using methods adapted from Jason Pell's
* multipart classes (see class description).
*
* @param saveDir the directory to save off the file
* @param servletRequest the request containing the multipart
* @throws java.io.IOException is thrown if encoding fails.
*/
@SuppressWarnings("unchecked")
@Override
public void parse(HttpServletRequest servletRequest, String saveDir) throws IOException {
DiskFileItemFactory fac = new DiskFileItemFactory();
// Make sure that the data is written to file
fac.setSizeThreshold(0);
if (saveDir != null) {
fac.setRepository(new File(saveDir));
}
ProgressMonitor monitor = null;
// Parse the request
try {
ServletFileUpload upload = new ServletFileUpload(fac);
upload.setSizeMax(maxSize);
monitor = new ProgressMonitor();
upload.setProgressListener(monitor);
servletRequest.getSession().setAttribute(ProgressMonitor.SESSION_PROGRESS_MONITOR, monitor);
List<FileItem> items = upload.parseRequest(createRequestContext(servletRequest));
for (FileItem item1 : items) {
FileItem item = item1;
if (log.isDebugEnabled()) {
log.debug("Found item " + item.getFieldName());
}
if (item.isFormField()) {
if (log.isDebugEnabled()) {
log.debug("Item is a normal form field");
}
List<String> values;
if (params.get(item.getFieldName()) != null) {
values = params.get(item.getFieldName());
} else {
values = new ArrayList<String>();
}
// note: see http://jira.opensymphony.com/browse/WW-633
// basically, in some cases the charset may be null, so
// we're just going to try to "other" method (no idea if this
// will work)
String charset = servletRequest.getCharacterEncoding();
if (charset != null) {
values.add(item.getString(charset));
} else {
values.add(item.getString());
}
params.put(item.getFieldName(), values);
} else {
if (log.isDebugEnabled()) {
log.debug("Item is a file upload");
}
List<FileItem> values;
if (files.get(item.getFieldName()) != null) {
values = files.get(item.getFieldName());
} else {
values = new ArrayList<FileItem>();
}
values.add(item);
files.put(item.getFieldName(), values);
}
}
} catch (FileUploadException e) {
e.printStackTrace();
if (monitor != null) monitor.abort();
log.error(e);
errors.add(e.getMessage());
} catch (Exception e) {
e.printStackTrace();
if (monitor != null) monitor.abort();
}
}
@Override
public int read(char[] cbuf, int off, int len) throws IOException {
int res = inReader.read(cbuf, off, len);
monitor.reportProgress(countingIn.getByteCount());
return res;
}
