/** Run function */
public void run() {
// Display the waiting item during the process instead of the compute button
snake_.start();
myCardLayout.show(cards, /*snake_.getName()*/ "snake");
try {
extractor_ = new SubnetExtractor((ImodNetwork) network_);
if (extractAllRegulators_) {
output_ = new Structure[1];
output_[0] = extractor_.extractRegulators();
} else if (seeds_ == null)
output_ = extractor_.runExtraction(subnetRootName_.getText(), size_, numSubnets_);
else output_ = extractor_.runExtraction(subnetRootName_.getText(), size_, seeds_);
if (output_ != null) done();
else log.info("Subnetwork extraction canceled !");
} catch (final java.lang.OutOfMemoryError oome) {
log.log(Level.SEVERE, oome.getMessage());
SubnetExtraction.this.escapeAction();
String title = "Memory Error";
String msg =
"Java doesn't have access to enough memory for the current operation.<br>"
+ "Large networks require a lot of memory, please increase the max heap<br>"
+ "size in your Java configuration. See the GeneNetWeaver documentation<br>"
+ "for details.";
msg = "<html>" + msg + "</html>";
JOptionPane.showMessageDialog(
GnwGuiSettings.getInstance().getGnwGui().getFrame(),
msg,
title,
JOptionPane.WARNING_MESSAGE);
}
}
/** Called when the activity is first created. */
@Override
public void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
setRequestedOrientation(ActivityInfo.SCREEN_ORIENTATION_LANDSCAPE);
mAlertBuilder = new AlertDialog.Builder(this);
gAlertBuilder = mAlertBuilder; // keep a static copy of this that other classes can use
if (core == null) {
core = (MuPDFCore) getLastNonConfigurationInstance();
if (savedInstanceState != null && savedInstanceState.containsKey("FileName")) {
mFileName = savedInstanceState.getString("FileName");
}
}
if (core == null) {
Intent intent = getIntent();
byte buffer[] = null;
if (Intent.ACTION_VIEW.equals(intent.getAction())) {
Uri uri = intent.getData();
System.out.println("URI to open is: " + uri);
if (uri.toString().startsWith("content://")) {
String reason = null;
try {
InputStream is = getContentResolver().openInputStream(uri);
int len = is.available();
buffer = new byte[len];
is.read(buffer, 0, len);
is.close();
} catch (java.lang.OutOfMemoryError e) {
System.out.println("Out of memory during buffer reading");
reason = e.toString();
} catch (Exception e) {
System.out.println("Exception reading from stream: " + e);
// Handle view requests from the Transformer Prime's file manager
// Hopefully other file managers will use this same scheme, if not
// using explicit paths.
// I'm hoping that this case below is no longer needed...but it's
// hard to test as the file manager seems to have changed in 4.x.
try {
Cursor cursor =
getContentResolver().query(uri, new String[] {"_data"}, null, null, null);
if (cursor.moveToFirst()) {
String str = cursor.getString(0);
if (str == null) {
reason = "Couldn't parse data in intent";
} else {
uri = Uri.parse(str);
}
}
} catch (Exception e2) {
System.out.println("Exception in Transformer Prime file manager code: " + e2);
reason = e2.toString();
}
}
if (reason != null) {
buffer = null;
Resources res = getResources();
AlertDialog alert = mAlertBuilder.create();
setTitle(String.format(res.getString(R.string.cannot_open_document_Reason), reason));
alert.setButton(
AlertDialog.BUTTON_POSITIVE,
getString(R.string.dismiss),
new DialogInterface.OnClickListener() {
public void onClick(DialogInterface dialog, int which) {
finish();
}
});
alert.show();
return;
}
}
if (buffer != null) {
core = openBuffer(buffer, intent.getType());
} else {
String path = Uri.decode(uri.getEncodedPath());
if (path == null) {
path = uri.toString();
}
core = openFile(path);
}
SearchTaskResult.set(null);
}
if (core != null && core.needsPassword()) {
requestPassword(savedInstanceState);
return;
}
if (core != null && core.countPages() == 0) {
core = null;
}
}
if (core == null) {
AlertDialog alert = mAlertBuilder.create();
alert.setTitle(R.string.cannot_open_document);
alert.setButton(
AlertDialog.BUTTON_POSITIVE,
getString(R.string.dismiss),
new DialogInterface.OnClickListener() {
public void onClick(DialogInterface dialog, int which) {
finish();
}
});
alert.setOnCancelListener(
new OnCancelListener() {
@Override
public void onCancel(DialogInterface dialog) {
finish();
}
});
alert.show();
return;
}
createUI(savedInstanceState);
// hide the proof button if this file can't be proofed
if (!core.canProof()) {
mProofButton.setVisibility(View.INVISIBLE);
}
if (isProofing()) {
// start the activity with a new array
mSepEnabled = null;
// show the separations button
mSepsButton.setVisibility(View.VISIBLE);
// hide some other buttons
mLinkButton.setVisibility(View.INVISIBLE);
mReflowButton.setVisibility(View.INVISIBLE);
mOutlineButton.setVisibility(View.INVISIBLE);
mSearchButton.setVisibility(View.INVISIBLE);
mMoreButton.setVisibility(View.INVISIBLE);
} else {
// hide the separations button
mSepsButton.setVisibility(View.INVISIBLE);
}
}