List of usage examples for java.awt FileDialog LOAD
int LOAD
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From source file:edu.ku.brc.specify.config.ResourceImportExportDlg.java
/** * /*from ww w .jav a2 s . c om*/ */ protected void importResource() { int levelIndex = levelCBX.getSelectedIndex(); if (levelIndex > -1) { String importedName = null; final String IMP_DIR_PREF = "RES_LAST_IMPORT_DIR"; String initalImportDir = AppPreferences.getLocalPrefs().get(IMP_DIR_PREF, getUserHomeDir()); FileDialog fileDlg = new FileDialog(this, getResourceString("RIE_IMPORT_RES"), FileDialog.LOAD); File impDir = new File(initalImportDir); if (StringUtils.isNotEmpty(initalImportDir) && impDir.exists()) { fileDlg.setDirectory(initalImportDir); } UIHelper.centerAndShow(fileDlg); String dirStr = fileDlg.getDirectory(); String fileName = fileDlg.getFile(); if (StringUtils.isNotEmpty(dirStr) && StringUtils.isNotEmpty(fileName)) { AppPreferences.getLocalPrefs().put(IMP_DIR_PREF, dirStr); String data = null; String fullFileName = dirStr + File.separator + fileName; File importFile = new File(fullFileName); if (importFile.exists()) { String repResourceName = getSpReportResourceName(importFile); boolean isSpReportRes = repResourceName != null; boolean isJRReportRes = false; try { data = FileUtils.readFileToString(importFile); isJRReportRes = isJasperReport(data); } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(ResourceImportExportDlg.class, ex); return; } boolean isReportRes = isJRReportRes || isSpReportRes; if (tabbedPane.getSelectedComponent() == viewsPanel) { int viewIndex = viewSetsList.getSelectedIndex(); if (viewIndex > -1) { boolean isAddItemForImport = viewSetsList.getSelectedValue() instanceof String; boolean isOK = false; SpViewSetObj vso = null; DataProviderSessionIFace session = null; try { session = DataProviderFactory.getInstance().createSession(); session.beginTransaction(); if (!isAddItemForImport) { vso = (SpViewSetObj) viewSetsList.getSelectedValue(); SpAppResourceDir appResDir = vso.getSpAppResourceDir(); importedName = vso.getName(); if (vso.getSpViewSetObjId() == null) { appResDir.getSpPersistedViewSets().add(vso); vso.setSpAppResourceDir(appResDir); } vso.setDataAsString(data, true); session.saveOrUpdate(appResDir); } else { SpAppResourceDir appResDir = dirs.get(levelIndex); vso = new SpViewSetObj(); vso.initialize(); vso.setLevel((short) levelIndex); vso.setName(FilenameUtils.getBaseName(importFile.getName())); appResDir.getSpPersistedViewSets().add(vso); vso.setSpAppResourceDir(appResDir); vso.setDataAsString(data); session.saveOrUpdate(appResDir); } session.saveOrUpdate(vso); for (SpAppResourceData ard : vso.getSpAppResourceDatas()) { session.saveOrUpdate(ard); } session.commit(); session.flush(); setHasChanged(true); isOK = true; completeMsg = getLocalizedMessage("RIE_RES_IMPORTED", importedName == null ? fileName : importedName); } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance() .capture(ResourceImportExportDlg.class, ex); session.rollback(); } finally { try { session.close(); } catch (Exception ex) { ex.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance() .capture(ResourceImportExportDlg.class, ex); } } if (isOK) { if (isAddItemForImport) { viewSetsModel.clear(); viewSetsModel.addElement(vso); } else { viewSetsModel.remove(viewIndex); viewSetsModel.insertElementAt(vso, viewIndex); } viewSetsList.repaint(); } } } else { boolean isResourcePanel = tabbedPane.getSelectedComponent() == repPanel; JList theList = isResourcePanel ? repList : resList; int resIndex = theList.getSelectedIndex(); Object selObj = theList.getSelectedValue(); if (resIndex > -1) { if (resIndex == 0) // means we are adding a new resource { try { SpecifyUser user = contextMgr.getClassObject(SpecifyUser.class); Agent agent = contextMgr.getClassObject(Agent.class); SpAppResourceDir dir = dirs.get(levelIndex); SpAppResource appRes = new SpAppResource(); appRes.initialize(); appRes.setName(fileName); appRes.setCreatedByAgent(agent); appRes.setSpecifyUser(user); if (dir.getId() == null) { dir.mergeTransientResourceAndViewSets(); } Pair<SpAppResource, String> retValues = checkForOverwriteOrNewName(dir, isSpReportRes ? repResourceName : fileName, isSpReportRes); if (retValues != null && retValues.first == null && retValues.second == null) { return; // Dialog was Cancelled } SpAppResource fndAppRes = retValues != null && retValues.first != null ? retValues.first : null; String newResName = retValues != null && retValues.second != null ? retValues.second : null; if (isReportRes) { if (fndAppRes != null) { if (isSpReportRes) { ReportsBaseTask.deleteReportAndResource(null, fndAppRes.getId()); } else { //XXX ??????????? if (fndAppRes.getSpAppResourceId() != null) { contextMgr.removeAppResourceSp(fndAppRes.getSpAppResourceDir(), fndAppRes); } } } /*else if (newResName == null) { return; }*/ if (isSpReportRes) { appRes = importSpReportZipResource(importFile, appRes, dir, newResName); if (appRes != null) { importedName = appRes.getName(); } } else { if (MainFrameSpecify.importJasperReport(importFile, false, newResName)) { importedName = importFile.getName(); } else { return; } } if (importedName != null) { CommandDispatcher.dispatch(new CommandAction(ReportsBaseTask.REPORTS, ReportsBaseTask.REFRESH, null)); CommandDispatcher.dispatch(new CommandAction(QueryTask.QUERY, QueryTask.REFRESH_QUERIES, null)); levelSelected(); } } else if (fndAppRes != null) // overriding { appRes.setMetaData(fndAppRes.getMetaData()); appRes.setDescription(fndAppRes.getDescription()); appRes.setFileName(fileName); appRes.setMimeType(appRes.getMimeType()); appRes.setName(fileName); appRes.setLevel(fndAppRes.getLevel()); } else if (!getMetaInformation(appRes, fileName)) { return; } if (!isReportRes) { appRes.setSpAppResourceDir(dir); dir.getSpAppResources().add(appRes); appRes.setDataAsString(data); contextMgr.saveResource(appRes); completeMsg = getLocalizedMessage("RIE_RES_IMPORTED", importedName == null ? fileName : importedName); } setHasChanged(true); } catch (Exception e) { e.printStackTrace(); edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance() .capture(ResourceImportExportDlg.class, e); } } else if (selObj instanceof AppResourceIFace) { //if (isResourcePanel) resIndex++; AppResourceIFace fndAppRes = null; for (AppResourceIFace appRes : resources) { if (appRes == selObj) { fndAppRes = appRes; break; } } if (fndAppRes != null) { String importedFileName = fndAppRes.getFileName(); String fName = FilenameUtils.getName(importedFileName); String dbBaseName = FilenameUtils.getBaseName(fileName); //log.debug("["+fName+"]["+dbBaseName+"]"); boolean doOverwrite = true; if (!dbBaseName.equals(fName)) { String msg = getLocalizedMessage("RIE_OVRDE_MSG", dbBaseName, fName); doOverwrite = displayConfirm(getResourceString("RIE_OVRDE_TITLE"), msg, getResourceString("RIE_OVRDE"), getResourceString("CANCEL"), JOptionPane.QUESTION_MESSAGE); } if (doOverwrite) { fndAppRes.setDataAsString(data); contextMgr.saveResource(fndAppRes); completeMsg = getLocalizedMessage("RIE_RES_IMPORTED", importedName == null ? fileName : importedName); } } else { UIRegistry.showError("Strange error - Couldn't resource."); } } } } if (importedName != null) { completeMsg = getLocalizedMessage("RIE_RES_IMPORTED", importedName == null ? fileName : importedName); } if (hasChanged()) { SwingUtilities.invokeLater(new Runnable() { @Override public void run() { okBtn.doClick(); } }); } } else { UIRegistry.showLocalizedError("FILE_NO_EXISTS", fullFileName); } } enableUI(); } }
From source file:com.jug.MoMA.java
/** * Shows a JFileChooser set up to accept the selection of folders. If * 'cancel' is pressed this method terminates the MotherMachine app. * * @param guiFrame/*from www. ja va 2 s. c o m*/ * parent frame * @param path * path to the folder to open initially * @return an instance of {@link File} pointing at the selected folder. */ private File showFolderChooser(final JFrame guiFrame, final String path) { File selectedFile = null; if (SystemUtils.IS_OS_MAC) { // --- ON MAC SYSTEMS --- ON MAC SYSTEMS --- ON MAC SYSTEMS --- ON MAC SYSTEMS --- ON MAC SYSTEMS --- System.setProperty("apple.awt.fileDialogForDirectories", "true"); final FileDialog fd = new FileDialog(guiFrame, "Select folder containing image sequence...", FileDialog.LOAD); fd.setDirectory(path); // fd.setLocation(50,50); fd.setVisible(true); selectedFile = new File(fd.getDirectory() + "/" + fd.getFile()); if (fd.getFile() == null) { System.exit(0); return null; } System.setProperty("apple.awt.fileDialogForDirectories", "false"); } else { // --- NOT ON A MAC --- NOT ON A MAC --- NOT ON A MAC --- NOT ON A MAC --- NOT ON A MAC --- NOT ON A MAC --- final JFileChooser chooser = new JFileChooser(); chooser.setCurrentDirectory(new java.io.File(path)); chooser.setDialogTitle("Select folder containing image sequence..."); chooser.setFileFilter(new FileFilter() { @Override public final boolean accept(final File file) { return file.isDirectory(); } @Override public String getDescription() { return "We only take directories"; } }); chooser.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY); chooser.setAcceptAllFileFilterUsed(false); if (chooser.showOpenDialog(guiFrame) == JFileChooser.APPROVE_OPTION) { selectedFile = chooser.getSelectedFile(); } else { System.exit(0); return null; } } return selectedFile; }
From source file:edu.ku.brc.specify.tasks.ReportsBaseTask.java
protected void importReport() { FileDialog fileDialog = new FileDialog((Frame) UIRegistry.get(UIRegistry.FRAME), getResourceString("CHOOSE_WORKBENCH_IMPORT_FILE"), FileDialog.LOAD); //Really shouldn't override workbench prefs with report stuff??? fileDialog.setDirectory(WorkbenchTask.getDefaultDirPath(WorkbenchTask.IMPORT_FILE_PATH)); fileDialog.setFilenameFilter(new java.io.FilenameFilter() { public boolean accept(File dir, String filename) { return FilenameUtils.getExtension(filename).equalsIgnoreCase("jrxml"); }//www.java 2s. c om }); UIHelper.centerAndShow(fileDialog); fileDialog.dispose(); String fileName = fileDialog.getFile(); String path = fileDialog.getDirectory(); if (StringUtils.isNotEmpty(path)) { AppPreferences localPrefs = AppPreferences.getLocalPrefs(); localPrefs.put(WorkbenchTask.IMPORT_FILE_PATH, path); } File file; if (StringUtils.isNotEmpty(fileName) && StringUtils.isNotEmpty(path)) { file = new File(path + File.separator + fileName); } else { return; } if (file.exists()) { if (MainFrameSpecify.importJasperReport(file, true, null)) { refreshCommands(); } //else -- assume feedback during importJasperReport() } }
From source file:edu.ku.brc.specify.tasks.QueryTask.java
/** * //from w ww . ja v a 2 s . c o m */ protected void importQueries() { UsageTracker.incrUsageCount("QB.IMPORT"); String path = AppPreferences.getLocalPrefs().get(XML_PATH_PREF, null); try { FileDialog fDlg = new FileDialog(((Frame) UIRegistry.getTopWindow()), "Open", FileDialog.LOAD); if (path != null) { fDlg.setDirectory(path); } fDlg.setVisible(true); String dirStr = fDlg.getDirectory(); String fileName = fDlg.getFile(); if (StringUtils.isEmpty(dirStr) || StringUtils.isEmpty(fileName)) { return; } path = dirStr + fileName; AppPreferences.getLocalPrefs().put(XML_PATH_PREF, path); Vector<Pair<SpQuery, Boolean>> queries = getQueriesFromFile(path, getTopLevelNodeSelector()); ToggleButtonChooserDlg<Pair<SpQuery, Boolean>> dlg = new ToggleButtonChooserDlg<Pair<SpQuery, Boolean>>( (Frame) UIRegistry.getMostRecentWindow(), "QY_IMPORT_QUERIES", "QY_SEL_QUERIES_IMP", queries, CustomDialog.OKCANCELHELP, ToggleButtonChooserPanel.Type.Checkbox); dlg.setAddSelectAll(true); dlg.setUseScrollPane(true); dlg.setHelpContext("QBImport"); UIHelper.centerAndShow(dlg); List<Pair<SpQuery, Boolean>> queriesList = dlg.getSelectedObjects(); if (queriesList == null || queriesList.size() == 0) { return; } Vector<String> names = new Vector<String>(); //For exportschemamappings, mapping name is assumed to be the same as associated query name List<Object> nameObjs = BasicSQLUtils.querySingleCol("select name from spquery order by 1"); for (Object q : nameObjs) { names.add((String) q); } adjustImportedQueryNames(queries, names); if (saveImportedQueries(queriesList)) { for (Pair<SpQuery, Boolean> query : queriesList) { RecordSet rs = new RecordSet(); rs.initialize(); rs.set(query.getFirst().getName(), SpQuery.getClassTableId(), RecordSet.GLOBAL); rs.addItem(query.getFirst().getSpQueryId()); addToNavBox(rs); } navBox.validate(); navBox.repaint(); } } catch (Exception ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(QueryTask.class, ex); ex.printStackTrace(); } }
From source file:base.BasePlayer.AddGenome.java
@Override public void mousePressed(MouseEvent e) { if (e.getSource() == tree) { if (selectedNode != null && selectedNode.toString().contains("Add new refe")) { try { FileDialog fs = new FileDialog(frame, "Select reference fasta-file", FileDialog.LOAD); fs.setDirectory(Main.downloadDir); fs.setVisible(true);//from w ww . ja v a 2 s. c o m String filename = fs.getFile(); fs.setFile("*.fasta;*.fa"); fs.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().contains(".fasta") || name.toLowerCase().contains(".fa"); } }); if (filename != null) { File addfile = new File(fs.getDirectory() + "/" + filename); if (addfile.exists()) { genomeFile = addfile; Main.downloadDir = genomeFile.getParent(); Main.writeToConfig("DownloadDir=" + genomeFile.getParent()); OutputRunner runner = new OutputRunner(genomeFile.getName().replace(".fasta", "") .replace(".fa", "").replace(".gz", ""), genomeFile, null); runner.createGenome = true; runner.execute(); } else { Main.showError("File does not exists.", "Error", frame); } } if (1 == 1) { return; } JFileChooser chooser = new JFileChooser(Main.downloadDir); chooser.setMultiSelectionEnabled(false); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); chooser.setAcceptAllFileFilterUsed(false); MyFilterFasta fastaFilter = new MyFilterFasta(); chooser.addChoosableFileFilter(fastaFilter); chooser.setDialogTitle("Select reference fasta-file"); if (Main.screenSize != null) { chooser.setPreferredSize(new Dimension((int) Main.screenSize.getWidth() / 3, (int) Main.screenSize.getHeight() / 3)); } int returnVal = chooser.showOpenDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { genomeFile = chooser.getSelectedFile(); Main.downloadDir = genomeFile.getParent(); Main.writeToConfig("DownloadDir=" + genomeFile.getParent()); OutputRunner runner = new OutputRunner( genomeFile.getName().replace(".fasta", "").replace(".gz", ""), genomeFile, null); runner.createGenome = true; runner.execute(); } } catch (Exception ex) { ex.printStackTrace(); } } else if (selectedNode != null && selectedNode.isLeaf() && selectedNode.toString().contains("Add new anno")) { try { FileDialog fs = new FileDialog(frame, "Select annotation gff3/gtf-file", FileDialog.LOAD); fs.setDirectory(Main.downloadDir); fs.setVisible(true); String filename = fs.getFile(); fs.setFile("*.gff3;*.gtf"); fs.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().contains(".gff3") || name.toLowerCase().contains(".gtf"); } }); if (filename != null) { File addfile = new File(fs.getDirectory() + "/" + filename); if (addfile.exists()) { annotationFile = addfile; Main.downloadDir = annotationFile.getParent(); Main.writeToConfig("DownloadDir=" + annotationFile.getParent()); OutputRunner runner = new OutputRunner(selectedNode.getParent().toString(), null, annotationFile); runner.createGenome = true; runner.execute(); } else { Main.showError("File does not exists.", "Error", frame); } } if (1 == 1) { return; } JFileChooser chooser = new JFileChooser(Main.downloadDir); chooser.setMultiSelectionEnabled(false); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); chooser.setAcceptAllFileFilterUsed(false); MyFilterGFF gffFilter = new MyFilterGFF(); chooser.addChoosableFileFilter(gffFilter); chooser.setDialogTitle("Select annotation gff3-file"); if (Main.screenSize != null) { chooser.setPreferredSize(new Dimension((int) Main.screenSize.getWidth() / 3, (int) Main.screenSize.getHeight() / 3)); } int returnVal = chooser.showOpenDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { annotationFile = chooser.getSelectedFile(); Main.downloadDir = annotationFile.getParent(); Main.writeToConfig("DownloadDir=" + annotationFile.getParent()); OutputRunner runner = new OutputRunner(selectedNode.getParent().toString(), null, annotationFile); runner.createGenome = true; runner.execute(); } } catch (Exception ex) { ex.printStackTrace(); } } } if (e.getSource() == genometable) { if (new File(".").getFreeSpace() / 1048576 < sizeHash.get(genometable.getValueAt(genometable.getSelectedRow(), 0))[0] / 1048576) { sizeError.setVisible(true); download.setEnabled(false); AddGenome.getLinks.setEnabled(false); } else { sizeError.setVisible(false); download.setEnabled(true); AddGenome.getLinks.setEnabled(true); } tree.clearSelection(); remove.setEnabled(false); checkUpdates.setEnabled(false); } }
From source file:base.BasePlayer.Main.java
public void actionPerformed(ActionEvent e) { //Logo.frame.setVisible(false); if (e.getSource() == pleiadesButton) { gotoURL("http://kaptah.local.lab.helsinki.fi/pleiades/"); } else if (e.getSource() == manage) { if (VariantHandler.frame == null) { VariantHandler.main(argsit); }/*w w w . j ava 2s .co m*/ VariantHandler.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantHandler.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); VariantHandler.frame.setState(JFrame.NORMAL); VariantHandler.frame.setVisible(true); Draw.calculateVars = true; Draw.updatevars = true; drawCanvas.repaint(); } else if (e.getSource() == tbrowser) { tablebrowser.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); tablebrowser.frame.setState(JFrame.NORMAL); tablebrowser.frame.setVisible(true); } else if (e.getSource() == bconvert) { bedconverter.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); bedconverter.frame.setState(JFrame.NORMAL); bedconverter.frame.setVisible(true); } else if (e.getSource() == peakCaller) { if (PeakCaller.frame == null) { PeakCaller.main(argsit); } PeakCaller.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); PeakCaller.frame.setState(JFrame.NORMAL); PeakCaller.frame.setVisible(true); } else if (e.getSource() == variantCaller) { //FileRead.checkSamples(); if (VariantCaller.frame == null) { VariantCaller.main(argsit); } VariantCaller.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - VariantCaller.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); VariantCaller.frame.setState(JFrame.NORMAL); VariantCaller.frame.setVisible(true); } else if (e.getSource() == average) { if (Average.frame == null) { Average.createAndShowGUI(); } Average.setSamples(); Average.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - Average.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); Average.frame.setState(JFrame.NORMAL); Average.frame.setVisible(true); } else if (e.getSource() == errorlog) { ErrorLog.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - ErrorLog.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); // VariantHandler.frame.setAlwaysOnTop(true); ErrorLog.frame.setState(JFrame.NORMAL); ErrorLog.frame.setVisible(true); } /* else if(e.getSource() == help) { JOptionPane.showMessageDialog(Main.chromDraw, "This is pre-release version of BasePlayer\nContact: help@baseplayer.fi\nUniversity of Helsinki", "Help", JOptionPane.INFORMATION_MESSAGE); }*/ else if (e.getSource() == settings) { Settings.frame.setLocation( frame.getLocationOnScreen().x + frame.getWidth() / 2 - Settings.frame.getWidth() / 2, frame.getLocationOnScreen().y + frame.getHeight() / 6); Settings.frame.setState(JFrame.NORMAL); Settings.frame.setVisible(true); } else if (e.getSource() == update) { try { Updater update = new Updater(); update.execute(); } catch (Exception ex) { ex.printStackTrace(); } } else if (e.getSource() == clearMemory) { FileRead.nullifyVarNodes(); //FileRead.removeNonListVariants();f System.gc(); chromDraw.repaint(); } else if (e.getSource() == zoomout) { zoomout(); } else if (e.getSource() == dosomething) { BedNode currentbed = bedCanvas.bedTrack.get(0).getHead().getNext(); VarNode currentvar = FileRead.head.getNext(); while (currentbed != null) { while (currentvar != null && currentvar.getPosition() < currentbed.getPosition()) { currentvar = currentvar.getNext(); } while (currentbed != null && currentvar.getPosition() > currentbed.getPosition() + currentbed.getLength()) { currentbed = currentbed.getNext(); } if (currentvar != null && currentvar.getPosition() >= currentbed.getPosition() && currentvar.getPosition() < currentbed.getPosition() + currentbed.getLength()) { currentvar.setBedhit(true); currentvar = currentvar.getNext(); } if (currentvar == null) { break; } currentbed = currentbed.getNext(); } } else if (e.getSource() == clear) { clearData(); } else if (e.getSource() == exit) { System.exit(0); } else if (e.getSource() == openbams) { try { if (!checkGenome()) return; if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } FileDialog fc = new FileDialog(frame, "Choose BAM file(s)", FileDialog.LOAD); fc.setDirectory(path); fc.setFile("*.bam;*.cram;*.link"); fc.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".bam") || name.toLowerCase().endsWith(".cram") || name.toLowerCase().endsWith(".link"); } }); fc.setMultipleMode(true); fc.setVisible(true); File[] openfiles = fc.getFiles(); if (openfiles != null && openfiles.length > 0) { path = openfiles[0].getParent(); writeToConfig("DefaultDir=" + path); FileRead filereader = new FileRead(openfiles); filereader.start = (int) drawCanvas.selectedSplit.start; filereader.end = (int) drawCanvas.selectedSplit.end; filereader.readBAM = true; filereader.execute(); } else { //Main.showError("File(s) does not exist.", "Error"); } } catch (Exception ex) { Main.showError(ex.getMessage(), "Error"); } } else if (e.getSource() == openvcfs) { try { if (!checkGenome()) return; if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } FileDialog fc = new FileDialog(frame, "Choose VCF file(s)", FileDialog.LOAD); fc.setDirectory(path); fc.setFile("*.vcf"); fc.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".vcf") || name.toLowerCase().endsWith(".vcf.gz"); } }); fc.setMultipleMode(true); fc.setVisible(true); File[] openfiles = fc.getFiles(); if (openfiles != null && openfiles.length > 0) { path = openfiles[0].getParent(); writeToConfig("DefaultDir=" + path); FileRead filereader = new FileRead(openfiles); filereader.start = (int) drawCanvas.selectedSplit.start; filereader.end = (int) drawCanvas.selectedSplit.end; filereader.readVCF = true; filereader.execute(); } else { //Main.showError("File(s) does not exist.", "Error"); } if (1 == 1) { return; } JFileChooser chooser = new JFileChooser(path); getText(chooser.getComponents()); chooser.setMultiSelectionEnabled(true); //chooser.setFileSelectionMode(JFileChooser.FILES_AND_DIRECTORIES); chooser.setFileSelectionMode(JFileChooser.FILES_ONLY); chooser.setAcceptAllFileFilterUsed(false); chooser.addChoosableFileFilter(vcfFilter); chooser.addChoosableFileFilter(bamFilter); chooser.addChoosableFileFilter(linkFilter); if (defaultSelectType == "vcf") { chooser.setFileFilter(vcfFilter); } else if (defaultSelectType == "bam") { chooser.setFileFilter(bamFilter); } else { chooser.setFileFilter(linkFilter); } chooser.setDialogTitle("Add samples"); chooser.setPreferredSize( new Dimension((int) screenSize.getWidth() / 3, (int) screenSize.getHeight() / 3)); int returnVal = chooser.showOpenDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { File vcffiles[] = chooser.getSelectedFiles(); if (vcffiles.length == 1 && !vcffiles[0].exists() && pleiades) { if (Main.chooserText.contains("`")) { Main.chooserText.replace("`", "?"); } if (Main.chooserText.contains(" ")) { Main.chooserText.replace(" ", "%20"); } if (Main.chooserText.contains("pleiades")) { try { URL url = new URL(Main.chooserText); //System.out.println(Main.chooserText); HttpURLConnection httpConn = (HttpURLConnection) url.openConnection(); httpConn.connect(); int responseCode = httpConn.getResponseCode(); if (responseCode == HttpsURLConnection.HTTP_OK) { String loading = drawCanvas.loadingtext; InputStream inputStream = httpConn.getInputStream(); BufferedReader reader = new BufferedReader(new InputStreamReader(inputStream)); Main.drawCanvas.loadingtext = loading + " 0MB"; String line; StringBuffer buffer = new StringBuffer(""); while ((line = reader.readLine()) != null) { buffer.append(line); } inputStream.close(); reader.close(); String split2; String[] split = buffer.toString().split("dataUnit"); String location; ArrayList<File> array = new ArrayList<File>(); File[] paths; FileSystemView fsv = FileSystemView.getFileSystemView(); paths = File.listRoots(); String loc = "/mnt"; boolean missingfiles = false; for (File path : paths) { if (fsv.getSystemDisplayName(path).contains("merit")) { loc = path.getCanonicalPath(); } } for (int i = 0; i < split.length; i++) { if (!split[i].contains("lastLocation")) { continue; } split2 = split[i].split("\"lastLocation\":\"")[1]; location = split2.substring(0, split2.indexOf("\"}")); String filename = ""; String testloc = location.replace("/mnt", loc) + "/wgspipeline/"; File testDir = new File(testloc); if (testDir.exists() && testDir.isDirectory()) { if (chooser.getFileFilter() .equals(chooser.getChoosableFileFilters()[1])) { File[] addDir = testDir.listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".bam") || name.toLowerCase().endsWith(".cram"); } }); if (addDir.length > 0) { filename = addDir[0].getName(); } } else { File[] addDir = testDir.listFiles(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".vcf.gz"); } }); if (addDir.length > 0) { filename = addDir[0].getName(); } } } location = testloc + "/" + filename; if (!new File(location).exists()) { if (!new File(location).exists()) { missingfiles = true; ErrorLog.addError("No sample files found in " + testloc); } else { array.add(new File(location)); } } else { array.add(new File(location)); } } File[] files = new File[array.size()]; for (int i = 0; i < files.length; i++) { files[i] = array.get(i); } FileRead filereader = new FileRead(files); filereader.start = (int) drawCanvas.selectedSplit.start; filereader.end = (int) drawCanvas.selectedSplit.end; if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[1])) { filereader.readBAM = true; } else { filereader.readVCF = true; } filereader.execute(); if (missingfiles) { JOptionPane.showMessageDialog(Main.drawScroll, "Missing files. Check Tools->View log", "Note", JOptionPane.INFORMATION_MESSAGE); } } } catch (Exception ex) { ex.printStackTrace(); } } return; } if (vcffiles.length > 0) { path = vcffiles[0].getParent(); writeToConfig("DefaultDir=" + path); FileRead filereader = new FileRead(vcffiles); if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[0])) { defaultSelectType = "vcf"; filereader.start = (int) drawCanvas.selectedSplit.start; filereader.end = (int) drawCanvas.selectedSplit.end; filereader.readVCF = true; filereader.execute(); } else if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[1])) { defaultSelectType = "bam"; filereader.readBAM = true; filereader.execute(); } else if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[2])) { defaultSelectType = "link"; filereader.readBAM = true; filereader.execute(); } } else { JOptionPane.showMessageDialog(Main.drawScroll, "The file does not exist. The file link may be broken.\nThe problem may also be the Java run time version in Linux.", "Note", JOptionPane.INFORMATION_MESSAGE); } } } catch (Exception ex) { ex.printStackTrace(); } } else if (e.getSource() == addcontrols) { if (!checkGenome()) return; if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } FileDialog fc = new FileDialog(frame, "Choose control file(s)", FileDialog.LOAD); fc.setDirectory(Main.controlDir); fc.setFile("*.vcf.gz"); fc.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".vcf.gz"); } }); fc.setMultipleMode(true); fc.setVisible(true); File[] openfiles = fc.getFiles(); if (openfiles != null && openfiles.length > 0) { controlDir = openfiles[0].getParent(); writeToConfig("DefaultControlDir=" + controlDir); Control.addFiles(openfiles); } if (1 == 1) { return; } JFileChooser chooser = new JFileChooser(controlDir); // JFileChooser chooser = new JFileChooser(path); chooser.setMultiSelectionEnabled(true); chooser.setAcceptAllFileFilterUsed(false); Control.MyFilter vcfFilter = new Control.MyFilter(); chooser.addChoosableFileFilter(vcfFilter); chooser.setDialogTitle("Add controls"); chooser.setPreferredSize( new Dimension((int) screenSize.getWidth() / 3, (int) screenSize.getHeight() / 3)); int returnVal = chooser.showOpenDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { File vcffiles[] = chooser.getSelectedFiles(); controlDir = vcffiles[0].getParent(); writeToConfig("DefaultControlDir=" + controlDir); if (chooser.getFileFilter().equals(chooser.getChoosableFileFilters()[0])) { Control.addFiles(vcffiles); } } } else if (e.getSource() == addtracks) { if (!checkGenome()) return; try { if (!checkGenome()) return; if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } FileDialog fc = new FileDialog(frame, "Choose track file(s)", FileDialog.LOAD); fc.setDirectory(Main.trackDir); fc.setFile( "*.bed;*.bedgraph.gz;*.gff.gz;*.gff3.gz;*.bigwig;*.bw;*.bigbed;*.bb;*.tsv.gz;*.tsv.bgz;*.txt"); fc.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".bed") || name.toLowerCase().endsWith(".bed.gz") || name.toLowerCase().endsWith(".bedgraph.gz") || name.toLowerCase().endsWith(".bedgraph.gz") || name.toLowerCase().endsWith(".bedgraph.gz") || name.toLowerCase().endsWith(".gff.gz") || name.toLowerCase().endsWith(".gff3.gz") || name.toLowerCase().endsWith(".bigwig") || name.toLowerCase().endsWith(".bw") || name.toLowerCase().endsWith(".bigbed") || name.toLowerCase().endsWith(".bb") || name.toLowerCase().endsWith(".tsv.gz") || name.toLowerCase().endsWith(".tsv.bgz") || name.toLowerCase().endsWith(".txt"); } }); fc.setMultipleMode(true); fc.setVisible(true); File[] openfiles = fc.getFiles(); if (openfiles != null && openfiles.length > 0) { trackDir = openfiles[0].getParent(); writeToConfig("DefaultTrackDir=" + trackDir); FileRead filereader = new FileRead(openfiles); filereader.readBED = true; filereader.execute(); } else { //Main.showError("File(s) does not exist.", "Error"); } } catch (Exception ex) { Main.showError(ex.getMessage(), "Error"); } if (1 == 1) { return; } if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } JFileChooser chooser = new JFileChooser(Main.trackDir); getText(chooser.getComponents()); chooser.setMultiSelectionEnabled(true); chooser.setAcceptAllFileFilterUsed(false); MyFilterBED bedFilter = new MyFilterBED(); MyFilterTXT txtFilter = new MyFilterTXT(); chooser.addChoosableFileFilter(bedFilter); chooser.addChoosableFileFilter(txtFilter); chooser.setDialogTitle("Add tracks"); chooser.setPreferredSize( new Dimension((int) screenSize.getWidth() / 3, (int) screenSize.getHeight() / 3)); int returnVal = chooser.showOpenDialog((Component) this.getParent()); try { if (returnVal == JFileChooser.APPROVE_OPTION) { File bedfiles[] = chooser.getSelectedFiles(); if (bedfiles[0].exists()) { trackDir = bedfiles[0].getParent(); writeToConfig("DefaultTrackDir=" + trackDir); FileRead filereader = new FileRead(bedfiles); filereader.readBED(bedfiles); } else { if (Main.chooserText.length() > 5 && Main.chooserText.endsWith(".bed.gz") || Main.chooserText.endsWith(".gff.gz") || Main.chooserText.endsWith(".gff3.gz") || Main.chooserText.endsWith(".bedgraph.gz")) { if (Main.chooserText.startsWith("http://") || Main.chooserText.startsWith("ftp://")) { URL url = new URL(Main.chooserText); SeekableStream stream = SeekableStreamFactory.getInstance().getStreamFor(url); TabixReader tabixReader = null; String index = null; try { tabixReader = new TabixReader(Main.chooserText, Main.chooserText + ".tbi", stream); index = Main.chooserText + ".tbi"; } catch (Exception ex) { try { tabixReader = new TabixReader(Main.chooserText, Main.chooserText.substring(0, Main.chooserText.indexOf(".gz")) + ".tbi", stream); index = Main.chooserText.substring(0, Main.chooserText.indexOf(".gz")) + ".tbi"; } catch (Exception exc) { exc.printStackTrace(); } } if (tabixReader != null && index != null) { FileRead filereader = new FileRead(bedfiles); filereader.readBED(Main.chooserText, index, false); tabixReader.close(); } } } else { if (Main.chooserText.contains("://")) { try { // bbreader = new BBFileReader(Main.chooserText, stream); } catch (Exception ex) { ex.printStackTrace(); } // if(bbreader != null) { FileRead filereader = new FileRead(bedfiles); filereader.readBED(Main.chooserText, "nan", false); // } // stream.close(); } } } } } catch (Exception ex) { ex.printStackTrace(); } } else if (e.getSource() == openProject) { if (!checkGenome()) return; if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } openProject(); } else if (e.getSource() == saveProjectAs) { if (VariantHandler.frame != null) { VariantHandler.frame.setState(Frame.ICONIFIED); } try { File savefile = null; FileDialog fs = new FileDialog(frame, "Save project as...", FileDialog.SAVE); fs.setDirectory(projectDir); fs.setFile("*.ses"); fs.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".ses"); } }); fs.setVisible(true); while (true) { String filename = fs.getFile(); if (filename != null) { savefile = new File(fs.getDirectory() + "/" + filename); projectDir = fs.getDirectory(); writeToConfig("DefaultProjectDir=" + projectDir); /* if(!Files.isWritable(Paths.get(savefile.getParent()))) { Main.showError("No permission to write.", "Error"); continue; }*/ if (!savefile.getAbsolutePath().endsWith(".ses")) { savefile = new File(savefile.getAbsolutePath() + ".ses"); } Serializer ser = new Serializer(); ser.serialize(savefile); break; } else { break; } } if (1 == 1) { return; } JFileChooser chooser = new JFileChooser(); chooser.setAcceptAllFileFilterUsed(false); MyFilterSES sesFilter = new MyFilterSES(); chooser.addChoosableFileFilter(sesFilter); chooser.setDialogTitle("Save project as..."); int returnVal = chooser.showSaveDialog((Component) this.getParent()); if (returnVal == JFileChooser.APPROVE_OPTION) { File outfile = chooser.getSelectedFile(); if (!outfile.getAbsolutePath().endsWith(".ses")) { outfile = new File(outfile.getAbsolutePath() + ".ses"); } Serializer ser = new Serializer(); ser.serialize(outfile); } } catch (Exception ex) { ex.printStackTrace(); } } else if (e.getSource() == saveProject) { if (drawCanvas.drawVariables.projectName.equals("Untitled")) { saveProjectAs.doClick(); } else { Serializer ser = new Serializer(); ser.serialize(drawCanvas.drawVariables.projectFile); } } /* else if(e.getSource() == welcome) { WelcomeScreen.main(args); WelcomeScreen.frame.setVisible(true); WelcomeScreen.frame.setLocation(frame.getLocationOnScreen().x+frame.getWidth()/2 - WelcomeScreen.frame.getWidth()/2, frame.getLocationOnScreen().y+frame.getHeight()/6); }*/ }
From source file:base.BasePlayer.Main.java
void openProject() { /*JFileChooser chooser = new JFileChooser(Main.projectDir); /* ww w . j a v a2 s . c om*/ chooser.setAcceptAllFileFilterUsed(false); MyFilterSES sesFilter = new MyFilterSES(); chooser.addChoosableFileFilter(sesFilter); chooser.setDialogTitle("Open project"); chooser.setPreferredSize(new Dimension((int)screenSize.getWidth()/3, (int)screenSize.getHeight()/3)); int returnVal = chooser.showOpenDialog((Component)this.getParent()); */ FileRead.asked = false; FileDialog fc = new FileDialog(frame, "Choose project file", FileDialog.LOAD); fc.setDirectory(Main.projectDir); fc.setFile("*.ses"); fc.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".ses"); } }); fc.setMultipleMode(false); fc.setVisible(true); String openfile = fc.getFile(); if (openfile != null) { File addfile = new File(fc.getDirectory() + "/" + openfile); projectDir = fc.getDirectory(); writeToConfig("DefaultProjectDir=" + projectDir); clearData(); OpenProject opener = new OpenProject(addfile); opener.execute(); } /* if (returnVal == JFileChooser.APPROVE_OPTION) { projectDir = chooser.getSelectedFile().getParent(); writeToConfig("DefaultProjectDir=" +projectDir); OpenProject opener = new OpenProject(chooser.getSelectedFile()); opener.execute(); }*/ }
From source file:no.java.swing.SingleSelectionFileDialog.java
private Result showNativeDialog(Component target, boolean open) { Window window = target == null ? null : (Frame) SwingUtilities.getWindowAncestor(target); FileDialog dialog;//from w w w.j a v a2s .co m if (window instanceof Frame) { dialog = new FileDialog((Frame) window); } else if (window instanceof Dialog) { dialog = new FileDialog((Dialog) window); } else { throw new IllegalStateException("Unknown window type"); } dialog.setDirectory(previousDirectory.getAbsolutePath()); dialog.setMode(open ? FileDialog.LOAD : FileDialog.SAVE); dialog.setVisible(true); if (rememberPreviousLocation) { previousDirectory = new File(dialog.getDirectory()); } if (dialog.getFile() == null) { return Result.CANCEL; } selected = new File(dialog.getFile()); return Result.APPROVE; }
From source file:org.broad.igv.hic.MainWindow.java
private void loadMenuItemActionPerformed(ActionEvent e) { FileDialog dlg = new FileDialog(this); dlg.setMode(FileDialog.LOAD); dlg.setVisible(true);/*from w w w . jav a2s.c om*/ String file = dlg.getFile(); if (file != null) { try { File f = new File(dlg.getDirectory(), dlg.getFile()); load(f.getAbsolutePath()); } catch (IOException e1) { e1.printStackTrace(); //To change body of catch statement use File | Settings | File Templates. } } }
From source file:org.jivesoftware.spark.plugin.fileupload.ChatRoomDecorator.java
private void getUploadUrl(ChatRoom room, Message.Type type) { FileDialog fd = new FileDialog((Frame) null, "Choose a file to upload", FileDialog.LOAD); fd.setMultipleMode(true);//from w w w . j a v a2s . co m fd.setVisible(true); File files[] = fd.getFiles(); for (File file : files) { handleUpload(file, room, type); } }