List of usage examples for java.awt FileDialog getFile
public String getFile()
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 w w . java2s . 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:com.declarativa.interprolog.gui.ListenerWindow.java
/** * For XSB only// w ww.j a va 2s .co m */ void load_dynFile() { String nome, directorio; File filetoreconsult = null; FileDialog d = new FileDialog(this, "load_dyn file..."); d.show(); nome = d.getFile(); directorio = d.getDirectory(); if (nome != null) { filetoreconsult = new File(directorio, nome); if (successfulCommand( "load_dyn('" + engine.unescapedFilePath(filetoreconsult.getAbsolutePath()) + "')")) { addToReloaders(filetoreconsult, "load_dyn"); } } }
From source file:com.declarativa.interprolog.gui.ListenerWindow.java
void reconsultFile() { String nome, directorio;// ww w . j a v a 2 s .co m File filetoreconsult = null; FileDialog d = new FileDialog(this, "Consult file..."); d.setVisible(true); nome = d.getFile(); directorio = d.getDirectory(); if (nome != null) { filetoreconsult = new File(directorio, nome); if (engine.consultAbsolute(filetoreconsult)) { addToReloaders(filetoreconsult, "consult"); } } }
From source file:com.declarativa.interprolog.gui.ListenerWindow.java
/** * *// ww w . jav a 2 s. c om * Generates the subgraph and splits the Program in Subgraphs (Graph * Analysis) */ public void GraphAnalysis2() { String fileToLoad, folder; File filetoreconsult = null; FileDialog d = new FileDialog(this, "Consult file..."); d.setVisible(true); fileToLoad = d.getFile(); folder = d.getDirectory(); if (fileToLoad != null) { ArgBuildManager manag = new ArgBuildManager(); manag.GraphAnalysis4Frag(folder, fileToLoad);//Call to the ArgBuildManager! } }
From source file:com.declarativa.interprolog.gui.ListenerWindow.java
/** * */*ww w . ja v a2s .c om*/ * Generates the subgraph and splits the Program in Subgraphs (Graph * Analysis) */ public void GraphAnalysis() { String fileToLoad, folder; File filetoreconsult = null; FileDialog d = new FileDialog(this, "Consult file..."); d.setVisible(true); fileToLoad = d.getFile(); folder = d.getDirectory(); if (fileToLoad != null) { ArgBuildManager manag = new ArgBuildManager(); manag.GraphFileRules(folder, fileToLoad);//Call to the ArgBuildManager! /* filetoreconsult = new File(folder, fileToLoad); if (engine.consultAbsolute(filetoreconsult)) { addToReloaders(filetoreconsult, "consult"); } */ //System.out.println("file:"+filetoreconsult.); } }
From source file:edu.ku.brc.specify.tasks.QueryTask.java
/** * //from w w w . 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:edu.ku.brc.specify.tasks.QueryTask.java
/** * /*from w ww .j a v a2 s .c o m*/ */ protected void exportQueries() { UsageTracker.incrUsageCount(getExportUsageKey()); Vector<String> list = new Vector<String>(); for (NavBoxItemIFace nbi : navBox.getItems()) { list.add(nbi.getTitle()); } List<String> selectedList = null; if (list.size() == 0) { UIRegistry.showLocalizedMsg(getNothingToExporti18nKey()); return; } if (list.size() == 1) { selectedList = list; } else { ToggleButtonChooserDlg<String> dlg = new ToggleButtonChooserDlg<String>( (Frame) UIRegistry.getMostRecentWindow(), getExportDlgTitlei18nKey(), getExportDlgMsgi18nKey(), list, CustomDialog.OKCANCELHELP, ToggleButtonChooserPanel.Type.Checkbox); dlg.setAddSelectAll(true); dlg.setUseScrollPane(true); dlg.setHelpContext(getExportHelpContext()); UIHelper.centerAndShow(dlg); selectedList = dlg.getSelectedObjects(); if (dlg.isCancelled() || selectedList.size() == 0) { return; } } String path = AppPreferences.getLocalPrefs().get(XML_PATH_PREF, null); FileDialog fDlg = new FileDialog(((Frame) UIRegistry.getTopWindow()), UIRegistry.getResourceString("SAVE"), FileDialog.SAVE); 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; } if (StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) { fileName += ".xml"; } path = dirStr + fileName; AppPreferences.getLocalPrefs().put(XML_PATH_PREF, path); Hashtable<String, Boolean> hash = new Hashtable<String, Boolean>(); for (String qTitle : selectedList) { hash.put(qTitle, true); } Vector<SpQuery> queries = new Vector<SpQuery>(); // Persist out to database DataProviderSessionIFace session = null; try { session = DataProviderFactory.getInstance().createSession(); for (NavBoxItemIFace nbi : navBox.getItems()) { if (hash.get(nbi.getTitle()) != null) { RecordSetIFace rs = (RecordSetIFace) nbi.getData(); if (rs != null) { SpQuery query = session.get(SpQuery.class, rs.getOnlyItem().getRecordId()); queries.add(query); } } } StringBuilder sb = new StringBuilder(); sb.append(getXMLExportFirstLine()); for (SpQuery q : queries) { q.toXML(sb); } sb.append(getXMLExportLastLine()); FileUtils.writeStringToFile(new File(path), sb.toString()); } catch (Exception ex) { edu.ku.brc.af.core.UsageTracker.incrHandledUsageCount(); edu.ku.brc.exceptions.ExceptionTracker.getInstance().capture(QueryTask.class, ex); // XXX Error dialog ex.printStackTrace(); } finally { if (session != null) { session.close(); } } }
From source file:processing.app.Base.java
/** * Prompt for a sketch to open, and open it in a new window. * * @throws Exception/*from w w w . j av a 2 s . c o m*/ */ public void handleOpenPrompt() throws Exception { // get the frontmost window frame for placing file dialog FileDialog fd = new FileDialog(activeEditor, tr("Open an Arduino sketch..."), FileDialog.LOAD); File lastFolder = new File( PreferencesData.get("last.folder", BaseNoGui.getSketchbookFolder().getAbsolutePath())); if (lastFolder.exists() && lastFolder.isFile()) { lastFolder = lastFolder.getParentFile(); } fd.setDirectory(lastFolder.getAbsolutePath()); // Only show .pde files as eligible bachelors fd.setFilenameFilter(new FilenameFilter() { public boolean accept(File dir, String name) { return name.toLowerCase().endsWith(".ino") || name.toLowerCase().endsWith(".pde"); } }); fd.setVisible(true); String directory = fd.getDirectory(); String filename = fd.getFile(); // User canceled selection if (filename == null) return; File inputFile = new File(directory, filename); PreferencesData.set("last.folder", inputFile.getAbsolutePath()); handleOpen(inputFile); }
From source file:base.BasePlayer.Main.java
void openProject() { /*JFileChooser chooser = new JFileChooser(Main.projectDir); /* w w w . ja v a2s . c o m*/ 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: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. ja v a 2s . c om 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); }*/ }