-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-\r
-//////////////////////////////////////////////////////////////////\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-import java.awt.*;\r
-import javax.swing.*;\r
-\r
-public class JalviewFileChooser\r
- extends JFileChooser\r
-{\r
-\r
- public JalviewFileChooser(String dir)\r
- {\r
- super(dir);\r
- }\r
-\r
- public JalviewFileChooser(String dir, String[] suffix, String[] desc,\r
- String selected)\r
- {\r
- super(dir);\r
-\r
- JalviewFileFilter chosen = null;\r
-\r
- for (int i = 0; i < suffix.length; i++)\r
- {\r
- JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);\r
- addChoosableFileFilter(jvf);\r
-\r
- if ( (selected != null) && selected.equalsIgnoreCase(desc[i]))\r
- {\r
- chosen = jvf;\r
- }\r
- }\r
-\r
- if (chosen != null)\r
- {\r
- setFileFilter(chosen);\r
- }\r
- }\r
-\r
- public void setFileFilter(javax.swing.filechooser.FileFilter filter)\r
- {\r
- super.setFileFilter(filter);\r
-\r
- try{\r
- if(getUI() instanceof javax.swing.plaf.basic.BasicFileChooserUI)\r
- {\r
- final javax.swing.plaf.basic.BasicFileChooserUI ui = (javax.swing.plaf.\r
- basic.BasicFileChooserUI) getUI();\r
- final String name = ui.getFileName().trim();\r
-\r
- if ( (name == null) || (name.length() == 0))\r
- {\r
- return;\r
- }\r
-\r
- EventQueue.invokeLater(new Thread()\r
- {\r
- public void run()\r
- {\r
- String currentName = ui.getFileName();\r
- if ( (currentName == null) || (currentName.length() == 0))\r
- {\r
- ui.setFileName(name);\r
- }\r
- }\r
- });\r
- }\r
- }catch(Exception ex)\r
- {\r
- // Some platforms do not have BasicFileChooserUI\r
- }\r
- }\r
-\r
-\r
- public String getSelectedFormat()\r
- {\r
- if(getFileFilter()==null)\r
- {\r
- return null;\r
- }\r
-\r
- String format = getFileFilter().getDescription();\r
-\r
- if (format.toUpperCase().startsWith("JALVIEW"))\r
- {\r
- format = "Jalview";\r
- }\r
- else if (format.toUpperCase().startsWith("FASTA"))\r
- {\r
- format = "FASTA";\r
- }\r
- else if (format.toUpperCase().startsWith("MSF"))\r
- {\r
- format = "MSF";\r
- }\r
- else if (format.toUpperCase().startsWith("CLUSTAL"))\r
- {\r
- format = "CLUSTAL";\r
- }\r
- else if (format.toUpperCase().startsWith("BLC"))\r
- {\r
- format = "BLC";\r
- }\r
- else if (format.toUpperCase().startsWith("PIR"))\r
- {\r
- format = "PIR";\r
- }\r
- else if (format.toUpperCase().startsWith("PFAM"))\r
- {\r
- format = "PFAM";\r
- }\r
-\r
- return format;\r
- }\r
-\r
- public int showSaveDialog(Component parent)\r
- throws HeadlessException\r
- {\r
- setDialogType(SAVE_DIALOG);\r
-\r
- int ret = showDialog(parent, null);\r
-\r
- if (getFileFilter() instanceof JalviewFileFilter)\r
- {\r
- JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();\r
-\r
- if (!jvf.accept(getSelectedFile()))\r
- {\r
- String withExtension = getSelectedFile() + "." +\r
- jvf.getAcceptableExtension();\r
- setSelectedFile(new File(withExtension));\r
- }\r
- }\r
-\r
- if ( (ret == JalviewFileChooser.APPROVE_OPTION) &&\r
- getSelectedFile().exists())\r
- {\r
- int confirm = JOptionPane.showConfirmDialog(parent,\r
- "Overwrite existing file?",\r
- "File exists",\r
- JOptionPane.YES_NO_OPTION);\r
-\r
- if (confirm != JOptionPane.YES_OPTION)\r
- {\r
- ret = JalviewFileChooser.CANCEL_OPTION;\r
- }\r
- }\r
-\r
- return ret;\r
- }\r
-}\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+//////////////////////////////////////////////////////////////////
+package jalview.io;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.EventQueue;
+import java.awt.HeadlessException;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyChangeEvent;
+import java.beans.PropertyChangeListener;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.concurrent.Callable;
+
+import javax.swing.BoxLayout;
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JCheckBox;
+import javax.swing.JFileChooser;
+import javax.swing.JList;
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SpringLayout;
+import javax.swing.filechooser.FileFilter;
+import javax.swing.plaf.basic.BasicFileChooserUI;
+
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.dialogrunner.DialogRunnerI;
+
+/**
+ * Enhanced file chooser dialog box.
+ *
+ * NOTE: bug on Windows systems when filechooser opened on directory to view
+ * files with colons in title.
+ *
+ * @author AMW
+ *
+ */
+public class JalviewFileChooser extends JFileChooser
+ implements DialogRunnerI, PropertyChangeListener
+{
+ private static final long serialVersionUID = 1L;
+
+ private Map<Object, Callable> callbacks = new HashMap<>();
+
+ File selectedFile = null;
+
+ /**
+ * backupfilesCheckBox = "Include backup files" checkbox includeBackupfiles =
+ * flag set by checkbox
+ */
+ private JCheckBox backupfilesCheckBox = null;
+
+ protected boolean includeBackupFiles = false;
+
+ /**
+ * Factory method to return a file chooser that offers readable alignment file
+ * formats
+ *
+ * @param directory
+ * @param selected
+ * @return
+ */
+ public static JalviewFileChooser forRead(String directory,
+ String selected)
+ {
+ return JalviewFileChooser.forRead(directory, selected, false);
+ }
+
+ public static JalviewFileChooser forRead(String directory,
+ String selected, boolean allowBackupFiles)
+ {
+ List<String> extensions = new ArrayList<>();
+ List<String> descs = new ArrayList<>();
+ for (FileFormatI format : FileFormats.getInstance().getFormats())
+ {
+ if (format.isReadable())
+ {
+ extensions.add(format.getExtensions());
+ descs.add(format.getName());
+ }
+ }
+
+ return new JalviewFileChooser(directory,
+ extensions.toArray(new String[extensions.size()]),
+ descs.toArray(new String[descs.size()]), selected, true,
+ allowBackupFiles);
+ }
+
+ /**
+ * Factory method to return a file chooser that offers writable alignment file
+ * formats
+ *
+ * @param directory
+ * @param selected
+ * @return
+ */
+ public static JalviewFileChooser forWrite(String directory,
+ String selected)
+ {
+ // TODO in Java 8, forRead and forWrite can be a single method
+ // with a lambda expression parameter for isReadable/isWritable
+ List<String> extensions = new ArrayList<>();
+ List<String> descs = new ArrayList<>();
+ for (FileFormatI format : FileFormats.getInstance().getFormats())
+ {
+ if (format.isWritable())
+ {
+ extensions.add(format.getExtensions());
+ descs.add(format.getName());
+ }
+ }
+ return new JalviewFileChooser(directory,
+ extensions.toArray(new String[extensions.size()]),
+ descs.toArray(new String[descs.size()]), selected, false);
+ }
+
+ public JalviewFileChooser(String dir)
+ {
+ super(safePath(dir));
+ setAccessory(new RecentlyOpened());
+ }
+
+ public JalviewFileChooser(String dir, String[] suffix, String[] desc,
+ String selected)
+ {
+ this(dir, suffix, desc, selected, true);
+ }
+
+ /**
+ * Constructor for a single choice of file extension and description
+ *
+ * @param extension
+ * @param desc
+ */
+ public JalviewFileChooser(String extension, String desc)
+ {
+ this(Cache.getProperty("LAST_DIRECTORY"), new String[] { extension },
+ new String[]
+ { desc }, desc, true);
+ }
+
+ JalviewFileChooser(String dir, String[] extensions, String[] descs,
+ String selected, boolean acceptAny)
+ {
+ this(dir, extensions, descs, selected, acceptAny, false);
+ }
+
+ public JalviewFileChooser(String dir, String[] extensions, String[] descs,
+ String selected, boolean acceptAny, boolean allowBackupFiles)
+ {
+ super(safePath(dir));
+ if (extensions.length == descs.length)
+ {
+ List<String[]> formats = new ArrayList<>();
+ for (int i = 0; i < extensions.length; i++)
+ {
+ formats.add(new String[] { extensions[i], descs[i] });
+ }
+ init(formats, selected, acceptAny, allowBackupFiles);
+ }
+ else
+ {
+ System.err.println("JalviewFileChooser arguments mismatch: "
+ + extensions + ", " + descs);
+ }
+ }
+
+ private static File safePath(String dir)
+ {
+ if (dir == null)
+ {
+ return null;
+ }
+
+ File f = new File(dir);
+ if (f.getName().indexOf(':') > -1)
+ {
+ return null;
+ }
+ return f;
+ }
+
+ /**
+ * Overridden for JalviewJS compatibility: only one thread in Javascript, so
+ * we can't wait for user choice in another thread and then perform the
+ * desired action
+ */
+ @Override
+ public int showOpenDialog(Component parent)
+ {
+ int value = super.showOpenDialog(this);
+
+ if (!Platform.isJS())
+ /**
+ * Java only
+ *
+ * @j2sIgnore
+ */
+ {
+ /*
+ * code here is not run in JalviewJS, instead
+ * propertyChange() is called for dialog action
+ */
+ handleResponse(value);
+ }
+ return value;
+ }
+
+ /**
+ *
+ * @param formats
+ * a list of {extensions, description} for each file format
+ * @param selected
+ * @param acceptAny
+ * if true, 'any format' option is included
+ */
+ void init(List<String[]> formats, String selected, boolean acceptAny)
+ {
+ init(formats, selected, acceptAny, false);
+ }
+
+ void init(List<String[]> formats, String selected, boolean acceptAny,
+ boolean allowBackupFiles)
+ {
+
+ JalviewFileFilter chosen = null;
+
+ // SelectAllFilter needs to be set first before adding further
+ // file filters to fix bug on Mac OSX
+ setAcceptAllFileFilterUsed(acceptAny);
+
+ for (String[] format : formats)
+ {
+ JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
+ if (allowBackupFiles)
+ {
+ jvf.setParentJFC(this);
+ }
+ addChoosableFileFilter(jvf);
+ if ((selected != null) && selected.equalsIgnoreCase(format[1]))
+ {
+ chosen = jvf;
+ }
+ }
+
+ if (chosen != null)
+ {
+ setFileFilter(chosen);
+ }
+
+ if (allowBackupFiles)
+ {
+ JPanel multi = new JPanel();
+ multi.setLayout(new BoxLayout(multi, BoxLayout.PAGE_AXIS));
+ if (backupfilesCheckBox == null)
+ {
+ try
+ {
+ includeBackupFiles = Boolean.parseBoolean(
+ Cache.getProperty(BackupFiles.NS + "_FC_INCLUDE"));
+ } catch (Exception e)
+ {
+ includeBackupFiles = false;
+ }
+ backupfilesCheckBox = new JCheckBox(
+ MessageManager.getString("label.include_backup_files"),
+ includeBackupFiles);
+ backupfilesCheckBox.setAlignmentX(Component.CENTER_ALIGNMENT);
+ JalviewFileChooser jfc = this;
+ backupfilesCheckBox.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ includeBackupFiles = backupfilesCheckBox.isSelected();
+ Cache.setProperty(BackupFiles.NS + "_FC_INCLUDE",
+ String.valueOf(includeBackupFiles));
+
+ FileFilter f = jfc.getFileFilter();
+ // deselect the selected file if it's no longer choosable
+ File selectedFile = jfc.getSelectedFile();
+ if (selectedFile != null && !f.accept(selectedFile))
+ {
+ jfc.setSelectedFile(null);
+ }
+ // fake the OK button changing (to force it to upate)
+ String s = jfc.getApproveButtonText();
+ jfc.firePropertyChange(APPROVE_BUTTON_TEXT_CHANGED_PROPERTY,
+ null, s);
+ // fake the file filter changing (its behaviour actually has)
+ jfc.firePropertyChange(FILE_FILTER_CHANGED_PROPERTY, null, f);
+
+ jfc.rescanCurrentDirectory();
+ jfc.revalidate();
+ jfc.repaint();
+ }
+ });
+ }
+ multi.add(new RecentlyOpened());
+ multi.add(backupfilesCheckBox);
+ setAccessory(multi);
+ }
+ else
+ {
+ // set includeBackupFiles=false to avoid other file choosers from picking
+ // up backup files (Just In Case)
+ includeBackupFiles = false;
+ setAccessory(new RecentlyOpened());
+ }
+ }
+
+ @Override
+ public void setFileFilter(javax.swing.filechooser.FileFilter filter)
+ {
+ super.setFileFilter(filter);
+
+ try
+ {
+ if (getUI() instanceof BasicFileChooserUI)
+ {
+ final BasicFileChooserUI fcui = (BasicFileChooserUI) getUI();
+ final String name = fcui.getFileName().trim();
+
+ if ((name == null) || (name.length() == 0))
+ {
+ return;
+ }
+
+ EventQueue.invokeLater(new Thread()
+ {
+ @Override
+ public void run()
+ {
+ String currentName = fcui.getFileName();
+ if ((currentName == null) || (currentName.length() == 0))
+ {
+ fcui.setFileName(name);
+ }
+ }
+ });
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ // Some platforms do not have BasicFileChooserUI
+ }
+ }
+
+ /**
+ * Returns the selected file format, or null if none selected
+ *
+ * @return
+ */
+ public FileFormatI getSelectedFormat()
+ {
+ if (getFileFilter() == null)
+ {
+ return null;
+ }
+
+ /*
+ * logic here depends on option description being formatted as
+ * formatName (extension, extension...)
+ * or the 'no option selected' value
+ * All Files
+ * @see JalviewFileFilter.getDescription
+ */
+ String format = getFileFilter().getDescription();
+ int parenPos = format.indexOf("(");
+ if (parenPos > 0)
+ {
+ format = format.substring(0, parenPos).trim();
+ try
+ {
+ return FileFormats.getInstance().forName(format);
+ } catch (IllegalArgumentException e)
+ {
+ System.err.println("Unexpected format: " + format);
+ }
+ }
+ return null;
+ }
+
+ @Override
+ public File getSelectedFile()
+ {
+ File f = super.getSelectedFile();
+ return f == null ? selectedFile : f;
+ }
+
+ @Override
+ public int showSaveDialog(Component parent) throws HeadlessException
+ {
+ this.setAccessory(null);
+ // Java 9,10,11 on OSX - clear selected file so name isn't auto populated
+ this.setSelectedFile(null);
+
+ return super.showSaveDialog(parent);
+ }
+
+ /**
+ * If doing a Save, and an existing file is chosen or entered, prompt for
+ * confirmation of overwrite. Proceed if Yes, else leave the file chooser
+ * open.
+ *
+ * @see https://stackoverflow.com/questions/8581215/jfilechooser-and-checking-for-overwrite
+ */
+ @Override
+ public void approveSelection()
+ {
+ if (getDialogType() != SAVE_DIALOG)
+ {
+ super.approveSelection();
+ return;
+ }
+
+ selectedFile = getSelectedFile();
+
+ if (selectedFile == null)
+ {
+ // Workaround for Java 9,10 on OSX - no selected file, but there is a
+ // filename typed in
+ try
+ {
+ String filename = ((BasicFileChooserUI) getUI()).getFileName();
+ if (filename != null && filename.length() > 0)
+ {
+ selectedFile = new File(getCurrentDirectory(), filename);
+ }
+ } catch (Throwable x)
+ {
+ System.err.println(
+ "Unexpected exception when trying to get filename.");
+ x.printStackTrace();
+ }
+ // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND
+ // THE
+ // USER PROMPTED FOR A NEW FILENAME
+ }
+
+ if (selectedFile == null)
+ {
+ return;
+ }
+
+ if (getFileFilter() instanceof JalviewFileFilter)
+ {
+ JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
+
+ if (!jvf.accept(selectedFile))
+ {
+ String withExtension = getSelectedFile().getName() + "."
+ + jvf.getAcceptableExtension();
+ selectedFile = (new File(getCurrentDirectory(), withExtension));
+ setSelectedFile(selectedFile);
+ }
+ }
+
+ if (selectedFile.exists())
+ {
+ int confirm = Cache.getDefault("CONFIRM_OVERWRITE_FILE", true)
+ ? JvOptionPane.showConfirmDialog(this,
+ MessageManager
+ .getString("label.overwrite_existing_file"),
+ MessageManager.getString("label.file_already_exists"),
+ JvOptionPane.YES_NO_OPTION)
+ : JOptionPane.YES_OPTION;
+
+ if (confirm != JvOptionPane.YES_OPTION)
+ {
+ return;
+ }
+ }
+
+ super.approveSelection();
+ }
+
+ void recentListSelectionChanged(Object selection)
+ {
+ setSelectedFile(null);
+ if (selection != null)
+ {
+ File file = new File((String) selection);
+ if (getFileFilter() instanceof JalviewFileFilter)
+ {
+ JalviewFileFilter jvf = (JalviewFileFilter) this.getFileFilter();
+
+ if (!jvf.accept(file))
+ {
+ setFileFilter(getChoosableFileFilters()[0]);
+ }
+ }
+
+ setSelectedFile(file);
+ }
+ }
+
+ class RecentlyOpened extends JPanel
+ {
+ private static final long serialVersionUID = 1L;
+
+ JList<String> list;
+
+ RecentlyOpened()
+ {
+ setPreferredSize(new Dimension(300, 100));
+ String historyItems = Cache.getProperty("RECENT_FILE");
+ StringTokenizer st;
+ Vector<String> recent = new Vector<>();
+
+ if (historyItems != null)
+ {
+ st = new StringTokenizer(historyItems, "\t");
+
+ while (st.hasMoreTokens())
+ {
+ recent.addElement(st.nextToken());
+ }
+ }
+
+ list = new JList<>(recent);
+
+ DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
+ dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
+ list.setCellRenderer(dlcr);
+
+ list.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mousePressed(MouseEvent evt)
+ {
+ recentListSelectionChanged(list.getSelectedValue());
+ }
+ });
+
+ this.setBorder(new javax.swing.border.TitledBorder(
+ MessageManager.getString("label.recently_opened")));
+
+ final JScrollPane scroller = new JScrollPane(list);
+
+ SpringLayout layout = new SpringLayout();
+ layout.putConstraint(SpringLayout.WEST, scroller, 5,
+ SpringLayout.WEST, this);
+ layout.putConstraint(SpringLayout.NORTH, scroller, 5,
+ SpringLayout.NORTH, this);
+
+ if (Platform.isAMacAndNotJS())
+ {
+ scroller.setPreferredSize(new Dimension(500, 100));
+ }
+ else
+ {
+ scroller.setPreferredSize(new Dimension(530, 200));
+ }
+
+ this.add(scroller);
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ scroller.getHorizontalScrollBar()
+ .setValue(scroller.getHorizontalScrollBar().getMaximum());
+ }
+ });
+
+ }
+
+ }
+
+ /*
+ @Override
+ public JalviewFileChooser setResponseHandler(Object response,
+ Runnable action)
+ {
+ callbacks.put(response, new Callable<Void>()
+ {
+ @Override
+ public Void call()
+ {
+ action.run();
+ return null;
+ }
+ });
+ return this;
+ }
+ */
+
+ @Override
+ public DialogRunnerI setResponseHandler(Object response, Callable action)
+ {
+ callbacks.put(response, action);
+ return this;
+ }
+
+ @Override
+ public void handleResponse(Object response)
+ {
+ /*
+ * this test is for NaN in Chrome
+ */
+ if (response != null && !response.equals(response))
+ {
+ return;
+ }
+ Callable action = callbacks.get(response);
+ if (action != null)
+ {
+ try
+ {
+ action.call();
+ } catch (Exception e)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * JalviewJS signals file selection by a property change event for property
+ * "SelectedFile". This methods responds to that by running the response
+ * action for 'OK' in the dialog.
+ *
+ * @param evt
+ */
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // TODO other properties need runners...
+ switch (evt.getPropertyName())
+ {
+ /*
+ * property name here matches that used in JFileChooser.js
+ */
+ case "SelectedFile":
+ handleResponse(APPROVE_OPTION);
+ break;
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff