X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FJalviewFileChooser.java;h=a7f8fa6f43ac905b2a174678bd84ecc777d2185f;hb=7047b076a62df177047ceb16c3611efe020bdd76;hp=556bb7254940ef0db86bd4477cb4b2bb15fcfcdc;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/io/JalviewFileChooser.java b/src/jalview/io/JalviewFileChooser.java
index 556bb72..a7f8fa6 100755
--- a/src/jalview/io/JalviewFileChooser.java
+++ b/src/jalview/io/JalviewFileChooser.java
@@ -1,276 +1,546 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
- */
-
-//////////////////////////////////////////////////////////////////
-package jalview.io;
-
-import java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-public class JalviewFileChooser
- extends JFileChooser
-{
-
- public JalviewFileChooser(String dir)
- {
- super(dir);
- setAccessory(new RecentlyOpened());
- }
-
- public JalviewFileChooser(String dir,
- String[] suffix,
- String[] desc,
- String selected,
- boolean selectAll)
- {
- super(dir);
- init(suffix, desc, selected, selectAll);
- }
-
- public JalviewFileChooser(String dir,
- String[] suffix,
- String[] desc,
- String selected)
- {
- super(dir);
- init(suffix, desc, selected, true);
- }
-
- void init(String[] suffix,
- String[] desc,
- String selected,
- boolean selectAll)
- {
-
- JalviewFileFilter chosen = null;
-
- //SelectAllFilter needs to be set first before adding further
- //file filters to fix bug on Mac OSX
- setAcceptAllFileFilterUsed(selectAll);
-
- for (int i = 0; i < suffix.length; i++)
- {
- JalviewFileFilter jvf = new JalviewFileFilter(suffix[i], desc[i]);
- addChoosableFileFilter(jvf);
-
- if ( (selected != null) && selected.equalsIgnoreCase(desc[i]))
- {
- chosen = jvf;
- }
- }
-
- if (chosen != null)
- {
- setFileFilter(chosen);
- }
-
- setAccessory(new RecentlyOpened());
- }
-
- public void setFileFilter(javax.swing.filechooser.FileFilter filter)
- {
- super.setFileFilter(filter);
-
- try
- {
- if (getUI() instanceof javax.swing.plaf.basic.BasicFileChooserUI)
- {
- final javax.swing.plaf.basic.BasicFileChooserUI ui = (javax.swing.plaf.
- basic.BasicFileChooserUI) getUI();
- final String name = ui.getFileName().trim();
-
- if ( (name == null) || (name.length() == 0))
- {
- return;
- }
-
- EventQueue.invokeLater(new Thread()
- {
- public void run()
- {
- String currentName = ui.getFileName();
- if ( (currentName == null) || (currentName.length() == 0))
- {
- ui.setFileName(name);
- }
- }
- });
- }
- }
- catch (Exception ex)
- {
- ex.printStackTrace();
- // Some platforms do not have BasicFileChooserUI
- }
- }
-
- public String getSelectedFormat()
- {
- if (getFileFilter() == null)
- {
- return null;
- }
-
- String format = getFileFilter().getDescription();
-
- if (format.toUpperCase().startsWith("JALVIEW"))
- {
- format = "Jalview";
- }
- else if (format.toUpperCase().startsWith("FASTA"))
- {
- format = "FASTA";
- }
- else if (format.toUpperCase().startsWith("MSF"))
- {
- format = "MSF";
- }
- else if (format.toUpperCase().startsWith("CLUSTAL"))
- {
- format = "CLUSTAL";
- }
- else if (format.toUpperCase().startsWith("BLC"))
- {
- format = "BLC";
- }
- else if (format.toUpperCase().startsWith("PIR"))
- {
- format = "PIR";
- }
- else if (format.toUpperCase().startsWith("PFAM"))
- {
- format = "PFAM";
- }
-
- return format;
- }
-
- public int showSaveDialog(Component parent)
- throws HeadlessException
- {
- this.setAccessory(null);
-
- setDialogType(SAVE_DIALOG);
-
- int ret = showDialog(parent, "Save");
-
- if (getFileFilter() instanceof JalviewFileFilter)
- {
- JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
-
- if (!jvf.accept(getSelectedFile()))
- {
- String withExtension = getSelectedFile() + "." +
- jvf.getAcceptableExtension();
- setSelectedFile(new File(withExtension));
- }
- }
-
- if ( (ret == JalviewFileChooser.APPROVE_OPTION) &&
- getSelectedFile().exists())
- {
- int confirm = JOptionPane.showConfirmDialog(parent,
- "Overwrite existing file?",
- "File exists",
- JOptionPane.YES_NO_OPTION);
-
- if (confirm != JOptionPane.YES_OPTION)
- {
- ret = JalviewFileChooser.CANCEL_OPTION;
- }
- }
-
- return ret;
- }
-
- void recentListSelectionChanged(String selection)
- {
- setSelectedFile(null);
-
- File file = new File(selection);
- if (getFileFilter() instanceof JalviewFileFilter)
- {
- JalviewFileFilter jvf = (JalviewFileFilter)this.getFileFilter();
-
- if (!jvf.accept(file))
- {
- setFileFilter(getChoosableFileFilters()[0]);
- }
- }
-
- setSelectedFile(file);
- }
-
- class RecentlyOpened
- extends JPanel
- {
- JList list;
- public RecentlyOpened()
- {
- String historyItems = jalview.bin.Cache.getProperty("RECENT_FILE");
- StringTokenizer st;
- Vector recent = new Vector();
-
- if (historyItems != null)
- {
- st = new StringTokenizer(historyItems, "\t");
-
- while (st.hasMoreTokens())
- {
- recent.addElement(st.nextElement());
- }
- }
-
- list = new JList(recent);
-
- DefaultListCellRenderer dlcr = new DefaultListCellRenderer();
- dlcr.setHorizontalAlignment(DefaultListCellRenderer.RIGHT);
- list.setCellRenderer(dlcr);
-
- list.addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- recentListSelectionChanged(list.getSelectedValue().toString());
- }
- });
-
- this.setBorder(new javax.swing.border.TitledBorder("Recently Opened"));
-
- final JScrollPane scroller = new JScrollPane(list);
- scroller.setPreferredSize(new Dimension(130, 200));
- this.add(scroller);
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
- scroller.getHorizontalScrollBar().setValue(
- scroller.getHorizontalScrollBar().getMaximum());
- }
- });
-
- }
-
- }
-}
+/*
+ * 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+//////////////////////////////////////////////////////////////////
+package jalview.io;
+
+import jalview.bin.Cache;
+import jalview.gui.JvOptionPane;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.util.dialogrunner.DialogRunner;
+import jalview.util.dialogrunner.DialogRunnerI;
+import jalview.util.dialogrunner.Response;
+import jalview.util.dialogrunner.RunResponse;
+
+import java.awt.Component;
+import java.awt.Dimension;
+import java.awt.EventQueue;
+import java.awt.HeadlessException;
+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.List;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.DefaultListCellRenderer;
+import javax.swing.JFileChooser;
+import javax.swing.JList;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.SpringLayout;
+import javax.swing.plaf.basic.BasicFileChooserUI;
+
+/**
+ * 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 PropertyChangeListener, DialogRunnerI
+{
+ DialogRunner runner = new DialogRunner<>(this);
+
+ /**
+ * 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)
+ {
+ List extensions = new ArrayList<>();
+ List 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);
+ }
+
+ /**
+ * 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 extensions = new ArrayList<>();
+ List 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 allFiles)
+ {
+ super(safePath(dir));
+ if (extensions.length == descs.length)
+ {
+ List formats = new ArrayList<>();
+ for (int i = 0; i < extensions.length; i++)
+ {
+ formats.add(new String[] { extensions[i], descs[i] });
+ }
+ init(formats, selected, allFiles);
+ }
+ else
+ {
+ System.err.println("JalviewFileChooser arguments mismatch: "
+ + extensions + ", " + descs);
+ }
+ }
+
+ @Override
+ public void propertyChange(PropertyChangeEvent evt)
+ {
+ // TODO other properties need runners...
+ switch (evt.getPropertyName())
+ {
+ case "SelectedFile":
+ runner.run(APPROVE_OPTION);
+ break;
+ }
+ }
+
+ 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)
+ {
+ runner.resetResponses();
+ int value = super.showOpenDialog(this);
+ /**
+ * @j2sNative
+ */
+ {
+ runner.firstRun(value);
+ }
+ return value;
+ }
+
+ /**
+ *
+ * @param formats
+ * a list of {extensions, description} for each file format
+ * @param selected
+ * @param allFiles
+ * if true, 'any format' option is included
+ */
+ void init(List formats, String selected, boolean allFiles)
+ {
+
+ JalviewFileFilter chosen = null;
+
+ // SelectAllFilter needs to be set first before adding further
+ // file filters to fix bug on Mac OSX
+ setAcceptAllFileFilterUsed(allFiles);
+
+ for (String[] format : formats)
+ {
+ JalviewFileFilter jvf = new JalviewFileFilter(format[0], format[1]);
+ addChoosableFileFilter(jvf);
+ if ((selected != null) && selected.equalsIgnoreCase(format[1]))
+ {
+ chosen = jvf;
+ }
+ }
+
+ if (chosen != null)
+ {
+ setFileFilter(chosen);
+ }
+
+ 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;
+ }
+
+ File ourselectedFile = null;
+
+ @Override
+ public File getSelectedFile()
+ {
+ File selfile = super.getSelectedFile();
+ if (selfile == null && ourselectedFile != null)
+ {
+ return ourselectedFile;
+ }
+ return selfile;
+ }
+
+ Component saveparent;
+ RunResponse overwriteCheck = new RunResponse(
+ JalviewFileChooser.APPROVE_OPTION)
+ {
+ @Override
+ public void run()
+ {
+ ourselectedFile = getSelectedFile();
+
+ if (getSelectedFile() == 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)
+ {
+ ourselectedFile = new File(getCurrentDirectory(), filename);
+ }
+ } catch (Throwable x)
+ {
+ System.err.println(
+ "Unexpected exception when trying to get filename.");
+ x.printStackTrace();
+ }
+ }
+ if (ourselectedFile == null)
+ {
+ returned = new Response(JalviewFileChooser.CANCEL_OPTION);
+ return;
+ }
+ // JBP Note - this code was executed regardless of 'SAVE' being pressed
+ // need to see if there were side effects
+ if (getFileFilter() instanceof JalviewFileFilter)
+ {
+ JalviewFileFilter jvf = (JalviewFileFilter) getFileFilter();
+
+ if (!jvf.accept(getSelectedFile()))
+ {
+ String withExtension = getSelectedFile() + "."
+ + jvf.getAcceptableExtension();
+ setSelectedFile(new File(withExtension));
+ }
+ }
+ // All good, so we continue to save
+ returned = new Response(JalviewFileChooser.APPROVE_OPTION);
+
+ // TODO: ENSURE THAT FILES SAVED WITH A ':' IN THE NAME ARE REFUSED AND THE
+ // USER PROMPTED FOR A NEW FILENAME
+ /**
+ * @j2sNative
+ */
+ {
+ if (getSelectedFile().exists())
+ {
+ // JAL-3048 - may not need to raise this for browser saves
+
+ // yes/no cancel
+ int confirm = JvOptionPane.showConfirmDialog(saveparent,
+ MessageManager.getString("label.overwrite_existing_file"),
+ MessageManager.getString("label.file_already_exists"),
+ JvOptionPane.YES_NO_OPTION);
+
+ if (confirm != JvOptionPane.YES_OPTION)
+ {
+ returned = new Response(JalviewFileChooser.CANCEL_OPTION);
+ }
+ }
+ }
+ };
+ };
+
+ /**
+ * 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 showSaveDialog(Component parent) throws HeadlessException
+ {
+ this.setAccessory(null);
+
+ /*
+ * Save dialog is opened until user picks a file format
+ */
+ if (!runner.isRegistered(overwriteCheck))
+ {
+ // first call for this instance
+ runner.firstResponse(overwriteCheck);
+ }
+ else
+ {
+ // reset response flags
+ runner.resetResponses();
+ }
+
+ setDialogType(SAVE_DIALOG);
+
+ // Java 9,10,11 on OSX - clear selected file so name isn't auto populated
+ this.setSelectedFile(null);
+
+ saveparent = parent;
+
+ int value = showDialog(parent, MessageManager.getString("action.save"));
+ /**
+ * @j2sNative
+ */
+ {
+ runner.firstRun(value);
+ }
+ return value;
+ }
+
+ 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
+ {
+ JList list;
+
+ public RecentlyOpened()
+ {
+
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_FILE");
+ StringTokenizer st;
+ Vector 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.isAMac())
+ {
+ scroller.setPreferredSize(new Dimension(500, 100));
+ }
+ else
+ {
+ scroller.setPreferredSize(new Dimension(130, 200));
+ }
+
+ this.add(scroller);
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ scroller.getHorizontalScrollBar()
+ .setValue(scroller.getHorizontalScrollBar().getMaximum());
+ }
+ });
+
+ }
+
+ }
+
+ @Override
+ public JalviewFileChooser response(RunResponse action)
+ {
+ return runner.response(action);
+ }
+
+}