diff --git a/uk/ac/sanger/artemis/components/filetree/FileList.java b/uk/ac/sanger/artemis/components/filetree/FileList.java
new file mode 100644
index 0000000000000000000000000000000000000000..e32322eadf835e5a280f60a7b19fa8e1bfa23497
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/FileList.java
@@ -0,0 +1,144 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* @author: Copyright (C) Tim Carver
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import uk.ac.sanger.artemis.j2ssh.SshFileManager;
+import java.util.Vector;
+import java.util.Collections;
+import java.io.IOException;
+import java.io.File;
+
+public class FileList
+{
+ /** vector containing directories */
+ private Vector vdir;
+ private Vector vfile;
+ private static SshFileManager ssh_client = new SshFileManager();
+
+ public FileList()
+ {
+ }
+
+ protected void getDirList(String dir)
+ {
+ try
+ {
+ ssh_client.remoteList(dir);
+ }
+ catch(IOException ioe)
+ {
+ ioe.printStackTrace();
+ }
+ vdir = ssh_client.getDirList();
+ vfile = ssh_client.getFileList();
+ Collections.sort(vfile);
+ }
+
+ /**
+ *
+ * Delete the given file / directory
+ *
+ */
+ protected boolean delete(String file)
+ {
+ return ssh_client.delete(file);
+ }
+
+ /**
+ *
+ * Make a directory
+ *
+ */
+ protected boolean mkdir(String dir)
+ {
+ return ssh_client.mkdir(dir);
+ }
+
+
+ /**
+ *
+ * Print working directory
+ *
+ */
+ protected String pwd()
+ {
+ return ssh_client.pwd();
+ }
+
+ /**
+ *
+ * Rename a file
+ *
+ */
+ protected boolean rename(String old_file, String new_file)
+ {
+ return ssh_client.rename(old_file, new_file);
+ }
+
+
+ /**
+ *
+ * Put a file
+ *
+ */
+ protected boolean put(String dir, File local_file)
+ {
+ return ssh_client.put(dir, local_file);
+ }
+
+
+ /**
+ *
+ * Get the file contents
+ *
+ */
+ protected byte[] getFileContents(String file)
+ {
+ return ssh_client.getFileContents(file);
+ }
+
+
+ /**
+ *
+ * Gets the list of files as a Vector
+ * @return list of files as a Vector
+ *
+ */
+ public Vector fileVector()
+ {
+ return vfile;
+ }
+
+
+ /**
+ *
+ * Gets whether this name is a directory
+ * @return true if it is a directory
+ *
+ */
+ public boolean isDirectory(String d)
+ {
+ return vdir.contains(d);
+ }
+
+
+}
diff --git a/uk/ac/sanger/artemis/components/filetree/FileManager.java b/uk/ac/sanger/artemis/components/filetree/FileManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..85aca7e09dbf8bf8fb5289c05775f71b01f22f7b
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/FileManager.java
@@ -0,0 +1,435 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* Copyright (C) Genome Research Limited
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import uk.ac.sanger.artemis.util.StringVector;
+import uk.ac.sanger.artemis.Options;
+
+import javax.swing.*;
+import java.io.File;
+import java.io.FileFilter;
+import java.awt.event.*;
+import java.awt.geom.*;
+import java.awt.*;
+
+public class FileManager extends JFrame
+{
+
+ /** busy cursor */
+ private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+ /** done cursor */
+ private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+
+ public FileManager(JFrame frame)
+ {
+ this(frame,getArtemisFilter());
+ }
+
+ /**
+ *
+ * File Manager Frame
+ * @param frame parent frame
+ *
+ */
+ public FileManager(JFrame frame, FileFilter filter)
+ {
+ super("File Manager");
+
+ FileTree ftree = new FileTree(new File(System.getProperty("user.dir")),
+ frame, filter);
+ JScrollPane jsp = new JScrollPane(ftree);
+ JPanel pane = (JPanel)getContentPane();
+ pane.setLayout(new BorderLayout());
+ pane.add(jsp, BorderLayout.CENTER);
+ setJMenuBar(makeMenuBar(pane,ftree));
+ pane.add(getFileFileterComboBox(ftree), BorderLayout.SOUTH);
+
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ jsp.setPreferredSize(new Dimension(210,
+ (int)(screen.getHeight()/2)));
+ pack();
+
+ int yloc = (int)((screen.getHeight()-getHeight())/2);
+ setLocation(0,yloc);
+ setVisible(true);
+ }
+
+ protected JComboBox getFileFileterComboBox(final FileTree ftree)
+ {
+ String[] filters = { "Artemis Files", "Sequence Files",
+ "Feature Files", "All Files" };
+ final JComboBox comboFilter = new JComboBox(filters);
+ comboFilter.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String select = (String)comboFilter.getSelectedItem();
+ if(select.equals("Artemis Files"))
+ ftree.setFilter(getArtemisFilter());
+ else if(select.equals("Sequence Files"))
+ ftree.setFilter(getSequenceFilter());
+ else if(select.equals("Feature Files"))
+ ftree.setFilter(getFeatureFilter());
+ else if(select.equals("All Files"))
+ {
+ ftree.setFilter(new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.getName().startsWith("."))
+ return false;
+ return true;
+ }
+ });
+ }
+ }
+ });
+ return comboFilter;
+ }
+
+ /**
+ *
+ * Get a file filter for sequence and feature suffixes.
+ * @return file filter
+ */
+ protected static FileFilter getArtemisFilter()
+ {
+ final StringVector sequence_suffixes =
+ Options.getOptions().getOptionValues("sequence_file_suffixes");
+
+ final StringVector feature_suffixes =
+ Options.getOptions().getOptionValues("feature_file_suffixes");
+
+ final FileFilter artemis_filter = new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.isDirectory() &&
+ !pathname.getName().startsWith("."))
+ return true;
+
+ for(int i = 0; i<sequence_suffixes.size(); ++i)
+ {
+ final String suffix = sequence_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+
+ for(int i = 0; i<feature_suffixes.size(); ++i)
+ {
+ final String suffix = feature_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+ return false;
+ }
+ };
+ return artemis_filter;
+ }
+
+
+ /**
+ *
+ * Get a file filter for feature suffixes.
+ * @return file filter
+ */
+ protected static FileFilter getFeatureFilter()
+ {
+ final StringVector feature_suffixes =
+ Options.getOptions().getOptionValues("feature_file_suffixes");
+
+ final FileFilter feature_filter = new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.isDirectory() &&
+ !pathname.getName().startsWith("."))
+ return true;
+
+ for(int i = 0; i<feature_suffixes.size(); ++i)
+ {
+ final String suffix = feature_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+ return false;
+ }
+ };
+ return feature_filter;
+ }
+
+ /**
+ *
+ * Get a file filter for sequence suffixes.
+ * @return file filter
+ */
+ protected static FileFilter getSequenceFilter()
+ {
+ final StringVector sequence_suffixes =
+ Options.getOptions().getOptionValues("sequence_file_suffixes");
+
+ final FileFilter seq_filter = new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.isDirectory() &&
+ !pathname.getName().startsWith("."))
+ return true;
+
+ for(int i = 0; i<sequence_suffixes.size(); ++i)
+ {
+ final String suffix = sequence_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+
+ return false;
+ }
+ };
+ return seq_filter;
+ }
+
+ /**
+ *
+ * Set up a menu and tool bar
+ * @param pane panel to add toolbar to
+ * @param ftree file tree display
+ *
+ */
+ private JMenuBar makeMenuBar(JPanel pane, final FileTree ftree)
+ {
+ JMenuBar mBar = new JMenuBar();
+ JMenu fileMenu = new JMenu("File");
+ mBar.add(fileMenu);
+
+ JMenuItem fileMenuGoto = new JMenuItem("Go to Directory ...");
+ fileMenuGoto.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String dir = ftree.getRoot().getAbsolutePath();
+ String newDir = JOptionPane.showInputDialog(FileManager.this,
+ "Go to Directory:",dir);
+
+ if(newDir == null)
+ return;
+
+ newDir = newDir.trim();
+ File newDirFile = new File(newDir);
+
+ if(newDirFile.exists() &&
+ newDirFile.canRead() &&
+ !newDir.equals(dir))
+ ftree.newRoot(newDir);
+ else
+ {
+ String error = null;
+ if(!newDirFile.exists())
+ error = new String(newDir+" doesn't exist!");
+ else if(!newDirFile.canRead())
+ error = new String(newDir+" cannot be read!");
+ else if(newDir.equals(dir))
+ error = new String("Same directory!");
+
+ if(error != null)
+ JOptionPane.showMessageDialog(FileManager.this,
+ error, "Warning",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ fileMenu.add(fileMenuGoto);
+ fileMenu.add(new JSeparator());
+
+ JMenuItem fileMenuClose = new JMenuItem("Close");
+ fileMenuClose.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setVisible(false);
+ }
+ });
+ fileMenu.add(fileMenuClose);
+
+ // tool bar set up
+ JToolBar toolBar = new JToolBar();
+ Dimension buttonSize = new Dimension(22,24);
+
+ JButton upBt = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+
+ g2.setColor(new Color(0,128,0));
+ float loc1[][] = { {11,18}, {7,18}, {7,14},
+ {3,14}, {11,4} };
+
+ g2.fill(makeShape(loc1));
+ g2.setColor(Color.green);
+
+ float loc2[][] = { {11,18}, {15,18}, {15,14},
+ {19,14}, {11,4} };
+ g2.fill(makeShape(loc2));
+
+ setSize(22,24);
+ }
+ };
+ upBt.setPreferredSize(buttonSize);
+ upBt.setMinimumSize(buttonSize);
+
+ upBt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ FileManager.this.setCursor(cbusy);
+ File root = ftree.getRoot();
+ String parent = root.getParent();
+ if(parent != null)
+ ftree.newRoot(parent);
+ FileManager.this.setCursor(cdone);
+ }
+ });
+ toolBar.add(upBt);
+
+// yeastpub
+ JButton shortCut1 = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+ Font font = new Font("Monospaced", Font.BOLD, 14);
+ g2.setFont(font);
+
+ g2.setColor(Color.black);
+ g2.drawString("Y",4,18);
+ g2.setColor(Color.red);
+ g2.drawString("P",10,15);
+ setSize(22,24);
+ }
+ };
+ shortCut1.setPreferredSize(buttonSize);
+ shortCut1.setMinimumSize(buttonSize);
+ shortCut1.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ftree.newRoot("/nfs/disk222/yeastpub");
+ }
+ });
+
+ if((new File("/nfs/disk222/yeastpub")).exists())
+ toolBar.add(shortCut1);
+
+// pathdata
+ JButton shortCut2 = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+ Font font = new Font("Monospaced", Font.BOLD, 14);
+ g2.setFont(font);
+
+ g2.setColor(Color.black);
+ g2.drawString("P",4,18);
+ g2.setColor(Color.red);
+ g2.drawString("D",10,15);
+ setSize(22,24);
+ }
+ };
+ shortCut2.setPreferredSize(buttonSize);
+ shortCut2.setMinimumSize(buttonSize);
+ shortCut2.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ftree.newRoot("/nfs/pathdata/");
+ }
+ });
+
+ if((new File("/nfs/pathdata/")).exists())
+ toolBar.add(shortCut2);
+
+// home button
+ JButton homeBt = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+
+ g2.setColor(Color.blue);
+ float loc1[][] = { {3,14}, {11,3}, {19,14},
+ {17,14}, {17,18}, {5,18}, {5,14} };
+ g2.fill(makeShape(loc1));
+
+ setSize(22,24);
+ }
+ };
+ homeBt.setPreferredSize(buttonSize);
+ homeBt.setMinimumSize(buttonSize);
+ homeBt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ftree.newRoot(System.getProperty("user.home"));
+ }
+ });
+ toolBar.add(homeBt);
+
+ toolBar.add(Box.createVerticalStrut(35));
+ pane.add(toolBar, BorderLayout.NORTH);
+
+ return mBar;
+ }
+
+ /**
+ *
+ * Used to draw a Shape.
+ *
+ */
+ public static GeneralPath makeShape(float loc[][])
+ {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_NON_ZERO);
+
+ path.moveTo(loc[0][0],loc[0][1]);
+
+ for(int i=1; i<loc.length; i++)
+ path.lineTo(loc[i][0],loc[i][1]);
+
+ return path;
+ }
+
+
+}
+
diff --git a/uk/ac/sanger/artemis/components/filetree/FileNode.java b/uk/ac/sanger/artemis/components/filetree/FileNode.java
new file mode 100644
index 0000000000000000000000000000000000000000..6542722e7c292e2c4d383102599d9c0a697e1529
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/FileNode.java
@@ -0,0 +1,159 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* Copyright (C) Genome Research Limited
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import java.awt.datatransfer.*;
+import javax.swing.tree.*;
+import java.io.*;
+import java.util.*;
+
+/**
+*
+* File node for local file tree manager
+*
+*/
+public class FileNode extends DefaultMutableTreeNode
+ implements Transferable, Serializable
+{
+ /** true if explored */
+ private boolean explored = false;
+ /** data flavour of a file node */
+ public static DataFlavor FILENODE =
+ new DataFlavor(FileNode.class, "Local file");
+ /** flavours file node and string */
+ static DataFlavor flavors[] = { FILENODE, DataFlavor.stringFlavor };
+
+ /**
+ *
+ * @param file file node file
+ *
+ */
+ public FileNode(File file)
+ {
+ setUserObject(file);
+ }
+
+ /** Determine if this is a directory */
+ public boolean getAllowsChildren() { return isDirectory(); }
+ /** Determine if this is a file */
+ public boolean isLeaf() { return !isDirectory(); }
+ /** Get the File this node represents */
+ public File getFile() { return (File)getUserObject(); }
+ /** Determine if this node has been explored */
+ public boolean isExplored() { return explored; }
+ /** Determine if this is a directory */
+ public boolean isDirectory()
+ {
+ File file = getFile();
+ return file.isDirectory();
+ }
+
+ /**
+ *
+ * Returns the name of the file
+ *
+ */
+ public String toString()
+ {
+ File file = (File)getUserObject();
+ String filename = file.toString();
+ int index = filename.lastIndexOf(File.separator);
+
+ return (index != -1 && index != filename.length()-1) ?
+ filename.substring(index+1) :
+ filename;
+ }
+
+ /**
+ *
+ * Explores a directory adding a FileNode for each
+ * child
+ *
+ */
+ public void explore(FileFilter filter)
+ {
+ if(!isDirectory())
+ return;
+
+ if(!isExplored())
+ {
+ File file = getFile();
+ explored = true;
+ File[] children;
+// filter files
+ children = file.listFiles(filter);
+
+// sort into alphabetic order
+ java.util.Arrays.sort(children);
+ for(int i=0; i < children.length; ++i)
+ add(new FileNode(children[i]));
+ }
+ }
+
+ /**
+ *
+ * Forces the directory to be re-explored
+ *
+ */
+ public void reExplore(FileFilter filter)
+ {
+ explored = false;
+ removeAllChildren();
+ explore(filter);
+ }
+
+// Transferable
+ public DataFlavor[] getTransferDataFlavors()
+ {
+ return flavors;
+ }
+
+ public boolean isDataFlavorSupported(DataFlavor f)
+ {
+ if(f.equals(FILENODE) || f.equals(DataFlavor.stringFlavor))
+ return true;
+ return false;
+ }
+
+ public Object getTransferData(DataFlavor d)
+ throws UnsupportedFlavorException, IOException
+ {
+ if(d.equals(FILENODE))
+ return this;
+ else if(d.equals(DataFlavor.stringFlavor))
+ return getFile().getAbsolutePath();
+ else throw new UnsupportedFlavorException(d);
+ }
+
+//Serializable
+ private void writeObject(java.io.ObjectOutputStream out) throws IOException
+ {
+ out.defaultWriteObject();
+ }
+
+ private void readObject(java.io.ObjectInputStream in)
+ throws IOException, ClassNotFoundException
+ {
+ in.defaultReadObject();
+ }
+
+}
diff --git a/uk/ac/sanger/artemis/components/filetree/FileTree.java b/uk/ac/sanger/artemis/components/filetree/FileTree.java
new file mode 100644
index 0000000000000000000000000000000000000000..cd86e466b3b628700df6f045f9f24d55b1bc347f
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/FileTree.java
@@ -0,0 +1,947 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* Copyright (C) Genome Research Limited
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import uk.ac.sanger.artemis.components.SwingWorker;
+import uk.ac.sanger.artemis.components.EntryEdit;
+import uk.ac.sanger.artemis.components.EntryFileDialog;
+
+import uk.ac.sanger.artemis.io.EntryInformation;
+import uk.ac.sanger.artemis.io.SimpleEntryInformation;
+import uk.ac.sanger.artemis.*;
+import uk.ac.sanger.artemis.util.InputStreamProgressListener;
+import uk.ac.sanger.artemis.util.InputStreamProgressEvent;
+import uk.ac.sanger.artemis.util.FileDocument;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+import uk.ac.sanger.artemis.sequence.NoSequenceException;
+import uk.ac.sanger.artemis.components.MessageDialog;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.tree.*;
+import java.io.*;
+import java.util.Vector;
+import java.util.Enumeration;
+import java.util.Hashtable;
+
+
+/**
+*
+* Creates a local file tree manager. This acts as a drag
+* source and sink for files.
+*
+*/
+public class FileTree extends JTree implements DragGestureListener,
+ DragSourceListener, DropTargetListener, ActionListener,
+ Autoscroll
+{
+
+ /** root directory */
+ private File root;
+ /** store of directories that are opened */
+ private Vector openNode;
+ /** file separator */
+ private String fs = new String(System.getProperty("file.separator"));
+ /** popup menu */
+ private JPopupMenu popup;
+ /** busy cursor */
+ private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+ /** done cursor */
+ private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+ /** AutoScroll margin */
+ private static final int AUTOSCROLL_MARGIN = 45;
+ /** used by AutoScroll method */
+ private Insets autoscrollInsets = new Insets( 0, 0, 0, 0 );
+ /** file filter */
+ private FileFilter filter = null;
+
+ /**
+ *
+ * @param rt root directory
+ * @param f frame
+ *
+ */
+ public FileTree(File rt, final JFrame f,
+ FileFilter filter)
+ {
+ this.root = rt;
+ this.filter = filter;
+
+ DragSource dragSource = DragSource.getDefaultDragSource();
+
+ dragSource.createDefaultDragGestureRecognizer(
+ this, // component where drag originates
+ DnDConstants.ACTION_COPY_OR_MOVE, // actions
+ this); // drag gesture recognizer
+
+ setDropTarget(new DropTarget(this,this));
+ DefaultTreeModel model = createTreeModel(root);
+ setModel(model);
+ createTreeModelListener();
+
+ this.getSelectionModel().setSelectionMode
+ (TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION);
+
+ // Popup menu
+ addMouseListener(new PopupListener());
+ popup = new JPopupMenu();
+
+ JMenuItem menuItem = new JMenuItem("Refresh");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ popup.add(new JSeparator());
+ //open menu
+ JMenu openMenu = new JMenu("Open With");
+ popup.add(openMenu);
+ menuItem = new JMenuItem("Jemboss Alignment Editor");
+ menuItem.addActionListener(this);
+ openMenu.add(menuItem);
+ menuItem = new JMenuItem("Artemis");
+ menuItem.addActionListener(this);
+ openMenu.add(menuItem);
+
+ menuItem = new JMenuItem("Rename...");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ menuItem = new JMenuItem("New Folder...");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ menuItem = new JMenuItem("Delete...");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ popup.add(new JSeparator());
+ menuItem = new JMenuItem("De-select All");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+
+ //Listen for when a file is selected
+ MouseListener mouseListener = new MouseAdapter()
+ {
+ public void mouseClicked(MouseEvent me)
+ {
+ if(me.getClickCount() == 2 && isFileSelection() &&
+ !me.isPopupTrigger())
+ {
+ f.setCursor(cbusy);
+ FileNode node = getSelectedNode();
+ String selected = node.getFile().getAbsolutePath();
+ showFilePane(selected);
+ f.setCursor(cdone);
+ }
+ }
+ };
+ this.addMouseListener(mouseListener);
+
+ addTreeExpansionListener(new TreeExpansionListener()
+ {
+ public void treeCollapsed(TreeExpansionEvent e){}
+ public void treeExpanded(TreeExpansionEvent e)
+ {
+ TreePath path = e.getPath();
+ if(path != null)
+ {
+ FileNode node = (FileNode)path.getLastPathComponent();
+
+ if(!node.isExplored())
+ {
+ f.setCursor(cbusy);
+ exploreNode(node);
+ f.setCursor(cdone);
+ }
+ }
+ }
+ });
+
+ }
+
+
+ /**
+ *
+ * Popup menu actions
+ * @param e action event
+ *
+ */
+ public void actionPerformed(ActionEvent e)
+ {
+
+ JMenuItem source = (JMenuItem)(e.getSource());
+ final FileNode node = getSelectedNode();
+
+ if(source.getText().equals("Refresh"))
+ {
+ if(node == null)
+ newRoot(root.getAbsolutePath());
+ else if(node.isLeaf())
+ refresh((FileNode)node.getParent());
+ else
+ refresh(node);
+ return;
+ }
+
+ if(node == null)
+ {
+ JOptionPane.showMessageDialog(null,"No file selected.",
+ "Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ final File f = node.getFile();
+
+ if(source.getText().equals("Jemboss Alignment Editor"))
+ {
+ org.emboss.jemboss.editor.AlignJFrame ajFrame =
+ new org.emboss.jemboss.editor.AlignJFrame(f);
+ ajFrame.setVisible(true);
+ }
+ else if(source.getText().equals("Artemis"))
+ {
+ setCursor(cbusy);
+ String selected = node.getFile().getAbsolutePath();
+ showFilePane(selected);
+ setCursor(cdone);
+ }
+ else if(source.getText().equals("Text Editor"))
+ showFilePane(f.getAbsolutePath());
+ else if(source.getText().equals("New Folder..."))
+ {
+ String path = null;
+ if(node.isLeaf())
+ path = f.getParent();
+ else
+ path = f.getAbsolutePath();
+
+ String inputValue = JOptionPane.showInputDialog(null,
+ "Folder Name","Create New Folder in "+path,
+ JOptionPane.QUESTION_MESSAGE);
+
+ if(inputValue != null && !inputValue.equals("") )
+ {
+ String fullname = path+fs+inputValue;
+ File dir = new File(fullname);
+
+ if(dir.exists())
+ JOptionPane.showMessageDialog(null, fullname+" alread exists!",
+ "Error", JOptionPane.ERROR_MESSAGE);
+ else
+ {
+ if(dir.mkdir())
+ addObject(inputValue,path,node);
+ else
+ JOptionPane.showMessageDialog(null,
+ "Cannot make the folder\n"+fullname,
+ "Error", JOptionPane.ERROR_MESSAGE);
+ }
+ }
+ }
+ else if(source.getText().equals("Delete..."))
+ {
+ File fn[] = getSelectedFiles();
+ String names = "";
+ for(int i=0; i<fn.length;i++)
+ names = names.concat(fn[i].getAbsolutePath()+"\n");
+ int n = JOptionPane.showConfirmDialog(null,
+ "Delete \n"+names+"?",
+ "Delete Files",
+ JOptionPane.YES_NO_OPTION);
+
+ FileNode nodes[] = getSelectedNodes();
+ if(n == JOptionPane.YES_OPTION)
+ for(int i=0; i<nodes.length;i++)
+ deleteFile(nodes[i]);
+ }
+ else if(source.getText().equals("De-select All"))
+ clearSelection();
+ else if(isFileSelection() && source.getText().equals("Rename..."))
+ {
+ String inputValue = (String)JOptionPane.showInputDialog(null,
+ "New File Name","Rename "+f.getName(),
+ JOptionPane.QUESTION_MESSAGE,null,null,f.getName());
+
+ if(inputValue != null && !inputValue.equals("") )
+ {
+ String path = f.getParent();
+ String fullname = path+fs+inputValue;
+ File newFile = new File(fullname);
+
+ try
+ {
+ renameFile(f,node,newFile.getCanonicalPath());
+ }
+ catch(IOException ioe){}
+ }
+ }
+ }
+
+
+ /**
+ *
+ * Delete a file from the tree
+ * @param node node to delete
+ *
+ */
+ public void deleteFile(final FileNode node)
+ {
+ File f = node.getFile();
+ if(f.delete())
+ {
+ Runnable deleteFileFromTree = new Runnable()
+ {
+ public void run () { deleteObject(node); };
+ };
+ SwingUtilities.invokeLater(deleteFileFromTree);
+ }
+ else
+ JOptionPane.showMessageDialog(null,"Cannot delete\n"+
+ f.getAbsolutePath(),"Warning",
+ JOptionPane.ERROR_MESSAGE);
+ }
+
+
+ /**
+ *
+ * Method to rename a file and update the filenode's.
+ * @param oldFile file to rename
+ * @param oldNode filenode to be removed
+ * @param newFullName name of the new file
+ *
+ */
+ private void renameFile(final File oldFile, final FileNode oldNode,
+ String newFullName)
+ {
+ final File fnew = new File(newFullName);
+ if(fnew.exists())
+ JOptionPane.showMessageDialog(null, newFullName+" alread exists!",
+ "Warning", JOptionPane.ERROR_MESSAGE);
+ else
+ {
+ if(oldFile.renameTo(fnew))
+ {
+ Runnable renameFileInTree = new Runnable()
+ {
+ public void run ()
+ {
+ addObject(fnew.getName(),fnew.getParent(),oldNode);
+ deleteObject(oldNode);
+ };
+ };
+ SwingUtilities.invokeLater(renameFileInTree);
+ }
+ else
+ JOptionPane.showMessageDialog(null,
+ "Cannot rename \n"+oldFile.getAbsolutePath()+
+ "\nto\n"+fnew.getAbsolutePath(), "Rename Error",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ return;
+ }
+
+
+ /**
+ *
+ * Define a directory root for the file tree
+ * @param newRoot directory to use as the root for
+ * the tree.
+ *
+ */
+ public void newRoot(String newRoot)
+ {
+ root = new File(newRoot);
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ model = createTreeModel(root);
+ setModel(model);
+ }
+
+ /**
+ *
+ * Get the current root node.
+ * @return directory root.
+ *
+ */
+ public File getRoot()
+ {
+ return root;
+ }
+
+ /**
+ *
+ * Refresh
+ * @param FileNode node to refresh
+ *
+ */
+ public void refresh(FileNode node)
+ {
+ node.reExplore(filter);
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ model.nodeStructureChanged(node);
+ }
+
+ /**
+ *
+ * Set the current file filter
+ *
+ */
+ public void setFilter(FileFilter filter)
+ {
+ this.filter = filter;
+ Enumeration en = openNode.elements();
+
+ while(en.hasMoreElements())
+ refresh((FileNode)en.nextElement());
+ }
+
+ /**
+ *
+ * Get FileNode of selected node
+ * @return node that is currently selected
+ *
+ */
+ public FileNode getSelectedNode()
+ {
+ TreePath path = getLeadSelectionPath();
+ if(path == null)
+ return null;
+ FileNode node = (FileNode)path.getLastPathComponent();
+ return node;
+ }
+
+
+ /**
+ *
+ * Get FileNodes of selected nodes
+ * @return node that is currently selected
+ *
+ */
+ public FileNode[] getSelectedNodes()
+ {
+ TreePath path[] = getSelectionPaths();
+ if(path == null)
+ return null;
+
+ int numberSelected = path.length;
+ FileNode nodes[] = new FileNode[numberSelected];
+ for(int i=0;i<numberSelected;i++)
+ nodes[i] = (FileNode)path[i].getLastPathComponent();
+
+ return nodes;
+ }
+
+
+ /**
+ *
+ * Get selected files
+ * @return node that is currently selected
+ *
+ */
+ public File[] getSelectedFiles()
+ {
+ FileNode[] fn = getSelectedNodes();
+ int numberSelected = fn.length;
+ File files[] = new File[numberSelected];
+ for(int i=0;i<numberSelected;i++)
+ files[i] = fn[i].getFile();
+
+ return files;
+ }
+
+
+ /**
+ *
+ * Return true if selected node is a file
+ * @return true is a file is selected, false if
+ * a directory is selected
+ *
+ */
+ public boolean isFileSelection()
+ {
+ TreePath path = getLeadSelectionPath();
+ if(path == null)
+ return false;
+
+ FileNode node = (FileNode)path.getLastPathComponent();
+ return node.isLeaf();
+ }
+
+
+ /**
+ *
+ * Make the given directory the root and create a new
+ * DefaultTreeModel.
+ * @param root root directory
+ * @param tree model with the root node set
+ * to the given directory
+ *
+ */
+ private DefaultTreeModel createTreeModel(File root)
+ {
+ FileNode rootNode = new FileNode(root);
+ rootNode.explore(filter);
+ openNode = new Vector();
+ openNode.add(rootNode);
+ return new DefaultTreeModel(rootNode);
+ }
+
+
+ /**
+ *
+ * Adding a file (or directory) to the file tree manager.
+ * This looks to see if the directory has already been opened
+ * and updates the filetree if it has.
+ * @param child new child to add in
+ * @param path path to where child is to be added
+ * @param node node to add child to
+ *
+ */
+ public DefaultMutableTreeNode addObject(String child,
+ String path, FileNode node)
+ {
+
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ if(node == null)
+ {
+ node = getNode(path);
+ if(node==null)
+ return null;
+ }
+
+ FileNode parentNode = getNode(path);
+ File newleaf = new File(path + fs + child);
+ FileNode childNode = null;
+
+ if(parentNode.isExplored())
+ {
+ childNode = new FileNode(newleaf);
+ int index = getAnIndex(parentNode,child);
+ if(index > -1)
+ model.insertNodeInto(childNode, parentNode, index);
+ }
+ else if(parentNode.isDirectory())
+ {
+ exploreNode(parentNode);
+ childNode = getNode(path + fs + child);
+ }
+
+ // Make sure the user can see the new node.
+ this.scrollPathToVisible(new TreePath(childNode.getPath()));
+ return childNode;
+ }
+
+
+ /**
+ *
+ * Delete a node from the JTree
+ * @param node node for deletion
+ *
+ */
+ public void deleteObject(FileNode node)
+ {
+ DefaultTreeModel model =(DefaultTreeModel)getModel();
+ FileNode parentNode = getNode(node.getFile().getParent());
+ model.removeNodeFromParent(node);
+ }
+
+
+ /**
+ *
+ * Explore a directory node
+ * @param dirNode direcory node to display
+ *
+ */
+ public void exploreNode(FileNode dirNode)
+ {
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ dirNode.explore(filter);
+ openNode.add(dirNode);
+ model.nodeStructureChanged(dirNode);
+ }
+
+ /**
+ *
+ * Gets the node from the existing explored nodes and their
+ * children.
+ * @param path path to a file or directory
+ * @return corresponding node if the directory or
+ * file is visible otherwise returns null.
+ *
+ */
+ private FileNode getNode(String path)
+ {
+ Enumeration en = openNode.elements();
+
+ while(en.hasMoreElements())
+ {
+ FileNode node = (FileNode)en.nextElement();
+ String nodeName = node.getFile().getAbsolutePath();
+ if(nodeName.equals(path))
+ return node;
+ }
+
+// check children of explored nodes
+ en = openNode.elements();
+ while(en.hasMoreElements())
+ {
+ FileNode child = getChildNode((FileNode)en.nextElement(),path);
+ if(child != null)
+ return child;
+ }
+
+ return null;
+ }
+
+
+ /**
+ *
+ * Gets the child node of a parent node
+ * @param parent parent node
+ * @param childName name of child
+ * @return the child node
+ *
+ */
+ private FileNode getChildNode(FileNode parent, String childName)
+ {
+ for(Enumeration children = parent.children(); children.hasMoreElements() ;)
+ {
+ FileNode childNode = (FileNode)children.nextElement();
+ String nodeName = childNode.getFile().getAbsolutePath();
+ if(childName.equals(nodeName))
+ return childNode;
+ }
+
+ return null;
+ }
+
+ /**
+ *
+ * Finds a new index for adding a new file to the file manager.
+ * @param parentNode parent directory node
+ * @param child new child node
+ * @return index of the child in the directory
+ *
+ */
+ private int getAnIndex(FileNode parentNode, String child)
+ {
+ //find the index for the child
+ int num = parentNode.getChildCount();
+ int childIndex = num;
+ for(int i=0;i<num;i++)
+ {
+ String nodeName =
+ ((FileNode)parentNode.getChildAt(i)).getFile().getName();
+ if(nodeName.compareTo(child) > 0)
+ {
+ childIndex = i;
+ break;
+ }
+ else if (nodeName.compareTo(child) == 0) //file already exists
+ {
+ childIndex = -1;
+ break;
+ }
+ }
+ return childIndex;
+ }
+
+
+ /**
+ *
+ * Read a file into a byte array.
+ * @param filename file name
+ * @return byte[] contents of file
+ *
+ */
+ protected static byte[] readByteFile(String filename)
+ {
+
+ File fn = new File(filename);
+ byte[] b = null;
+ try
+ {
+ long s = fn.length();
+ if(s == 0)
+ return b;
+ b = new byte[(int)s];
+ FileInputStream fi = new FileInputStream(fn);
+ fi.read(b);
+ fi.close();
+ }
+ catch (IOException ioe)
+ {
+ System.out.println("Cannot read file: " + filename);
+ }
+ return b;
+ }
+
+ /**
+ *
+ * Opens a JFrame with the file contents displayed.
+ * @param filename file name to display
+ *
+ */
+ private void showFilePane(final String filename)
+ {
+ SwingWorker entryWorker = new SwingWorker()
+ {
+ EntryEdit entry_edit;
+ public Object construct()
+ {
+ try
+ {
+ EntryInformation new_entry_information =
+ new SimpleEntryInformation(Options.getArtemisEntryInformation());
+
+ final Entry entry = new Entry(EntryFileDialog.getEntryFromFile(
+ null, new FileDocument(new File(filename)),
+ new_entry_information, true));
+ if(entry == null)
+ return null;
+
+ final EntryGroup entry_group =
+ new SimpleEntryGroup(entry.getBases());
+
+ entry_group.add(entry);
+ entry_edit = new EntryEdit(entry_group);
+ return null;
+ }
+ catch(NoSequenceException e)
+ {
+ new MessageDialog(null, "read failed: entry contains no sequence");
+ }
+ catch(OutOfRangeException e)
+ {
+ new MessageDialog(null, "read failed: one of the features in " +
+ " the entry has an out of range " +
+ "location: " + e.getMessage());
+
+ }
+ catch(NullPointerException npe){}
+
+ return null;
+ }
+
+ public void finished()
+ {
+ if(entry_edit != null)
+ entry_edit.setVisible(true);
+ }
+ };
+ entryWorker.start();
+
+ }
+
+
+////////////////////
+// DRAG AND DROP
+////////////////////
+// drag source
+ public void dragGestureRecognized(DragGestureEvent e)
+ {
+ // ignore if mouse popup trigger
+ InputEvent ie = e.getTriggerEvent();
+ if(ie instanceof MouseEvent)
+ if(((MouseEvent)ie).isPopupTrigger())
+ return;
+
+ // drag only files
+ if(isFileSelection())
+ e.startDrag(DragSource.DefaultCopyDrop, // cursor
+ (Transferable)getSelectedNode(), // transferable data
+ this); // drag source listener
+ }
+ public void dragDropEnd(DragSourceDropEvent e) {}
+ public void dragEnter(DragSourceDragEvent e) {}
+ public void dragExit(DragSourceEvent e) {}
+ public void dragOver(DragSourceDragEvent e) {}
+ public void dropActionChanged(DragSourceDragEvent e) {}
+
+// drop sink
+ public void dragEnter(DropTargetDragEvent e)
+ {
+ if(e.isDataFlavorSupported(FileNode.FILENODE))
+ e.acceptDrag(DnDConstants.ACTION_COPY_OR_MOVE);
+ }
+
+ public void drop(DropTargetDropEvent e)
+ {
+
+ Transferable t = e.getTransferable();
+ final FileNode dropNode = getSelectedNode();
+ if(dropNode == null)
+ {
+ e.rejectDrop();
+ return;
+ }
+
+ //local drop
+ if(t.isDataFlavorSupported(FileNode.FILENODE))
+ {
+ try
+ {
+ FileNode fn = (FileNode)t.getTransferData(FileNode.FILENODE);
+ fn = getNode(fn.getFile().getAbsolutePath());
+
+ if (dropNode.isLeaf())
+ {
+ e.rejectDrop();
+ return;
+ }
+
+ String dropDir = dropNode.getFile().getAbsolutePath();
+ String newFullName = dropDir+fs+fn.toString();
+ renameFile(fn.getFile(),fn,newFullName);
+ }
+ catch(Exception ufe){}
+ }
+ else
+ {
+ e.rejectDrop();
+ return;
+ }
+
+ }
+
+
+ /**
+ *
+ * When a suitable DataFlavor is offered over a remote file
+ * node the node is highlighted/selected and the drag
+ * accepted. Otherwise the drag is rejected.
+ *
+ */
+ public void dragOver(DropTargetDragEvent e)
+ {
+ if(e.isDataFlavorSupported(FileNode.FILENODE))
+ {
+ Point ploc = e.getLocation();
+ TreePath ePath = getPathForLocation(ploc.x,ploc.y);
+ if (ePath == null)
+ {
+ e.rejectDrag();
+ return;
+ }
+ FileNode node = (FileNode)ePath.getLastPathComponent();
+ if(!node.isDirectory())
+ e.rejectDrag();
+ else
+ {
+ setSelectionPath(ePath);
+ e.acceptDrag(DnDConstants.ACTION_COPY_OR_MOVE);
+ }
+ }
+ else
+ e.rejectDrag();
+
+ return;
+ }
+
+ public void dropActionChanged(DropTargetDragEvent e) {}
+ public void dragExit(DropTargetEvent e){}
+
+
+////////////////////
+// AUTO SCROLLING //
+////////////////////
+ /**
+ *
+ * Handles the auto scrolling of the JTree.
+ * @param location The location of the mouse.
+ *
+ */
+ public void autoscroll( Point location )
+ {
+ int top = 0, left = 0, bottom = 0, right = 0;
+ Dimension size = getSize();
+ Rectangle rect = getVisibleRect();
+ int bottomEdge = rect.y + rect.height;
+ int rightEdge = rect.x + rect.width;
+ if( location.y - rect.y < AUTOSCROLL_MARGIN && rect.y > 0 )
+ top = AUTOSCROLL_MARGIN;
+ if( location.x - rect.x < AUTOSCROLL_MARGIN && rect.x > 0 )
+ left = AUTOSCROLL_MARGIN;
+ if( bottomEdge - location.y < AUTOSCROLL_MARGIN && bottomEdge < size.height )
+ bottom = AUTOSCROLL_MARGIN;
+ if( rightEdge - location.x < AUTOSCROLL_MARGIN && rightEdge < size.width )
+ right = AUTOSCROLL_MARGIN;
+ rect.x += right - left;
+ rect.y += bottom - top;
+ scrollRectToVisible( rect );
+ }
+
+
+ /**
+ *
+ * Gets the insets used for the autoscroll.
+ * @return The insets.
+ *
+ */
+ public Insets getAutoscrollInsets()
+ {
+ Dimension size = getSize();
+ Rectangle rect = getVisibleRect();
+ autoscrollInsets.top = rect.y + AUTOSCROLL_MARGIN;
+ autoscrollInsets.left = rect.x + AUTOSCROLL_MARGIN;
+ autoscrollInsets.bottom = size.height - (rect.y+rect.height) + AUTOSCROLL_MARGIN;
+ autoscrollInsets.right = size.width - (rect.x+rect.width) + AUTOSCROLL_MARGIN;
+ return autoscrollInsets;
+ }
+
+ /**
+ *
+ * Popup menu listener
+ *
+ */
+ class PopupListener extends MouseAdapter
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ maybeShowPopup(e);
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ maybeShowPopup(e);
+ }
+
+ private void maybeShowPopup(MouseEvent e)
+ {
+ if(e.isPopupTrigger())
+ popup.show(e.getComponent(),
+ e.getX(), e.getY());
+ }
+ }
+
+ public static void main(String[] args)
+ {
+ JFrame tree_frame = new JFrame("File Manager");
+ FileTree ftree = new FileTree(new File(System.getProperty("user.home")),
+ tree_frame,null);
+ JScrollPane jsp = new JScrollPane(ftree);
+ tree_frame.getContentPane().add(jsp);
+ tree_frame.pack();
+ tree_frame.setVisible(true);
+ }
+
+}
+
diff --git a/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java b/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
new file mode 100644
index 0000000000000000000000000000000000000000..b105a2e9c78404e48805148f64a1ad96c3bac0be
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/LocalAndRemoteFileManager.java
@@ -0,0 +1,541 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* Copyright (C) Genome Research Limited
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import uk.ac.sanger.artemis.util.StringVector;
+import uk.ac.sanger.artemis.Options;
+
+import javax.swing.*;
+import java.io.File;
+import java.io.FileFilter;
+import java.awt.event.*;
+import java.awt.geom.*;
+import java.awt.*;
+
+public class LocalAndRemoteFileManager extends JFrame
+{
+
+ /** busy cursor */
+ private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+ /** done cursor */
+ private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+
+ public LocalAndRemoteFileManager(JFrame frame)
+ {
+ this(frame,getArtemisFilter());
+ }
+
+ /**
+ *
+ * File Manager Frame
+ * @param frame parent frame
+ *
+ */
+ public LocalAndRemoteFileManager(JFrame frame, FileFilter filter)
+ {
+ super("File Manager");
+
+ final JPanel localPanel = new JPanel(new BorderLayout());
+ FileTree ftree = new FileTree(new File(System.getProperty("user.dir")),
+ frame, filter);
+ JScrollPane localTree = new JScrollPane(ftree);
+ localPanel.add(localTree,BorderLayout.CENTER);
+
+ final JPanel remotePanel = new JPanel(new BorderLayout());
+
+ FileList flist = new FileList();
+ String pwd = flist.pwd();
+ SshFileTree sshtree = new SshFileTree(pwd);
+ JScrollPane remoteTree = new JScrollPane(sshtree);
+ remotePanel.add(remoteTree,BorderLayout.CENTER);
+
+ final JSplitPane treePane = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,
+ localPanel,remotePanel);
+
+ JPanel pane = (JPanel)getContentPane();
+ pane.setLayout(new BorderLayout());
+ pane.add(treePane, BorderLayout.CENTER);
+
+ Dimension screen = Toolkit.getDefaultToolkit().getScreenSize();
+ Dimension panelSize = new Dimension(210, (int)(screen.getHeight()/3));
+ setJMenuBar(makeMenuBar(pane,ftree,sshtree,localPanel,remotePanel,treePane,panelSize));
+ localPanel.add(getFileFileterComboBox(ftree), BorderLayout.SOUTH);
+
+ remoteTree.setPreferredSize(panelSize);
+ localTree.setPreferredSize(panelSize);
+
+ pack();
+
+ int yloc = (int)((screen.getHeight()-getHeight())/2);
+ setLocation(0,yloc);
+ setVisible(true);
+ }
+
+ protected JComboBox getFileFileterComboBox(final FileTree ftree)
+ {
+ String[] filters = { "Artemis Files", "Sequence Files",
+ "Feature Files", "All Files" };
+ final JComboBox comboFilter = new JComboBox(filters);
+ comboFilter.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String select = (String)comboFilter.getSelectedItem();
+ if(select.equals("Artemis Files"))
+ ftree.setFilter(getArtemisFilter());
+ else if(select.equals("Sequence Files"))
+ ftree.setFilter(getSequenceFilter());
+ else if(select.equals("Feature Files"))
+ ftree.setFilter(getFeatureFilter());
+ else if(select.equals("All Files"))
+ {
+ ftree.setFilter(new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.getName().startsWith("."))
+ return false;
+ return true;
+ }
+ });
+ }
+ }
+ });
+ return comboFilter;
+ }
+
+ /**
+ *
+ * Get a file filter for sequence and feature suffixes.
+ * @return file filter
+ */
+ protected static FileFilter getArtemisFilter()
+ {
+ final StringVector sequence_suffixes =
+ Options.getOptions().getOptionValues("sequence_file_suffixes");
+
+ final StringVector feature_suffixes =
+ Options.getOptions().getOptionValues("feature_file_suffixes");
+
+ final FileFilter artemis_filter = new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.isDirectory() &&
+ !pathname.getName().startsWith("."))
+ return true;
+
+ for(int i = 0; i<sequence_suffixes.size(); ++i)
+ {
+ final String suffix = sequence_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+
+ for(int i = 0; i<feature_suffixes.size(); ++i)
+ {
+ final String suffix = feature_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+ return false;
+ }
+ };
+ return artemis_filter;
+ }
+
+
+ /**
+ *
+ * Get a file filter for feature suffixes.
+ * @return file filter
+ */
+ protected static FileFilter getFeatureFilter()
+ {
+ final StringVector feature_suffixes =
+ Options.getOptions().getOptionValues("feature_file_suffixes");
+
+ final FileFilter feature_filter = new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.isDirectory() &&
+ !pathname.getName().startsWith("."))
+ return true;
+
+ for(int i = 0; i<feature_suffixes.size(); ++i)
+ {
+ final String suffix = feature_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+ return false;
+ }
+ };
+ return feature_filter;
+ }
+
+ /**
+ *
+ * Get a file filter for sequence suffixes.
+ * @return file filter
+ */
+ protected static FileFilter getSequenceFilter()
+ {
+ final StringVector sequence_suffixes =
+ Options.getOptions().getOptionValues("sequence_file_suffixes");
+
+ final FileFilter seq_filter = new FileFilter()
+ {
+ public boolean accept(File pathname)
+ {
+ if(pathname.isDirectory() &&
+ !pathname.getName().startsWith("."))
+ return true;
+
+ for(int i = 0; i<sequence_suffixes.size(); ++i)
+ {
+ final String suffix = sequence_suffixes.elementAt(i);
+
+ if(pathname.getName().endsWith("." + suffix) ||
+ pathname.getName().endsWith("." + suffix + ".gz"))
+ return true;
+ }
+
+ return false;
+ }
+ };
+ return seq_filter;
+ }
+
+ /**
+ *
+ * Set up a menu and tool bar
+ * @param pane panel to add toolbar to
+ * @param ftree file tree display
+ *
+ */
+ private JMenuBar makeMenuBar(JPanel pane, final FileTree ftree, final SshFileTree sshtree,
+ final JPanel localPanel, final JPanel remotePanel,
+ final JSplitPane treePane, final Dimension panelSize)
+ {
+ JMenuBar mBar = new JMenuBar();
+ JMenu fileMenu = new JMenu("File");
+ mBar.add(fileMenu);
+
+ JMenuItem fileMenuGoto = new JMenuItem("Go to Directory ...");
+ fileMenuGoto.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ String dir = ftree.getRoot().getAbsolutePath();
+ String newDir = JOptionPane.showInputDialog(LocalAndRemoteFileManager.this,
+ "Go to Directory:",dir);
+
+ if(newDir == null)
+ return;
+
+ newDir = newDir.trim();
+ File newDirFile = new File(newDir);
+
+ if(newDirFile.exists() &&
+ newDirFile.canRead() &&
+ !newDir.equals(dir))
+ ftree.newRoot(newDir);
+ else
+ {
+ String error = null;
+ if(!newDirFile.exists())
+ error = new String(newDir+" doesn't exist!");
+ else if(!newDirFile.canRead())
+ error = new String(newDir+" cannot be read!");
+ else if(newDir.equals(dir))
+ error = new String("Same directory!");
+
+ if(error != null)
+ JOptionPane.showMessageDialog(LocalAndRemoteFileManager.this,
+ error, "Warning",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ }
+ });
+ fileMenu.add(fileMenuGoto);
+ fileMenu.add(new JSeparator());
+
+ JRadioButtonMenuItem prefV = new JRadioButtonMenuItem("Vertical Split");
+ fileMenu.add(prefV);
+ prefV.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ treePane.remove(remotePanel);
+ treePane.remove(localPanel);
+ treePane.setOrientation(JSplitPane.VERTICAL_SPLIT);
+ treePane.setTopComponent(localPanel);
+ treePane.setBottomComponent(remotePanel);
+ remotePanel.setPreferredSize(panelSize);
+ localPanel.setPreferredSize(panelSize);
+
+ pack();
+ treePane.setDividerLocation(0.5);
+ }
+ });
+// prefV.setSelected(true);
+ ButtonGroup group = new ButtonGroup();
+ group.add(prefV);
+
+ JRadioButtonMenuItem prefH = new JRadioButtonMenuItem("Horizontal Split");
+ fileMenu.add(prefH);
+ prefH.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ treePane.remove(remotePanel);
+ treePane.remove(localPanel);
+ treePane.setOrientation(JSplitPane.HORIZONTAL_SPLIT);
+ treePane.setLeftComponent(localPanel);
+ treePane.setRightComponent(remotePanel);
+
+ remotePanel.setPreferredSize(panelSize);
+ localPanel.setPreferredSize(panelSize);
+
+ pack();
+ treePane.setDividerLocation(0.5);
+ }
+ });
+ group.add(prefH);
+ prefH.setSelected(true);
+
+ JMenuItem fileMenuClose = new JMenuItem("Close");
+ fileMenuClose.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ setVisible(false);
+ }
+ });
+ fileMenu.add(fileMenuClose);
+
+ // remote tool bar set up
+ JToolBar remoteToolBar = new JToolBar();
+ Dimension buttonSize = new Dimension(22,24);
+
+ JButton remoteUpBt = new UpButton();
+ remoteUpBt.setPreferredSize(buttonSize);
+ remoteUpBt.setMinimumSize(buttonSize);
+
+ remoteUpBt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LocalAndRemoteFileManager.this.setCursor(cbusy);
+ sshtree.up();
+ LocalAndRemoteFileManager.this.setCursor(cdone);
+ }
+ });
+ remoteToolBar.add(remoteUpBt);
+
+ remoteToolBar.add(Box.createVerticalStrut(35));
+ remotePanel.add(remoteToolBar, BorderLayout.NORTH);
+
+ // local tool bar set up
+ JToolBar toolBar = new JToolBar();
+
+ JButton upBt = new UpButton();
+ upBt.setPreferredSize(buttonSize);
+ upBt.setMinimumSize(buttonSize);
+
+ upBt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ LocalAndRemoteFileManager.this.setCursor(cbusy);
+ File root = ftree.getRoot();
+ String parent = root.getParent();
+ if(parent != null)
+ ftree.newRoot(parent);
+ LocalAndRemoteFileManager.this.setCursor(cdone);
+ }
+ });
+ toolBar.add(upBt);
+
+// yeastpub
+ JButton shortCut1 = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+ Font font = new Font("Monospaced", Font.BOLD, 14);
+ g2.setFont(font);
+
+ g2.setColor(Color.black);
+ g2.drawString("Y",4,18);
+ g2.setColor(Color.red);
+ g2.drawString("P",10,15);
+ setSize(22,24);
+ }
+ };
+ shortCut1.setPreferredSize(buttonSize);
+ shortCut1.setMinimumSize(buttonSize);
+ shortCut1.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ftree.newRoot("/nfs/disk222/yeastpub");
+ }
+ });
+
+ if((new File("/nfs/disk222/yeastpub")).exists())
+ toolBar.add(shortCut1);
+
+// pathdata
+ JButton shortCut2 = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+ Font font = new Font("Monospaced", Font.BOLD, 14);
+ g2.setFont(font);
+
+ g2.setColor(Color.black);
+ g2.drawString("P",4,18);
+ g2.setColor(Color.red);
+ g2.drawString("D",10,15);
+ setSize(22,24);
+ }
+ };
+ shortCut2.setPreferredSize(buttonSize);
+ shortCut2.setMinimumSize(buttonSize);
+ shortCut2.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ftree.newRoot("/nfs/pathdata/");
+ }
+ });
+
+ if((new File("/nfs/pathdata/")).exists())
+ toolBar.add(shortCut2);
+
+// home button
+ JButton homeBt = new JButton()
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+
+ g2.setColor(Color.blue);
+ float loc1[][] = { {3,14}, {11,3}, {19,14},
+ {17,14}, {17,18}, {5,18}, {5,14} };
+ g2.fill(makeShape(loc1));
+
+ setSize(22,24);
+ }
+ };
+ homeBt.setPreferredSize(buttonSize);
+ homeBt.setMinimumSize(buttonSize);
+ homeBt.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ftree.newRoot(System.getProperty("user.home"));
+ }
+ });
+ toolBar.add(homeBt);
+
+ toolBar.add(Box.createVerticalStrut(35));
+ localPanel.add(toolBar, BorderLayout.NORTH);
+
+ return mBar;
+ }
+
+ /**
+ *
+ * Used to draw a Shape.
+ *
+ */
+ public static GeneralPath makeShape(float loc[][])
+ {
+ GeneralPath path = new GeneralPath(GeneralPath.WIND_NON_ZERO);
+
+ path.moveTo(loc[0][0],loc[0][1]);
+
+ for(int i=1; i<loc.length; i++)
+ path.lineTo(loc[i][0],loc[i][1]);
+
+ return path;
+ }
+
+ class UpButton extends JButton
+ {
+ public void paintComponent(Graphics g)
+ {
+ super.paintComponent(g);
+ Graphics2D g2 = (Graphics2D)g;
+
+ g2.setColor(new Color(0,128,0));
+ float loc1[][] = { {11,18}, {7,18}, {7,14},
+ {3,14}, {11,4} };
+
+ g2.fill(makeShape(loc1));
+ g2.setColor(Color.green);
+
+ float loc2[][] = { {11,18}, {15,18}, {15,14},
+ {19,14}, {11,4} };
+ g2.fill(makeShape(loc2));
+
+ setSize(22,24);
+ }
+ }
+
+ public static void main(String args[])
+ {
+ final javax.swing.LookAndFeel look_and_feel =
+ javax.swing.UIManager.getLookAndFeel();
+
+ final javax.swing.plaf.FontUIResource font_ui_resource =
+ Options.getOptions().getFontUIResource();
+
+ java.util.Enumeration keys = UIManager.getDefaults().keys();
+ while(keys.hasMoreElements())
+ {
+ Object key = keys.nextElement();
+ Object value = UIManager.get(key);
+ if(value instanceof javax.swing.plaf.FontUIResource)
+ UIManager.put(key, font_ui_resource);
+ }
+
+ JFrame frame = new LocalAndRemoteFileManager(null);
+ frame.pack();
+ frame.setVisible(true);
+ }
+}
+
diff --git a/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java b/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
new file mode 100644
index 0000000000000000000000000000000000000000..4e7a678a716f57b9e8dbee715831beaddb72b90f
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/RemoteFileNode.java
@@ -0,0 +1,266 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* @author: Copyright (C) Tim Carver
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import java.awt.datatransfer.*;
+import javax.swing.tree.*;
+import java.io.*;
+import java.util.*;
+
+/**
+*
+* File node for remote file tree manager
+*
+*/
+public class RemoteFileNode extends DefaultMutableTreeNode
+ implements Transferable, Serializable
+{
+ /** true if node is explored */
+ private boolean explored = false;
+ /** true if node is a directory */
+ private boolean isDir = false;
+ /** full name of node */
+ private String fullname;
+ /** path to the file on the server */
+ private String serverPathToFile;
+ /** root directory */
+ private String rootdir;
+
+ /** parent directory listing */
+ private transient FileList parentList; // make transient for
+ /** jemboss properties */
+ private transient Properties mysettings; // Transferable to work
+ /** remote server file roots */
+ private transient String froots;
+ /** file separator for server files */
+ private String fs = "/";
+
+ final public static DataFlavor REMOTEFILENODE =
+ new DataFlavor(RemoteFileNode.class, "Remote file");
+ static DataFlavor remoteFlavors[] = { REMOTEFILENODE,
+ DataFlavor.stringFlavor };
+
+
+ /**
+ *
+ * @param mysettings jemboss properties
+ * @param froots remote server file roots
+ * @param file file for this node
+ * @param parentList parent directory listing
+ * @param parent parent to this node
+ *
+ */
+ public RemoteFileNode(Properties mysettings, String froots,
+ String file, FileList parentList, String parent)
+ {
+ this(mysettings, froots, file, parentList, parent, false);
+ }
+
+ /**
+ *
+ * @param mysettings jemboss properties
+ * @param froots remote server file roots
+ * @param file file for this node
+ * @param parentList parent directory listing
+ * @param parent parent to this node
+ * @param ldir true if the node is a directory
+ *
+ */
+ public RemoteFileNode(Properties mysettings, String froots,
+ String file, FileList parentList, String parent,
+ boolean ldir)
+ {
+ this.mysettings = mysettings;
+ this.froots = froots;
+ this.parentList = parentList;
+ isDir = ldir;
+ rootdir = froots;
+ serverPathToFile = froots;
+
+ if(parent != null)
+ {
+ if(parent.endsWith("/."))
+ parent = parent.substring(0,parent.length()-1);
+ else if(parent.endsWith(fs))
+ parent = parent.substring(0,parent.length());
+
+ if(parent.equals("."))
+ fullname = file;
+ else
+ {
+ fullname = parent + fs + file;
+ if(serverPathToFile.endsWith(fs))
+ serverPathToFile = serverPathToFile.concat(parent);
+ else
+ serverPathToFile = serverPathToFile.concat(fs+parent);
+ }
+ }
+
+ if(parentList != null)
+ {
+ if(parentList.isDirectory(file))
+ isDir = true;
+ }
+ else if(parent == null)
+ fullname = ".";
+
+ setUserObject(file);
+ }
+
+ /** @return true if node is a directory */
+ public boolean getAllowsChildren() { return isDir; }
+ /** @return true if node is a file */
+ public boolean isLeaf() { return !isDir; }
+ /** @return true if node is a directory */
+ public boolean isDirectory() { return isDir; }
+ /** @return the node name */
+ public String getFile() { return (String)getUserObject(); }
+ /** @return root directory */
+ public String getRootDir() { return rootdir; }
+ /** @return full name of the node */
+ public String getFullName() { return fullname; }
+ /** @return path on server */
+ public String getPathName() { return serverPathToFile; }
+ /** @return true if explored */
+ public boolean isExplored() { return explored; }
+
+ protected void setDir(boolean isDir)
+ {
+ this.isDir = isDir;
+ }
+
+ /**
+ *
+ * Get the server name
+ * @return server name
+ *
+ */
+ public String getServerName()
+ {
+ String prefix = serverPathToFile;
+ if(!prefix.endsWith(fs))
+ prefix = prefix.concat(fs);
+
+ if(fullname.equals("."))
+ return prefix;
+
+ return prefix + (String)getUserObject();
+ }
+
+ /**
+ *
+ * Explore the node and add new child nodes
+ *
+ */
+ public void explore()
+ {
+ if(!isDir)
+ return;
+
+ if(!explored)
+ {
+ FileList flist = new FileList();
+
+ String dir;
+ if(getRootDir().equals(""))
+ dir = new String("~/"+getFullName());
+ else
+ dir = new String(getRootDir()+"/"+getFullName());
+ dir = dir.trim();
+
+ flist.getDirList(dir);
+ Vector children = flist.fileVector();
+ for(int i=0;i<children.size();i++)
+ add(new RemoteFileNode(mysettings,froots,(String)children.get(i),
+ flist,fullname));
+ }
+ explored = true;
+ }
+
+ protected boolean delete()
+ {
+ FileList flist = new FileList();
+ return flist.delete(getRootDir()+"/"+getFullName());
+ }
+
+ protected boolean mkdir(String dir)
+ {
+ FileList flist = new FileList();
+ return flist.mkdir(dir);
+ }
+
+ protected boolean rename(String new_file)
+ {
+ FileList flist = new FileList();
+ return flist.rename(getRootDir()+"/"+getFullName(), new_file);
+ }
+
+ protected boolean put(File local_file)
+ {
+ FileList flist = new FileList();
+ return flist.put(getRootDir()+"/"+getFullName(), local_file);
+ }
+
+
+ public byte[] getFileContents()
+ {
+ FileList flist = new FileList();
+ return flist.getFileContents(getRootDir()+"/"+getFullName());
+ }
+
+// Transferable
+ public DataFlavor[] getTransferDataFlavors()
+ {
+ return remoteFlavors;
+ }
+
+ public boolean isDataFlavorSupported(DataFlavor f)
+ {
+ if(f.equals(REMOTEFILENODE) || f.equals(DataFlavor.stringFlavor))
+ return true;
+ return false;
+ }
+
+ public Object getTransferData(DataFlavor d)
+ throws UnsupportedFlavorException, IOException
+ {
+ if(d.equals(REMOTEFILENODE))
+ return this;
+ else if(d.equals(DataFlavor.stringFlavor))
+ return getServerName();
+ else throw new UnsupportedFlavorException(d);
+ }
+
+// Serializable
+ private void writeObject(java.io.ObjectOutputStream out) throws IOException
+ {
+ out.defaultWriteObject();
+ }
+
+ private void readObject(java.io.ObjectInputStream in)
+ throws IOException, ClassNotFoundException
+ {
+ in.defaultReadObject();
+ }
+
+}
+
diff --git a/uk/ac/sanger/artemis/components/filetree/SshFileTree.java b/uk/ac/sanger/artemis/components/filetree/SshFileTree.java
new file mode 100644
index 0000000000000000000000000000000000000000..19be4f2a0d514dccb5912bb23ac831eef8762594
--- /dev/null
+++ b/uk/ac/sanger/artemis/components/filetree/SshFileTree.java
@@ -0,0 +1,1000 @@
+/********************************************************************
+*
+* This library is free software; you can redistribute it and/or
+* modify it under the terms of the GNU Library General Public
+* License as published by the Free Software Foundation; either
+* version 2 of the License, or (at your option) any later version.
+*
+* This library 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
+* Library General Public License for more details.
+*
+* You should have received a copy of the GNU Library General Public
+* License along with this library; if not, write to the
+* Free Software Foundation, Inc., 59 Temple Place - Suite 330,
+* Boston, MA 02111-1307, USA.
+*
+* @author: Copyright (C) Tim Carver
+*
+********************************************************************/
+
+package uk.ac.sanger.artemis.components.filetree;
+
+import uk.ac.sanger.artemis.components.SwingWorker;
+import uk.ac.sanger.artemis.components.EntryEdit;
+import uk.ac.sanger.artemis.components.EntryFileDialog;
+import uk.ac.sanger.artemis.io.EntryInformation;
+import uk.ac.sanger.artemis.io.SimpleEntryInformation;
+import uk.ac.sanger.artemis.*;
+import uk.ac.sanger.artemis.util.RemoteFileDocument;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+import uk.ac.sanger.artemis.sequence.NoSequenceException;
+import uk.ac.sanger.artemis.components.MessageDialog;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.datatransfer.*;
+import java.awt.dnd.*;
+import javax.swing.*;
+import javax.swing.event.*;
+import javax.swing.tree.*;
+import java.io.*;
+import java.util.*;
+
+
+/**
+*
+* Creates a remote file tree which is a drag source & sink
+*
+*/
+public class SshFileTree extends JTree implements DragGestureListener,
+ DragSourceListener, DropTargetListener, ActionListener,
+ Autoscroll
+{
+
+ /** properties */
+ private Properties mysettings;
+ /** remote directory roots */
+ private static String froots;
+ /** popup menu */
+ private JPopupMenu popup;
+ /** file separator */
+ private String fs = new String(System.getProperty("file.separator"));
+ /** line separator */
+ private String ls = new String(System.getProperty("line.separator"));
+ /** store of directories that are opened */
+ private Vector openNode;
+ /** busy cursor */
+ private Cursor cbusy = new Cursor(Cursor.WAIT_CURSOR);
+ /** done cursor */
+ private Cursor cdone = new Cursor(Cursor.DEFAULT_CURSOR);
+ /** AutoScroll margin */
+ private static final int AUTOSCROLL_MARGIN = 45;
+ /** used by AutoScroll method */
+ private Insets autoscrollInsets = new Insets( 0, 0, 0, 0 );
+
+
+ /**
+ *
+ * @param froots remote directory roots
+ *
+ */
+ public SshFileTree(String froots)
+ {
+ this.froots = froots;
+
+ DragSource dragSource = DragSource.getDefaultDragSource();
+ dragSource.createDefaultDragGestureRecognizer(
+ this, // component where drag originates
+ DnDConstants.ACTION_COPY_OR_MOVE, // actions
+ this); // drag gesture recognizer
+
+ setDropTarget(new DropTarget(this,this));
+ DefaultTreeModel model = createTreeModel(froots);
+ setModel(model);
+ createTreeModelListener();
+
+ this.getSelectionModel().setSelectionMode
+ (TreeSelectionModel.DISCONTIGUOUS_TREE_SELECTION);
+
+// popup menu
+ addMouseListener(new PopupListener());
+ popup = new JPopupMenu();
+ JMenuItem menuItem = new JMenuItem("Refresh");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ popup.add(new JSeparator());
+//open menu
+ JMenu openMenu = new JMenu("Open With");
+ popup.add(openMenu);
+ menuItem = new JMenuItem("Jemboss Aligmnment Editor");
+ menuItem.addActionListener(this);
+ openMenu.add(menuItem);
+ menuItem = new JMenuItem("Artemis");
+ menuItem.addActionListener(this);
+ openMenu.add(menuItem);
+
+ menuItem = new JMenuItem("Rename...");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ menuItem = new JMenuItem("New Folder...");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ menuItem = new JMenuItem("Delete...");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+ popup.add(new JSeparator());
+ menuItem = new JMenuItem("De-select All");
+ menuItem.addActionListener(this);
+ popup.add(menuItem);
+
+
+ //Listen for when a file is selected
+ addMouseListener(new MouseListener()
+ {
+ public void mouseClicked(MouseEvent me)
+ {
+ if(me.getClickCount() == 2 && isFileSelection())
+ {
+ RemoteFileNode node = (RemoteFileNode)getLastSelectedPathComponent();
+ if(node==null)
+ return;
+ setCursor(cbusy);
+ if(node.isLeaf())
+ showFilePane(node);
+ setCursor(cdone);
+ }
+ }
+ public void mousePressed(MouseEvent me){}
+ public void mouseEntered(MouseEvent me){}
+ public void mouseExited(MouseEvent me){}
+ public void mouseReleased(MouseEvent me){}
+ });
+
+ addTreeExpansionListener(new TreeExpansionListener()
+ {
+ public void treeExpanded(TreeExpansionEvent e)
+ {
+ TreePath path = e.getPath();
+ if(path != null)
+ {
+ setCursor(cbusy);
+ RemoteFileNode node = (RemoteFileNode)path.getLastPathComponent();
+
+ if(!node.isExplored())
+ exploreNode(node);
+ setCursor(cdone);
+ }
+ }
+ public void treeCollapsed(TreeExpansionEvent e){}
+ });
+
+ }
+
+
+ /**
+ *
+ * This is used to refresh the file manager
+ *
+ */
+ public void refreshRoot()
+ {
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ model = createTreeModel(froots);
+ setModel(model);
+ }
+
+
+ /**
+ *
+ * Define a directory root for the file tree
+ * @param newRoot directory to use as the root for
+ * the tree.
+ *
+ */
+ public void up()
+ {
+ File current = new File(froots);
+ froots = current.getParentFile().getAbsolutePath();
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ model = createTreeModel(froots);
+ setModel(model);
+ }
+
+ /**
+ *
+ * Popup menu actions
+ * @param e action event
+ *
+ */
+ public void actionPerformed(ActionEvent e)
+ {
+
+ JMenuItem source = (JMenuItem)(e.getSource());
+ final RemoteFileNode node = getSelectedNode();
+ if(node == null)
+ {
+ JOptionPane.showMessageDialog(null,"No file selected.",
+ "Warning",
+ JOptionPane.WARNING_MESSAGE);
+ return;
+ }
+
+ final String fn = node.getFullName();
+ final String parent = node.getPathName();
+ String rootPath = node.getRootDir();
+ RemoteFileNode pn = node;
+
+ if(source.getText().equals("Refresh"))
+ {
+ refreshRoot();
+ }
+ else if(source.getText().equals("Jemboss Aligmnment Editor"))
+ {
+ final byte[] contents = node.getFileContents();
+ org.emboss.jemboss.editor.AlignJFrame ajFrame =
+ new org.emboss.jemboss.editor.AlignJFrame(new String(contents), fn);
+ ajFrame.setVisible(true);
+ }
+ else if(source.getText().equals("Artemis"))
+ showFilePane(node);
+ else if(source.getText().equals("New Folder..."))
+ {
+ final String inputValue = JOptionPane.showInputDialog(null,
+ "Folder Name","Create New Folder in",
+ JOptionPane.QUESTION_MESSAGE);
+
+ String dropDest = null;
+
+ if(node.isLeaf())
+ {
+ pn = (RemoteFileNode)node.getParent();
+ dropDest = pn.getFullName() + "/" + inputValue; //assumes unix file sep.!
+ }
+ else
+ dropDest = node.getFullName() + "/" + inputValue;
+
+ String newNode = pn.getServerName();
+ if(!newNode.endsWith("/"))
+ newNode = newNode.concat("/");
+ newNode = newNode.concat(inputValue);
+
+ if(nodeExists(pn,newNode))
+ return;
+
+ if(inputValue != null && !inputValue.equals("") )
+ {
+ final RemoteFileNode pnn = pn;
+ node.mkdir(newNode);
+
+ Runnable addDirToTree = new Runnable()
+ {
+ public void run () { addObject(pnn,inputValue,true); };
+ };
+ SwingUtilities.invokeLater(addDirToTree);
+ }
+ }
+ else if(source.getText().equals("Delete..."))
+ {
+ RemoteFileNode nodes[] = getSelectedNodes();
+ String sname = "";
+ for(int i=0;i<nodes.length;i++)
+ sname = sname.concat(nodes[i].getServerName()+ls);
+
+ int n = JOptionPane.showConfirmDialog(null,
+ "Delete"+ls+sname+"?", "Delete "+sname,
+ JOptionPane.YES_NO_OPTION);
+ if(n == JOptionPane.YES_OPTION)
+ for(int i=0;i<nodes.length;i++)
+ deleteNode(nodes[i]);
+ }
+ else if(source.getText().equals("De-select All"))
+ clearSelection();
+ else if(source.getText().equals("Rename..."))
+ {
+ if(node.isLeaf())
+ {
+ String inputValue = (String)JOptionPane.showInputDialog(null,
+ "New File Name","Rename "+fn,
+ JOptionPane.QUESTION_MESSAGE,null,null,fn);
+
+ pn = (RemoteFileNode)node.getParent();
+
+ if(inputValue != null && !inputValue.equals("") )
+ {
+ String newfile = null;
+ if(parent.endsWith("/"))
+ newfile = parent+inputValue;
+ else
+ newfile = parent+"/"+inputValue;
+ String dir = ((RemoteFileNode)node.getParent()).getFullName();
+ if(inputValue.indexOf("/") > 0)
+ {
+ int index = inputValue.lastIndexOf("/");
+ dir = inputValue.substring(0,index);
+ }
+
+ RemoteFileNode parentNode = getNode(dir);
+ if(!nodeExists(parentNode,newfile))
+ rename(rootPath,fn,parent,inputValue,node,parentNode);
+ }
+ }
+ }
+ }
+
+
+ /**
+ *
+ * Delete a node (file or directory) from the tree
+ * and from the server
+ * @param node node to remove
+ *
+ */
+ private void deleteNode(final RemoteFileNode node)
+ {
+ setCursor(cbusy);
+
+ boolean deleted = false;
+ deleted = node.delete();
+
+ if(!deleted && !node.isLeaf())
+ JOptionPane.showMessageDialog(null,"Cannot delete"+ls+
+ node.getServerName()+
+ ls+"this directory is not empty","Warning",
+ JOptionPane.ERROR_MESSAGE);
+ else if(deleted)
+ {
+ Runnable deleteFileFromTree = new Runnable()
+ {
+ public void run () { deleteObject(node); };
+ };
+ SwingUtilities.invokeLater(deleteFileFromTree);
+ }
+
+ setCursor(cdone);
+ }
+
+
+ /**
+ *
+ * Explore a directory node
+ * @param dirNode direcory node to display
+ *
+ */
+ public void exploreNode(RemoteFileNode dirNode)
+ {
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ dirNode.explore();
+ openNode.add(dirNode);
+ model.nodeStructureChanged(dirNode);
+ }
+
+
+ /**
+ *
+ * Test if a child node exists
+ * @param parentNode parent node
+ * @param child child to test for
+ *
+ */
+ public boolean nodeExists(RemoteFileNode parentNode,String child)
+ {
+ RemoteFileNode childNode = getChildNode(parentNode,child);
+ if(childNode != null)
+ {
+ String ls = System.getProperty("line.separator");
+ JOptionPane.showMessageDialog(null, child+ls+" already exists!",
+ "File Exists",
+ JOptionPane.ERROR_MESSAGE);
+ return true;
+ }
+
+ return false;
+ }
+
+
+ /**
+ *
+ * Rename a node from the tree
+ * @param rootPath root path
+ * @param fullname full name of node to rename
+ * @param pathToNewFile path to new file
+ * @param newfile new file name
+ * @param node node to rename
+ *
+ */
+ private void rename(String rootPath, final String fullname,
+ String pathToNewFile, final String newfile,
+ final RemoteFileNode node, final RemoteFileNode parentNode)
+ {
+ setCursor(cbusy);
+ node.rename(pathToNewFile+"/"+newfile);
+ setCursor(cdone);
+ Runnable deleteFileFromTree = new Runnable()
+ {
+ public void run ()
+ {
+ addObject(parentNode,newfile,false);
+ deleteObject(node);
+ };
+ };
+ SwingUtilities.invokeLater(deleteFileFromTree);
+ }
+
+
+ /**
+ *
+ * Adding a file (or directory) to the file tree manager.
+ * This looks to see if the directory has already been opened
+ * and updates the filetree if it has.
+ * @param parentNode parent node
+ * @param child file to add to the tree
+ * @param ldir true if child is a directory
+ *
+ */
+ public void addObject(RemoteFileNode parentNode,String child,
+ boolean ldir)
+ {
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+
+ if(parentNode == null)
+ return;
+
+ String path = parentNode.getFullName();
+ //create new file node
+ if(path.equals(" "))
+ path = "";
+
+ if(child.indexOf("/") > -1)
+ child = child.substring(child.lastIndexOf("/")+1);
+
+ RemoteFileNode childNode = null;
+ if(!parentNode.isExplored())
+ {
+ exploreNode(parentNode);
+ childNode = getNode(parentNode.getServerName() + "/" + child);
+ }
+ else
+ {
+ childNode = new RemoteFileNode(mysettings,froots,
+ child,null,path,ldir);
+
+ //find the index for the child
+ int num = parentNode.getChildCount();
+ int childIndex = num;
+ for(int i=0;i<num;i++)
+ {
+ String nodeName = ((RemoteFileNode)parentNode.getChildAt(i)).getFile();
+ if(nodeName.compareTo(child) > 0)
+ {
+ childIndex = i;
+ break;
+ }
+ else if(nodeName.compareTo(child) == 0) //file already exists
+ {
+ childIndex = -1;
+ break;
+ }
+ }
+ if(childIndex != -1)
+ model.insertNodeInto(childNode,parentNode,childIndex);
+ }
+
+ // Make sure the user can see the new node.
+ this.scrollPathToVisible(new TreePath(childNode.getPath()));
+
+ return;
+ }
+
+
+ /**
+ *
+ * Delete a node from the tree
+ * @param node node to remove
+ *
+ */
+ public void deleteObject(RemoteFileNode node)
+ {
+ RemoteFileNode parentNode = (RemoteFileNode)node.getParent();
+ DefaultTreeModel model = (DefaultTreeModel)getModel();
+ model.removeNodeFromParent(node);
+// model.nodeStructureChanged(parentNode);
+ return;
+ }
+
+
+ /**
+ *
+ * Get RemoteFileNode of selected node
+ * @return node that is currently selected
+ *
+ */
+ public RemoteFileNode getSelectedNode()
+ {
+ TreePath path = getLeadSelectionPath();
+ if(path == null)
+ return null;
+ RemoteFileNode node = (RemoteFileNode)path.getLastPathComponent();
+ return node;
+ }
+
+
+ /**
+ *
+ * Get RemoteFileNodes of selected nodes
+ * @return node that is currently selected
+ *
+ */
+ public RemoteFileNode[] getSelectedNodes()
+ {
+ TreePath path[] = getSelectionPaths();
+ if(path == null)
+ return null;
+
+ int numberSelected = path.length;
+ RemoteFileNode nodes[] = new RemoteFileNode[numberSelected];
+ for(int i=0;i<numberSelected;i++)
+ nodes[i] = (RemoteFileNode)path[i].getLastPathComponent();
+
+ return nodes;
+ }
+
+
+ /**
+ *
+ * Determine if selected node is a file
+ * @return true if the selected node is a file
+ *
+ */
+ public boolean isFileSelection()
+ {
+ TreePath path = getLeadSelectionPath();
+ if(path == null)
+ return false;
+ RemoteFileNode node = (RemoteFileNode)path.getLastPathComponent();
+ return !node.isDirectory();
+ }
+
+
+ /**
+ *
+ * Get the selected node file name
+ * @return file name
+ *
+ */
+ public String getFilename()
+ {
+ TreePath path = getLeadSelectionPath();
+ RemoteFileNode node = (RemoteFileNode)path.getLastPathComponent();
+ return node.getServerName();
+ }
+
+
+ /**
+ *
+ * Creates the tree model for the given root
+ * @param root root to create model for
+ * @return tree model
+ *
+ */
+ private DefaultTreeModel createTreeModel(String root)
+ {
+ setCursor(cbusy);
+
+ File f = new File(root);
+ RemoteFileNode rootNode = new RemoteFileNode(mysettings,froots,
+ f.getName(),null,null);
+
+ rootNode.setDir(true);
+ rootNode.explore();
+ openNode = new Vector();
+ openNode.add(rootNode);
+ setCursor(cdone);
+ return new DefaultTreeModel(rootNode);
+ }
+
+ /**
+ *
+ * Gets the node from the existing explored nodes and their children.
+ * @param path path to a file or directory
+ * @return corresponding node if the directory or
+ * file is visible otherwise returns null.
+ *
+ */
+ private RemoteFileNode getNode(String path)
+ {
+ Enumeration en = openNode.elements();
+
+ while(en.hasMoreElements())
+ {
+ RemoteFileNode node = (RemoteFileNode)en.nextElement();
+ String nodeName = node.getFullName();
+
+ if(nodeName.equals(path))
+ return node;
+ }
+
+// check children of explored nodes
+ en = openNode.elements();
+ while(en.hasMoreElements())
+ {
+ RemoteFileNode child = getChildNode((RemoteFileNode)en.nextElement(),path);
+ if(child != null)
+ return child;
+ }
+
+ return null;
+ }
+
+
+ /**
+ *
+ * Gets the child node of a parent node
+ * @param parent parent node
+ * @param childName name of child
+ * @return the child node
+ *
+ */
+ private RemoteFileNode getChildNode(RemoteFileNode parent, String childName)
+ {
+ for(Enumeration children = parent.children();
+ children.hasMoreElements() ;)
+ {
+ RemoteFileNode childNode = (RemoteFileNode)children.nextElement();
+ String nodeName = childNode.getServerName();
+ if(childName.equals(nodeName))
+ return childNode;
+ }
+
+ return null;
+ }
+
+
+ /**
+ *
+ * Opens a JFrame with the file contents displayed.
+ * @param filename file name
+ * @param mysettings jemboss properties
+ *
+ */
+ public static void showFilePane(final RemoteFileNode node)
+ {
+ SwingWorker entryWorker = new SwingWorker()
+ {
+ EntryEdit entry_edit;
+ public Object construct()
+ {
+ try
+ {
+ EntryInformation new_entry_information =
+ new SimpleEntryInformation(Options.getArtemisEntryInformation());
+
+ final Entry entry = new Entry(EntryFileDialog.getEntryFromFile(
+ null, new RemoteFileDocument(node),
+ new_entry_information, true));
+ if(entry == null)
+ return null;
+
+ final EntryGroup entry_group =
+ new SimpleEntryGroup(entry.getBases());
+
+ entry_group.add(entry);
+ entry_edit = new EntryEdit(entry_group);
+ return null;
+ }
+ catch(NoSequenceException e)
+ {
+ new MessageDialog(null, "read failed: entry contains no sequence");
+ }
+ catch(OutOfRangeException e)
+ {
+ new MessageDialog(null, "read failed: one of the features in " +
+ " the entry has an out of range " +
+ "location: " + e.getMessage());
+
+ }
+ catch(NullPointerException npe){}
+
+ return null;
+ }
+
+ public void finished()
+ {
+ if(entry_edit != null)
+ entry_edit.setVisible(true);
+ }
+ };
+ entryWorker.start();
+ }
+
+
+////////////////////
+// DRAG AND DROP
+////////////////////
+ public void dragGestureRecognized(DragGestureEvent e)
+ {
+ // ignore if mouse popup trigger
+ InputEvent ie = e.getTriggerEvent();
+ if(ie instanceof MouseEvent)
+ if(((MouseEvent)ie).isPopupTrigger())
+ return;
+
+ // drag only files
+ if(isFileSelection())
+ e.startDrag(DragSource.DefaultCopyDrop, // cursor
+ (Transferable)getSelectedNode(), // transferable data
+ this); // drag source listener
+ }
+
+// Source
+ public void dragDropEnd(DragSourceDropEvent e) {}
+ public void dragEnter(DragSourceDragEvent e) {}
+ public void dragExit(DragSourceEvent e) {}
+ public void dragOver(DragSourceDragEvent e) {}
+ public void dropActionChanged(DragSourceDragEvent e) {}
+
+// Target
+ public void dragEnter(DropTargetDragEvent e)
+ {
+ if(e.isDataFlavorSupported(FileNode.FILENODE) ||
+ e.isDataFlavorSupported(RemoteFileNode.REMOTEFILENODE))
+ e.acceptDrag(DnDConstants.ACTION_COPY_OR_MOVE);
+ }
+
+ public void drop(DropTargetDropEvent e)
+ {
+ Transferable t = e.getTransferable();
+
+ if(t.isDataFlavorSupported(RemoteFileNode.REMOTEFILENODE))
+ {
+ try
+ {
+ Point ploc = e.getLocation();
+ TreePath dropPath = getPathForLocation(ploc.x,ploc.y);
+ if(dropPath != null)
+ {
+ RemoteFileNode fn =
+ (RemoteFileNode)t.getTransferData(RemoteFileNode.REMOTEFILENODE);
+
+ fn = getNode(fn.getServerName()); // need to get the instance of
+ // this directly to manipulate tree
+ String dropDest = null;
+ RemoteFileNode fdropPath = (RemoteFileNode)dropPath.getLastPathComponent();
+ String dropRoot = fdropPath.getRootDir();
+ String dropFile = null;
+ if(fdropPath.getFile().equals(" "))
+ dropFile = fn.getFile();
+ else
+ dropFile = fdropPath.getFile()+"/"+fn.getFile();
+
+ if(!nodeExists(fdropPath,fdropPath.getServerName()+fn.getFile()))
+ rename(fn.getRootDir(),fn.getFullName(),
+ fdropPath.getPathName(),
+ dropFile, fn, fdropPath);
+ }
+ }
+ catch(Exception ex){}
+ }
+ else if(t.isDataFlavorSupported(FileNode.FILENODE))
+ {
+ try
+ {
+ Point ploc = e.getLocation();
+ TreePath dropPath = getPathForLocation(ploc.x,ploc.y);
+ if (dropPath != null)
+ {
+ FileNode fn = (FileNode)t.getTransferData(FileNode.FILENODE);
+ File lfn = fn.getFile();
+
+ String dropDest = null;
+ RemoteFileNode fdropPath = (RemoteFileNode)dropPath.getLastPathComponent();
+ String dropRoot = fdropPath.getRootDir();
+
+ RemoteFileNode pn = fdropPath;
+ if(fdropPath.isLeaf())
+ {
+ pn = (RemoteFileNode)fdropPath.getParent();
+ dropDest = pn.getFullName() + "/" + lfn.getName(); //assumes unix file sep.!
+ }
+ else
+ dropDest = fdropPath.getFullName()+ "/" + lfn.getName();
+
+ if(!nodeExists(pn,pn.getServerName()+lfn.getName()))
+ {
+ pn.put(lfn);
+ try
+ {
+
+// Vector params = new Vector();
+// byte[] fileData = getLocalFile(lfn);
+// params.addElement("fileroot=" + dropRoot);
+// params.addElement(dropDest);
+// params.addElement(fileData);
+
+// setCursor(cbusy);
+// PrivateRequest gReq = new PrivateRequest(mysettings,"EmbreoFile",
+// "put_file",params);
+// setCursor(cdone);
+ //add file to remote file tree
+ RemoteFileNode parentNode = fdropPath;
+ if(parentNode.isLeaf())
+ parentNode = (RemoteFileNode)fdropPath.getParent();
+ else
+ parentNode = fdropPath;
+
+ if(parentNode.isExplored())
+ addObject(parentNode,lfn.getName(),false);
+ else
+ {
+ exploreNode(parentNode);
+ RemoteFileNode childNode = getNode(parentNode.getServerName()
+ + "/" + lfn.getName());
+ scrollPathToVisible(new TreePath(childNode.getPath()));
+ }
+ }
+ catch (Exception exp)
+ {
+ setCursor(cdone);
+ System.out.println("SshFileTree: caught exception " + dropRoot +
+ " Destination: " + dropDest + " Local File " + lfn.toString());
+ }
+ }
+ else
+ e.rejectDrop();
+ }
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+ else
+ e.rejectDrop();
+
+ }
+
+ /**
+ *
+ * When a suitable DataFlavor is offered over a remote file
+ * node the node is highlighted/selected and the drag
+ * accepted. Otherwise the drag is rejected.
+ *
+ */
+ public void dragOver(DropTargetDragEvent e)
+ {
+ if (e.isDataFlavorSupported(FileNode.FILENODE))
+ {
+ Point ploc = e.getLocation();
+ TreePath ePath = getPathForLocation(ploc.x,ploc.y);
+ if (ePath == null)
+ e.rejectDrag();
+ else
+ {
+ setSelectionPath(ePath);
+ e.acceptDrag(DnDConstants.ACTION_COPY_OR_MOVE);
+ }
+ }
+ else if(e.isDataFlavorSupported(RemoteFileNode.REMOTEFILENODE))
+ {
+ Point ploc = e.getLocation();
+ TreePath ePath = getPathForLocation(ploc.x,ploc.y);
+ if (ePath == null)
+ {
+ e.rejectDrag();
+ return;
+ }
+ RemoteFileNode node = (RemoteFileNode)ePath.getLastPathComponent();
+ if(!node.isDirectory())
+ e.rejectDrag();
+ else
+ {
+ setSelectionPath(ePath);
+ e.acceptDrag(DnDConstants.ACTION_COPY_OR_MOVE);
+ }
+ }
+ else
+ e.rejectDrag();
+
+ }
+
+ public void dropActionChanged(DropTargetDragEvent e) {}
+ public void dragExit(DropTargetEvent e){}
+
+
+////////////////////
+// AUTO SCROLLING //
+////////////////////
+ /**
+ *
+ * Handles the auto scrolling of the JTree.
+ * @param location The location of the mouse.
+ *
+ */
+ public void autoscroll( Point location )
+ {
+ int top = 0, left = 0, bottom = 0, right = 0;
+ Dimension size = getSize();
+ Rectangle rect = getVisibleRect();
+ int bottomEdge = rect.y + rect.height;
+ int rightEdge = rect.x + rect.width;
+ if( location.y - rect.y < AUTOSCROLL_MARGIN && rect.y > 0 )
+ top = AUTOSCROLL_MARGIN;
+ if( location.x - rect.x < AUTOSCROLL_MARGIN && rect.x > 0 )
+ left = AUTOSCROLL_MARGIN;
+ if( bottomEdge - location.y < AUTOSCROLL_MARGIN && bottomEdge < size.height )
+ bottom = AUTOSCROLL_MARGIN;
+ if( rightEdge - location.x < AUTOSCROLL_MARGIN && rightEdge < size.width )
+ right = AUTOSCROLL_MARGIN;
+ rect.x += right - left;
+ rect.y += bottom - top;
+ scrollRectToVisible( rect );
+ }
+
+
+ /**
+ *
+ * Gets the insets used for the autoscroll.
+ * @return The insets.
+ *
+ */
+ public Insets getAutoscrollInsets()
+ {
+ Dimension size = getSize();
+ Rectangle rect = getVisibleRect();
+ autoscrollInsets.top = rect.y + AUTOSCROLL_MARGIN;
+ autoscrollInsets.left = rect.x + AUTOSCROLL_MARGIN;
+ autoscrollInsets.bottom = size.height - (rect.y+rect.height) + AUTOSCROLL_MARGIN;
+ autoscrollInsets.right = size.width - (rect.x+rect.width) + AUTOSCROLL_MARGIN;
+ return autoscrollInsets;
+ }
+
+ /**
+ *
+ * Popup menu listener
+ *
+ */
+ class PopupListener extends MouseAdapter
+ {
+ public void mousePressed(MouseEvent e)
+ {
+ maybeShowPopup(e);
+ }
+
+ public void mouseReleased(MouseEvent e)
+ {
+ maybeShowPopup(e);
+ }
+
+ private void maybeShowPopup(MouseEvent e)
+ {
+ if(e.isPopupTrigger())
+ popup.show(e.getComponent(),
+ e.getX(), e.getY());
+ }
+ }
+
+ public static void main(String args[])
+ {
+ final javax.swing.LookAndFeel look_and_feel =
+ javax.swing.UIManager.getLookAndFeel();
+
+ final javax.swing.plaf.FontUIResource font_ui_resource =
+ Options.getOptions().getFontUIResource();
+
+ java.util.Enumeration keys = UIManager.getDefaults().keys();
+ while(keys.hasMoreElements())
+ {
+ Object key = keys.nextElement();
+ Object value = UIManager.get(key);
+ if(value instanceof javax.swing.plaf.FontUIResource)
+ UIManager.put(key, font_ui_resource);
+ }
+
+ JFrame frame = new JFrame("SSH :: File Manager");
+ JScrollPane jsp = new JScrollPane(new SshFileTree("/nfs/team81/tjc"));
+ frame.getContentPane().add(jsp);
+ frame.pack();
+ frame.setVisible(true);
+ }
+
+}