-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
- * AM Waterhouse\r
- *******************/\r
-\r
-\r
+ * This program is free software; you can redistribute it and/or\r
+ * modify it under the terms of the GNU General Public License\r
+ * as published by the Free Software Foundation; either version 2\r
+ * of the License, or (at your option) any later version.\r
+ *\r
+ * This program is distributed in the hope that it will be useful,\r
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
+ * GNU General Public License for more details.\r
+ *\r
+ * You should have received a copy of the GNU General Public License\r
+ * along with this program; if not, write to the Free Software\r
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
+ */\r
package jalview.gui;\r
\r
-import jalview.gui.*;\r
import jalview.io.*;\r
-import jalview.datamodel.*;\r
-import javax.swing.*;\r
+\r
import java.awt.*;\r
-import java.awt.event.*;\r
+import java.awt.datatransfer.*;\r
import java.awt.dnd.*;\r
+import java.awt.event.*;\r
+import java.util.*;\r
+\r
import javax.swing.*;\r
-import java.awt.datatransfer.*;\r
-import jalview.bin.Cache;\r
\r
\r
-public class Desktop extends jalview.jbgui.GDesktop implements DropTargetListener\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
+public class Desktop extends jalview.jbgui.GDesktop\r
+ implements DropTargetListener, ClipboardOwner\r
{\r
- public static JDesktopPane desktop;\r
- static int openFrameCount = 0;\r
- static final int xOffset = 30, yOffset = 30;\r
-\r
- public Desktop()\r
- {\r
- Image image =null;\r
- try{\r
- java.net.URL url = getClass().getResource("/images/logo.gif");\r
- if(url!=null)\r
+ /** DOCUMENT ME!! */\r
+ public static Desktop instance;\r
+ public static JDesktopPane desktop;\r
+ static int openFrameCount = 0;\r
+ static final int xOffset = 30;\r
+ static final int yOffset = 30;\r
+ public static jalview.ws.Discoverer discoverer;\r
+\r
+ public static Object [] jalviewClipboard;\r
+\r
+ static int fileLoadingCount= 0;\r
+\r
+ /**\r
+ * Creates a new Desktop object.\r
+ */\r
+ public Desktop()\r
+ {\r
+ instance = this;\r
+\r
+ Image image = null;\r
+\r
+ try\r
+ {\r
+ java.net.URL url = getClass().getResource("/images/logo.gif");\r
+\r
+ if (url != null)\r
+ {\r
+ image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
+\r
+ MediaTracker mt = new MediaTracker(this);\r
+ mt.addImage(image, 0);\r
+ mt.waitForID(0);\r
+ setIconImage(image);\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION"));\r
+ setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
+ desktop = new JDesktopPane();\r
+ desktop.setBackground(Color.white);\r
+ getContentPane().setLayout(new BorderLayout());\r
+ getContentPane().add(desktop, BorderLayout.CENTER);\r
+ desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
+\r
+ // This line prevents Windows Look&Feel resizing all new windows to maximum\r
+ // if previous window was maximised\r
+ desktop.setDesktopManager(new DefaultDesktopManager());\r
+\r
+ Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
+ String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
+ String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
+ String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
+ String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
+\r
+ if ((x != null) && (y != null) && (width != null) && (height != null))\r
+ {\r
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
+ Integer.parseInt(width), Integer.parseInt(height));\r
+ }\r
+ else\r
+ {\r
+ setBounds((int) (screenSize.width - 900) / 2,\r
+ (int) (screenSize.height - 650) / 2, 900, 650);\r
+ }\r
+\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ quit();\r
+ }\r
+ });\r
+\r
+ this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
+\r
+ /////////Add a splashscreen on startup\r
+ /////////Add a splashscreen on startup\r
+ JInternalFrame frame = new JInternalFrame();\r
+\r
+ SplashScreen splash = new SplashScreen(frame, image);\r
+ frame.setContentPane(splash);\r
+ frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
+ frame.setLocation((int) ((getWidth() - 750) / 2),\r
+ (int) ((getHeight() - 160) / 2));\r
+\r
+ addInternalFrame(frame, "", 750, 160, false);\r
+\r
+ discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed.\r
+\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param frame DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ * @param w DOCUMENT ME!\r
+ * @param h DOCUMENT ME!\r
+ */\r
+ public static synchronized void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h)\r
+ {\r
+ addInternalFrame(frame, title, w, h, true);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param frame DOCUMENT ME!\r
+ * @param title DOCUMENT ME!\r
+ * @param w DOCUMENT ME!\r
+ * @param h DOCUMENT ME!\r
+ * @param resizable DOCUMENT ME!\r
+ */\r
+ public static synchronized void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h, boolean resizable)\r
+ {\r
+\r
+ frame.setTitle(title);\r
+ if(frame.getWidth()<1 || frame.getHeight()<1)\r
+ {\r
+ frame.setSize(w, h);\r
+ }\r
+ // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN\r
+ // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN\r
+ // IF JALVIEW IS RUNNING HEADLESS\r
+ /////////////////////////////////////////////////\r
+ if (System.getProperty("java.awt.headless") != null\r
+ && System.getProperty("java.awt.headless").equals("true"))\r
{\r
- image = java.awt.Toolkit.getDefaultToolkit().createImage(url);\r
- MediaTracker mt = new MediaTracker(this);\r
- mt.addImage(image, 0);\r
- mt.waitForID(0);\r
- setIconImage(image);\r
+ return;\r
}\r
\r
- }catch(Exception ex){}\r
\r
- setTitle("Jalview 2005");\r
- setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- desktop = new JDesktopPane();\r
- desktop.setBackground(Color.white);\r
- setContentPane(desktop);\r
- desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE);\r
+ openFrameCount++;\r
+\r
+ frame.setVisible(true);\r
+ frame.setClosable(true);\r
+ frame.setResizable(resizable);\r
+ frame.setMaximizable(resizable);\r
+ frame.setIconifiable(resizable);\r
+ frame.setFrameIcon(null);\r
+\r
+ if (frame.getX()<1 && frame.getY()<1)\r
+ {\r
+ frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset);\r
+ }\r
+\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameActivated(javax.swing.event.\r
+ InternalFrameEvent evt)\r
+ {\r
+ JInternalFrame itf = desktop.getSelectedFrame();\r
+ if (itf != null)\r
+ itf.requestFocus();\r
+\r
+ }\r
+\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\r
+ JInternalFrame itf = desktop.getSelectedFrame();\r
+ if (itf != null)\r
+ itf.requestFocus();\r
+ }\r
+ ;\r
+ });\r
+\r
+ menuItem.addActionListener(new ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ frame.setSelected(true);\r
+ frame.setIcon(false);\r
+ }\r
+ catch (java.beans.PropertyVetoException ex)\r
+ {\r
+\r
+ }\r
+ }\r
+ });\r
+\r
+ windowMenu.add(menuItem);\r
+\r
+ desktop.add(frame);\r
+ frame.toFront();\r
+ try{\r
+ frame.setSelected(true);\r
+ frame.requestFocus();\r
+ }catch(java.beans.PropertyVetoException ve)\r
+ {}\r
+ }\r
+\r
+ public void lostOwnership(Clipboard clipboard, Transferable contents)\r
+ {\r
+ Desktop.jalviewClipboard = null;\r
+ }\r
\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {}\r
\r
- // This line prevents Windows Look&Feel resizing all new windows to maximum\r
- // if previous window was maximised\r
- desktop.setDesktopManager( new DefaultDesktopManager() );\r
+ public void dragExit(DropTargetEvent evt)\r
+ {}\r
\r
+ public void dragOver(DropTargetDragEvent evt)\r
+ {}\r
\r
- Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize();\r
- String x = jalview.bin.Cache.getProperty("SCREEN_X");\r
- String y = jalview.bin.Cache.getProperty("SCREEN_Y");\r
- String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH");\r
- String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT");\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {}\r
\r
- if(x!=null && y!=null && width!=null && height!=null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param evt DOCUMENT ME!\r
+ */\r
+ public void drop(DropTargetDropEvent evt)\r
{\r
- setBounds( Integer.parseInt(x), Integer.parseInt(y),\r
- Integer.parseInt(width), Integer.parseInt(height));\r
+ Transferable t = evt.getTransferable();\r
+ java.util.List files = null;\r
+\r
+ try\r
+ {\r
+ DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String");\r
+ if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ //Works on Windows and MacOSX\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
+ }\r
+ else if (t.isDataFlavorSupported(uriListFlavor))\r
+ {\r
+ // This is used by Unix drag system\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
+ String data = (String) t.getTransferData(uriListFlavor);\r
+ files = new java.util.ArrayList(1);\r
+ for (java.util.StringTokenizer st = new java.util.StringTokenizer(\r
+ data,\r
+ "\r\n");\r
+ st.hasMoreTokens(); )\r
+ {\r
+ String s = st.nextToken();\r
+ if (s.startsWith("#"))\r
+ {\r
+ // the line is a comment (as per the RFC 2483)\r
+ continue;\r
+ }\r
+\r
+ java.net.URI uri = new java.net.URI(s);\r
+ java.io.File file = new java.io.File(uri);\r
+ files.add(file);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+\r
+ if (files != null)\r
+ {\r
+ try\r
+ {\r
+ for (int i = 0; i < files.size(); i++)\r
+ {\r
+ String file = files.get(i).toString();\r
+ String protocol = FormatAdapter.FILE;\r
+ String format = null;\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ format = "Jalview";\r
+\r
+ }\r
+ else\r
+ {\r
+ format = new IdentifyFile().Identify(file,\r
+ protocol);\r
+ }\r
+\r
+\r
+ new FileLoader().LoadFile(file, protocol, format);\r
+\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
}\r
- else\r
- setBounds( (int)(screenSize.width-900)/2,\r
- (int)(screenSize.height-650)/2,\r
- 900 ,\r
- 650);\r
\r
-this.addWindowListener(new WindowAdapter()\r
-{\r
-public void windowClosing(WindowEvent evt)\r
-{\r
- jalview.bin.Cache.setProperty("SCREEN_X",\r
- getBounds().x + "");\r
- jalview.bin.Cache.setProperty("SCREEN_Y",\r
- getBounds().y + "");\r
- jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
- jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
-}\r
-});\r
-setVisible(true);\r
-\r
-this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this));\r
-\r
-/////////Add a splashscreen on startup\r
- /////////Add a splashscreen on startup\r
- JInternalFrame frame = new JInternalFrame();\r
-\r
- SplashScreen splash = new SplashScreen(frame, image);\r
- frame.setContentPane(splash);\r
- frame.setLayer(JLayeredPane.PALETTE_LAYER);\r
- addInternalFrame(frame, "", 750,160, false);\r
- frame.setLocation( (int)((getWidth()-750) /2), (int)((getHeight()-160) /2));\r
- }\r
- public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
- {\r
- addInternalFrame(frame, title, w, h, true);\r
- }\r
-\r
- public static void addInternalFrame(final JInternalFrame frame, String title,\r
- int w,\r
- int h,\r
- boolean resizable )\r
- {\r
- desktop.add(frame);\r
- openFrameCount++;\r
- try {\r
- frame.setSelected(true);\r
- } catch (java.beans.PropertyVetoException e) {}\r
- frame.setTitle(title);\r
- frame.setSize(w,h);\r
- frame.setClosable(true);\r
- frame.setResizable(resizable);\r
- frame.setMaximizable(resizable);\r
- frame.setIconifiable(resizable);\r
- frame.setFrameIcon(null);\r
- frame.setLocation(xOffset*openFrameCount, yOffset*openFrameCount);\r
- frame.toFront();\r
- final JMenuItem menuItem = new JMenuItem(title);\r
- frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- };\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputLocalFileMenuItem_actionPerformed(AlignViewport viewport)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"),\r
+ new String[]\r
+ {\r
+ "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc",\r
+ "jar"\r
+ },\r
+ new String[]\r
+ {\r
+ "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"\r
+ }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Open local file");\r
+ chooser.setToolTipText("Open");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getPath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+\r
+ String format = null;\r
+ if (chooser.getSelectedFormat().equals("Jalview"))\r
+ {\r
+ format = "Jalview";\r
+ }\r
+ else\r
+ {\r
+ format = new IdentifyFile().Identify(choice, FormatAdapter.FILE);\r
+ }\r
+\r
+ if (viewport != null)\r
+ new FileLoader().LoadFile(viewport, choice, FormatAdapter.FILE, format);\r
+ else\r
+ new FileLoader().LoadFile(choice, FormatAdapter.FILE, format);\r
+ }\r
+ }\r
+\r
+\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputURLMenuItem_actionPerformed(AlignViewport viewport)\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ // This construct allows us to have a wider textfield\r
+ // for viewing\r
+ JLabel label = new JLabel("Enter URL of Input File");\r
+ final JComboBox history = new JComboBox();\r
+\r
+ JPanel panel = new JPanel(new GridLayout(2,1));\r
+ panel.add(label);\r
+ panel.add(history);\r
+ history.setPreferredSize(new Dimension(400,20));\r
+ history.setEditable(true);\r
+ history.addItem("http://www.");\r
+\r
+ String historyItems = jalview.bin.Cache.getProperty("RECENT_URL");\r
+\r
+ StringTokenizer st;\r
+\r
+ if (historyItems != null)\r
{\r
- try{ frame.setSelected(true); frame.setIcon(false); }\r
- catch(java.beans.PropertyVetoException ex){};\r
+ st = new StringTokenizer(historyItems, "\t");\r
+\r
+ while (st.hasMoreTokens())\r
+ {\r
+ history.addItem(st.nextElement());\r
+ }\r
}\r
- });\r
\r
- frame.setVisible(true);\r
- windowMenu.add(menuItem);\r
- }\r
+ int reply = JOptionPane.showInternalConfirmDialog(desktop,\r
+ panel, "Input Alignment From URL",\r
+ JOptionPane.OK_CANCEL_OPTION );\r
+\r
+\r
+ if (reply != JOptionPane.OK_OPTION )\r
+ {\r
+ return;\r
+ }\r
+\r
+ String url = history.getSelectedItem().toString();\r
+\r
+ if (url.toLowerCase().endsWith(".jar"))\r
+ {\r
+ if (viewport != null)\r
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, "Jalview");\r
+ else\r
+ new FileLoader().LoadFile(url, FormatAdapter.URL, "Jalview");\r
+ }\r
+ else\r
+ {\r
+ String format = new IdentifyFile().Identify(url, FormatAdapter.URL);\r
+\r
+ if (format.equals("URL NOT FOUND"))\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + url,\r
+ "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+\r
+ return;\r
+ }\r
+\r
+ if (viewport != null)\r
+ new FileLoader().LoadFile(viewport, url, FormatAdapter.URL, format);\r
+ else\r
+ new FileLoader().LoadFile(url, FormatAdapter.URL, format);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void inputTextboxMenuItem_actionPerformed(AlignViewport viewport)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput(viewport);\r
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
+ }\r
\r
- public void dragEnter(DropTargetDragEvent evt){}\r
- public void dragExit(DropTargetEvent evt){}\r
- public void dragOver(DropTargetDragEvent evt){}\r
- public void dropActionChanged(DropTargetDragEvent evt){}\r
- public void drop(DropTargetDropEvent evt)\r
-{\r
- Transferable t = evt.getTransferable();\r
- if(!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
- return;\r
-\r
- evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
- try{\r
- java.util.List files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor);\r
-\r
- for (int i = 0; i < files.size(); i++)\r
- {\r
- String file = files.get(i).toString();\r
- String protocol = "File";\r
- if(file.endsWith(".jar"))\r
- Jalview2XML.LoadJalviewAlign(file);\r
- else\r
+ /*\r
+ * Exit the program\r
+ */\r
+ public void quit()\r
+ {\r
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + "");\r
+ System.exit(0);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void aboutMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ StringBuffer message = new StringBuffer("JalView version " +\r
+ jalview.bin.Cache.getProperty(\r
+ "VERSION") +\r
+ "; last updated: " +\r
+ jalview.bin.\r
+ Cache.getDefault("BUILD_DATE", "unknown"));\r
+\r
+ if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals(\r
+ jalview.bin.Cache.getProperty("VERSION")))\r
{\r
- String format = jalview.io.IdentifyFile.Identify(file, protocol);\r
- LoadFile(file, protocol, format);\r
+ message.append("\n\n!! Jalview version "\r
+ + jalview.bin.Cache.getProperty("LATEST_VERSION")\r
+ + " is available for download from http://www.jalview.org !!\n");\r
+\r
}\r
- }\r
-\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"fa, fasta, fastq", "aln", "pfam", "msf", "pir","blc","jar"},\r
- new String[]{"Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview"}\r
- ,jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT"));\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- if(chooser.getSelectedFormat().equals("Jalview"))\r
- {\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- else\r
- {\r
- String format = IdentifyFile.Identify(choice, "File");\r
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- }\r
-\r
- class LoadingThread extends Thread\r
- {\r
- String file, protocol, format;\r
-\r
- public LoadingThread(String file, String protocol, String format)\r
- {\r
- this.file = file;\r
- this.protocol = protocol;\r
- this.format = format;\r
- }\r
- public void run()\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
-\r
- if (sequences != null && sequences.length>0)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.currentFileFormat = format;\r
- af.statusBar.setText("Successfully loaded file " + file);\r
- try{\r
- af.setMaximum(Preferences.showFullscreen);\r
- }catch(Exception ex){}\r
-\r
- }\r
- else\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't open file.\n"\r
- + "Formats currently supported are\n"\r
- + "Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM" // JBPNote - message should be generated through FormatAdapter!\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
- }\r
-\r
-\r
- public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- String url = JOptionPane.showInternalInputDialog(Desktop.desktop,"Enter url of input file",\r
- "Input alignment from URL",\r
- JOptionPane.QUESTION_MESSAGE,\r
- null, null,\r
- "http://www.").toString();\r
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- if (format.equals("URL NOT FOUND"))\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,"Couldn't locate " + url,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-\r
- LoadFile(url, "URL", format);\r
- }\r
-\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
- int accept = JOptionPane.showInternalOptionDialog(Desktop.desktop, cap, "Cut & paste Alignment File",\r
- JOptionPane.YES_NO_CANCEL_OPTION,\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- new Object[]{"Accept", "Cancel", }, null);\r
-\r
-\r
- if(accept == JOptionPane.YES_OPTION)\r
- {\r
- String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains( format ))\r
- sequences = FormatAdapter.readFile(cap.getText(), "Paste", format);\r
-\r
-\r
- if(sequences!=null)\r
+\r
+ message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." +\r
+ "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." +\r
+ "\nFor all issues relating to Jalview, email help@jalview.org" +\r
+ "\n\nIf you use JalView, please cite:" +\r
+ "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" +\r
+ "\nBioinformatics, 2004 20;426-7.");\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+\r
+ message.toString(), "About Jalview",\r
+ JOptionPane.INFORMATION_MESSAGE);\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void documentationMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
+ java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help");\r
+ javax.help.HelpSet hs = new javax.help.HelpSet(cl, url);\r
+\r
+ javax.help.HelpBroker hb = hs.createHelpBroker();\r
+ hb.setCurrentID("home");\r
+ hb.setDisplayed(true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void preferences_actionPerformed(ActionEvent e)\r
+ {\r
+ new Preferences();\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void saveState_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "jar" },\r
+ new String[] { "Jalview Project" }, "Jalview Project");\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save State");\r
+\r
+ int value = chooser.showSaveDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ java.io.File choice = chooser.getSelectedFile();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
+ new Jalview2XML().SaveState(choice);\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void loadState_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty(\r
+ "LAST_DIRECTORY"), new String[] { "jar" },\r
+ new String[] { "Jalview Project" }, "Jalview Project");\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Restore state");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
+ {\r
+ String choice = chooser.getSelectedFile().getAbsolutePath();\r
+ jalview.bin.Cache.setProperty("LAST_DIRECTORY",\r
+ chooser.getSelectedFile().getParent());\r
+ new Jalview2XML().LoadJalviewAlign(choice);\r
+ }\r
+ }\r
+\r
+ /* public void vamsasLoad_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty("LAST_DIRECTORY"));\r
+\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Load Vamsas file");\r
+ chooser.setToolTipText("Import");\r
+\r
+ int value = chooser.showOpenDialog(this);\r
+\r
+ if (value == JalviewFileChooser.APPROVE_OPTION)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- addInternalFrame(af, "Cut & Paste input - "+format,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
+ jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null);\r
+ vs.load(\r
+ chooser.getSelectedFile().getAbsolutePath()\r
+ );\r
}\r
- else\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop, "Couldn't read the pasted text.\n"\r
- +"Formats currently supported are\n"\r
- +"Fasta, MSF, Clustal, BLC, PIR, MSP, and PFAM",\r
- "Error parsing text", JOptionPane.WARNING_MESSAGE);\r
\r
- }\r
- }\r
+ }*/\r
\r
-/*\r
-* Exit the program\r
-*/\r
- public void quit_actionPerformed(ActionEvent e)\r
- {\r
- if(jalview.bin.Jalview.applet!=null)\r
- jalview.bin.Jalview.applet.destroy();\r
- else\r
- System.exit(0);\r
- }\r
-\r
-\r
-\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "JalView 2005 version " + jalview.bin.Cache.VERSION+"; last updated: "+jalview.bin.Cache.BUILD_DATE\r
- +"\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton."\r
- +"\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee."\r
- +"\nIf you use JalView, please cite:"\r
- +"\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\""\r
- +"\nBioinformatics, 2004 12;426-7.",\r
- "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
-\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- ClassLoader cl = jalview.gui.Desktop.class.getClassLoader();\r
- java.net.URL url = javax.help.HelpSet.findHelpSet(cl,"help/help");\r
- javax.help.HelpSet hs = new javax.help.HelpSet(cl,url);\r
-\r
- javax.help.HelpBroker hb = hs.createHelpBroker();\r
- hb.setLocation(new Point(200, 50));\r
- hb.setSize(new Dimension(800,700));\r
- hb.setCurrentID("home");\r
- hb.setDisplayed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- protected void preferences_actionPerformed(ActionEvent e)\r
- {\r
- Preferences pref = new Preferences();\r
- }\r
-\r
- public void saveState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
- getProperty("LAST_DIRECTORY"),\r
- new String[]\r
- {"jar"}, new String[]{"Jalview Project"}, "Jalview Project");\r
-\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Save State");\r
- int value = chooser.showSaveDialog(this);\r
- if (value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- java.io.File choice = chooser.getSelectedFile();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent());\r
- Jalview2XML.SaveState(choice);\r
- }\r
-\r
- }\r
-\r
-\r
- public void loadState_actionPerformed(ActionEvent e)\r
- {\r
- JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"),\r
- new String[]{"jar"}, new String[]{"Jalview Project"}, "Jalview Project");\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Restore state");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JalviewFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getAbsolutePath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", chooser.getSelectedFile().getParent());\r
- Jalview2XML.LoadJalviewAlign(choice);\r
- }\r
- }\r
-}\r
\r
+ public void inputSequence_actionPerformed(ActionEvent e)\r
+ {\r
+ new SequenceFetcher(null);\r
+ }\r
+\r
+ JPanel progressPanel;\r
+\r
+ public void startLoading(final String fileName)\r
+ {\r
+ if (fileLoadingCount == 0)\r
+ {\r
+ progressPanel = new JPanel(new BorderLayout());\r
+ JProgressBar progressBar = new JProgressBar();\r
+ progressBar.setIndeterminate(true);\r
+\r
+ progressPanel.add(new JLabel("Loading File: " + fileName + " "),\r
+ BorderLayout.WEST);\r
+\r
+ progressPanel.add(progressBar, BorderLayout.CENTER);\r
+\r
+ instance.getContentPane().add(progressPanel, BorderLayout.SOUTH);\r
+ }\r
+ fileLoadingCount++;\r
+ validate();\r
+ }\r
+\r
+ public void stopLoading()\r
+ {\r
+ fileLoadingCount--;\r
+ if (fileLoadingCount < 1)\r
+ {\r
+ if(progressPanel!=null)\r
+ {\r
+ this.getContentPane().remove(progressPanel);\r
+ progressPanel = null;\r
+ }\r
+ fileLoadingCount = 0;\r
+ }\r
+ validate();\r
+ }\r
+\r
+}\r
\r
git://source.jalview.org / jalview.git / blobdiff