From 366b11bb8e79ff5bb1a9e6c50b648c3d4101862c Mon Sep 17 00:00:00 2001 From: amwaterhouse Date: Wed, 8 Mar 2006 16:58:51 +0000 Subject: [PATCH] IdentifyFile should not be static --- src/jalview/bin/Jalview.java | 4 +- src/jalview/bin/JalviewLite.java | 109 ++- src/jalview/gui/AlignFrame.java | 5 +- src/jalview/gui/Desktop.java | 1214 +++++++++++++++++----------------- src/jalview/gui/SequenceFetcher.java | 2 +- src/jalview/ws/JPredClient.java | 2 +- 6 files changed, 697 insertions(+), 639 deletions(-) diff --git a/src/jalview/bin/Jalview.java b/src/jalview/bin/Jalview.java index 0272751..a734054 100755 --- a/src/jalview/bin/Jalview.java +++ b/src/jalview/bin/Jalview.java @@ -163,7 +163,7 @@ public class Jalview if (file.endsWith(".jar")) format = "Jalview"; else - format = jalview.io.IdentifyFile.Identify(file, protocol); + format = new jalview.io.IdentifyFile().Identify(file, protocol); System.out.println("Opening: " + format + " file " + file); @@ -238,7 +238,7 @@ public class Jalview } else { - format = jalview.io.IdentifyFile.Identify(file, protocol); + format = new jalview.io.IdentifyFile().Identify(file, protocol); desktop.LoadFile(file, protocol, format); } } diff --git a/src/jalview/bin/JalviewLite.java b/src/jalview/bin/JalviewLite.java index c4e17fb..858c391 100755 --- a/src/jalview/bin/JalviewLite.java +++ b/src/jalview/bin/JalviewLite.java @@ -45,7 +45,13 @@ public class JalviewLite extends Applet String file = "No file"; Button launcher = new Button("Start Jalview"); + //The currentAlignFrame is static, it will change + //if and when the user selects a new window static AlignFrame currentAlignFrame; + + //This is the first frame to be displayed, and does not change + AlignFrame initialAlignFrame; + boolean embedded = false; @@ -82,8 +88,6 @@ public class JalviewLite extends Applet this.setBackground(new Color(r, g, b)); file = getParameter("file"); - if(file.indexOf("://")==-1) - file = getCodeBase() + file; final JalviewLite applet = this; if(getParameter("embedded")!=null @@ -91,7 +95,7 @@ public class JalviewLite extends Applet { embedded = true; LoadingThread loader = new LoadingThread(file, - "URL", + AppletFormatAdapter.URL, applet); loader.start(); } @@ -104,7 +108,7 @@ public class JalviewLite extends Applet public void actionPerformed(ActionEvent e) { LoadingThread loader = new LoadingThread(file, - "URL", + AppletFormatAdapter.URL, applet); loader.start(); } @@ -126,10 +130,11 @@ public class JalviewLite extends Applet System.exit(1); } - String format = jalview.io.IdentifyFile.Identify(args[0],"File"); + String format = new jalview.io.IdentifyFile().Identify(args[0],AppletFormatAdapter.FILE); + SequenceI[] sequences = null; try{ - sequences = new AppletFormatAdapter().readFile(args[0], "File", format); + sequences = new AppletFormatAdapter().readFile(args[0], AppletFormatAdapter.FILE, format); }catch(java.io.IOException ex) { ex.printStackTrace(); @@ -167,7 +172,7 @@ public class JalviewLite extends Applet currentAlignFrame = null; } lastFrameX -=40; - lastFrameY-=40; + lastFrameY -=40; frame.setMenuBar(null); frame.dispose(); } @@ -181,6 +186,23 @@ public class JalviewLite extends Applet frame.setVisible(true); } + public String getSelectedSequences() + { + StringBuffer result = new StringBuffer(""); + + if(initialAlignFrame.viewport.getSelectionGroup()!=null) + { + SequenceI[] seqs = initialAlignFrame.viewport.getSelectionGroup(). + getSequencesInOrder( + initialAlignFrame.viewport.getAlignment()); + + for (int i = 0; i < seqs.length; i++) + result.append(seqs[i].getName() + "¬"); + } + + return result.toString(); + } + public String getAlignment(String format) { return getAlignment(format, "true"); @@ -239,14 +261,18 @@ public class JalviewLite extends Applet String format; JalviewLite applet; - public LoadingThread(String file, - String protocol, - JalviewLite applet) + public LoadingThread(String _file, + String _protocol, + JalviewLite _applet) { - this.file = file; - this.protocol = protocol; - format = jalview.io.IdentifyFile.Identify(file, "URL"); - this.applet = applet; + file = _file; + if(inArchive(file)) + protocol = AppletFormatAdapter.CLASSLOADER; + else + protocol = _protocol; + + format = new jalview.io.IdentifyFile().Identify(file, protocol); + applet = _applet; } public void run() @@ -263,6 +289,9 @@ public class JalviewLite extends Applet { currentAlignFrame = new AlignFrame(new Alignment(sequences), applet, file); + + initialAlignFrame = currentAlignFrame; + if (embedded) currentAlignFrame.setEmbedded(); @@ -272,12 +301,18 @@ public class JalviewLite extends Applet String treeFile = applet.getParameter("treeFile"); if (treeFile != null) { - if (treeFile.indexOf("://") == -1) - treeFile = getCodeBase() + treeFile; - try { - jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, "URL"); + if(inArchive(treeFile)) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + protocol = AppletFormatAdapter.URL; + treeFile = addProtocol(treeFile); + } + + jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile, protocol); + fin.parse(); if (fin.getTree() != null) @@ -299,8 +334,8 @@ public class JalviewLite extends Applet String param = getParameter("features"); if (param != null) { - if (param.indexOf("://") == -1) - param = getCodeBase() + param; + if( !inArchive(param) ) + param = addProtocol( param ); currentAlignFrame.parseFeaturesFile(param); } @@ -308,8 +343,8 @@ public class JalviewLite extends Applet param = getParameter("annotations"); if (param != null) { - if (param.indexOf("://") == -1) - param = getCodeBase() + param; + if( !inArchive(param) ) + param = addProtocol( param ); new AnnotationReader().readAnnotationFile( currentAlignFrame.viewport.getAlignment(), @@ -322,14 +357,19 @@ public class JalviewLite extends Applet String pdbfile = applet.getParameter("PDBFILE"); if(pdbfile!=null) { - if(pdbfile.indexOf("://")==-1) - pdbfile = getCodeBase() + pdbfile; + if( inArchive(pdbfile) ) + protocol = AppletFormatAdapter.CLASSLOADER; + else + { + protocol = AppletFormatAdapter.URL; + pdbfile = addProtocol(pdbfile); + } String sequence = applet.getParameter("PDBSEQ"); if(sequence!=null) { - new MCview.AppletPDBViewer(pdbfile, "URL", + new MCview.AppletPDBViewer(pdbfile, protocol, (Sequence)currentAlignFrame.getAlignViewport().getAlignment().findName(sequence), currentAlignFrame.getSeqcanvas()); } @@ -343,5 +383,24 @@ public class JalviewLite extends Applet repaint(); } } + + /** + * Discovers whether the given file is in the Applet Archive + * @param file String + * @return boolean + */ + boolean inArchive(String file) + { + return ( getClass().getResourceAsStream("/" + file) != null ); + } + + String addProtocol(String file) + { + if (file.indexOf("://") == -1) + file = getCodeBase() + file; + + return file; + } + } } diff --git a/src/jalview/gui/AlignFrame.java b/src/jalview/gui/AlignFrame.java index e500422..b714aea 100755 --- a/src/jalview/gui/AlignFrame.java +++ b/src/jalview/gui/AlignFrame.java @@ -691,7 +691,7 @@ public class AlignFrame if(str.length()<1) return; - String format = IdentifyFile.Identify(str, "Paste"); + String format = new IdentifyFile().Identify(str, "Paste"); SequenceI[] sequences; if(Desktop.jalviewClipboard!=null) @@ -926,7 +926,6 @@ public class AlignFrame viewport.setSelectionGroup(null); alignPanel.seqPanel.seqCanvas.highlightSearchResults(null); alignPanel.idPanel.idCanvas.searchResults = null; - alignPanel.annotationPanel.activeRes = null; PaintRefresher.Refresh(null, viewport.alignment); } @@ -2735,7 +2734,7 @@ public void drop(DropTargetDropEvent evt) if (!isGroupsFile) { String protocol = "File"; - String format = jalview.io.IdentifyFile.Identify(file, protocol); + String format = new IdentifyFile().Identify(file, protocol); SequenceI[] sequences = new FormatAdapter().readFile(file, protocol, format); FastaFile ff = new FastaFile(); diff --git a/src/jalview/gui/Desktop.java b/src/jalview/gui/Desktop.java index a60d4e7..9085b1e 100755 --- a/src/jalview/gui/Desktop.java +++ b/src/jalview/gui/Desktop.java @@ -1,607 +1,607 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ -package jalview.gui; - -import jalview.io.*; - -import java.awt.*; -import java.awt.datatransfer.*; -import java.awt.dnd.*; -import java.awt.event.*; - -import javax.swing.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class Desktop extends jalview.jbgui.GDesktop - implements DropTargetListener -{ - /** DOCUMENT ME!! */ - public static JDesktopPane desktop; - static int openFrameCount = 0; - static final int xOffset = 30; - static final int yOffset = 30; - public static jalview.ws.Discoverer discoverer; - - public static Object [] jalviewClipboard; - - - /** - * Creates a new Desktop object. - */ - public Desktop() - { - Image image = null; - - - try - { - java.net.URL url = getClass().getResource("/images/logo.gif"); - - if (url != null) - { - image = java.awt.Toolkit.getDefaultToolkit().createImage(url); - - MediaTracker mt = new MediaTracker(this); - mt.addImage(image, 0); - mt.waitForID(0); - setIconImage(image); - } - } - catch (Exception ex) - { - } - - setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION")); - setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); - desktop = new JDesktopPane(); - desktop.setBackground(Color.white); - setContentPane(desktop); - desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); - - // This line prevents Windows Look&Feel resizing all new windows to maximum - // if previous window was maximised - desktop.setDesktopManager(new DefaultDesktopManager()); - - Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); - String x = jalview.bin.Cache.getProperty("SCREEN_X"); - String y = jalview.bin.Cache.getProperty("SCREEN_Y"); - String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH"); - String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT"); - - if ((x != null) && (y != null) && (width != null) && (height != null)) - { - setBounds(Integer.parseInt(x), Integer.parseInt(y), - Integer.parseInt(width), Integer.parseInt(height)); - } - else - { - setBounds((int) (screenSize.width - 900) / 2, - (int) (screenSize.height - 650) / 2, 900, 650); - } - - this.addWindowListener(new WindowAdapter() - { - public void windowClosing(WindowEvent evt) - { - quit(); - } - }); - - this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); - - /////////Add a splashscreen on startup - /////////Add a splashscreen on startup - JInternalFrame frame = new JInternalFrame(); - - SplashScreen splash = new SplashScreen(frame, image); - frame.setContentPane(splash); - frame.setLayer(JLayeredPane.PALETTE_LAYER); - frame.setLocation((int) ((getWidth() - 750) / 2), - (int) ((getHeight() - 160) / 2)); - - addInternalFrame(frame, "", 750, 160, false); - - discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed. - - } - - /** - * DOCUMENT ME! - * - * @param frame DOCUMENT ME! - * @param title DOCUMENT ME! - * @param w DOCUMENT ME! - * @param h DOCUMENT ME! - */ - public static synchronized void addInternalFrame(final JInternalFrame frame, - String title, int w, int h) - { - addInternalFrame(frame, title, w, h, true); - } - - /** - * DOCUMENT ME! - * - * @param frame DOCUMENT ME! - * @param title DOCUMENT ME! - * @param w DOCUMENT ME! - * @param h DOCUMENT ME! - * @param resizable DOCUMENT ME! - */ - public static synchronized void addInternalFrame(final JInternalFrame frame, - String title, int w, int h, boolean resizable) - { - - frame.setTitle(title); - if(frame.getWidth()<1 || frame.getHeight()<1) - { - frame.setSize(w, h); - } - // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN - // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN - // IF JALVIEW IS RUNNING HEADLESS - ///////////////////////////////////////////////// - if (System.getProperty("java.awt.headless") != null - && System.getProperty("java.awt.headless").equals("true")) - { - return; - } - - - openFrameCount++; - - frame.setVisible(true); - frame.setClosable(true); - frame.setResizable(resizable); - frame.setMaximizable(resizable); - frame.setIconifiable(resizable); - frame.setFrameIcon(null); - - if (frame.getX()<1 && frame.getY()<1) - { - frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset); - } - - final JMenuItem menuItem = new JMenuItem(title); - frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameActivated(javax.swing.event. - InternalFrameEvent evt) - { - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - itf.requestFocus(); - - } - - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent evt) - { - openFrameCount--; - windowMenu.remove(menuItem); - JInternalFrame itf = desktop.getSelectedFrame(); - if (itf != null) - itf.requestFocus(); - } - ; - }); - - menuItem.addActionListener(new ActionListener() - { - public void actionPerformed(ActionEvent e) - { - try - { - frame.setSelected(true); - frame.setIcon(false); - } - catch (java.beans.PropertyVetoException ex) - { - - } - } - }); - - windowMenu.add(menuItem); - - desktop.add(frame); - frame.toFront(); - try{ - frame.setSelected(true); - frame.requestFocus(); - }catch(java.beans.PropertyVetoException ve) - {} - } - - public void dragEnter(DropTargetDragEvent evt) - {} - - public void dragExit(DropTargetEvent evt) - {} - - public void dragOver(DropTargetDragEvent evt) - {} - - public void dropActionChanged(DropTargetDragEvent evt) - {} - - /** - * DOCUMENT ME! - * - * @param evt DOCUMENT ME! - */ - public void drop(DropTargetDropEvent evt) - { - Transferable t = evt.getTransferable(); - java.util.List files = null; - - try - { - DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String"); - if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) - { - //Works on Windows and MacOSX - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor); - } - else if (t.isDataFlavorSupported(uriListFlavor)) - { - // This is used by Unix drag system - evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); - String data = (String) t.getTransferData(uriListFlavor); - files = new java.util.ArrayList(1); - for (java.util.StringTokenizer st = new java.util.StringTokenizer( - data, - "\r\n"); - st.hasMoreTokens(); ) - { - String s = st.nextToken(); - if (s.startsWith("#")) - { - // the line is a comment (as per the RFC 2483) - continue; - } - - java.net.URI uri = new java.net.URI(s); - java.io.File file = new java.io.File(uri); - files.add(file); - } - } - } - catch (Exception e) - { - e.printStackTrace(); - } - - if (files != null) - { - try - { - for (int i = 0; i < files.size(); i++) - { - String file = files.get(i).toString(); - String protocol = "File"; - String format = null; - - if (file.endsWith(".jar")) - { - format = "Jalview"; - - } - else - { - format = jalview.io.IdentifyFile.Identify(file, - protocol); - } - LoadFile(file, protocol, format); - } - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void inputLocalFileMenuItem_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), - new String[] - { - "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", - "jar" - }, - new String[] - { - "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" - }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Open local file"); - chooser.setToolTipText("Open"); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getPath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - - String format = null; - if (chooser.getSelectedFormat().equals("Jalview")) - { - format = "Jalview"; - } - else - { - format = IdentifyFile.Identify(choice, "File"); - } - - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); - LoadFile(choice, "File", format); - } - } - - /** - * DOCUMENT ME! - * - * @param file DOCUMENT ME! - * @param protocol DOCUMENT ME! - * @param format DOCUMENT ME! - */ - public void LoadFile(String file, String protocol, String format) - { - FileLoader fileLoader = new FileLoader(); - fileLoader.LoadFile(file, protocol, format); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void inputURLMenuItem_actionPerformed(ActionEvent e) - { - // This construct allows us to have a wider textfield - // for viewing - JLabel label = new JLabel("Enter URL of Input File"); - JTextField textinput = new JTextField("http://www.", 40); - JPanel panel = new JPanel(new BorderLayout()); - panel.add(label, BorderLayout.NORTH); - panel.add(textinput, BorderLayout.SOUTH); - - - int reply = JOptionPane.showInternalConfirmDialog(desktop, - panel, "Input Alignment From URL", - JOptionPane.OK_CANCEL_OPTION ); - - - if (reply != JOptionPane.OK_OPTION ) - { - return; - } - - String url = textinput.getText(); - - if (url.toLowerCase().endsWith(".jar")) - { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview"); - Jalview2XML.LoadJalviewAlign(url); - } - else - { - - String format = IdentifyFile.Identify(url, "URL"); - - if (format.equals("URL NOT FOUND")) - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't locate " + url, - "URL not found", - JOptionPane.WARNING_MESSAGE); - - return; - } - - LoadFile(url, "URL", format); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void inputTextboxMenuItem_actionPerformed(ActionEvent e) - { - CutAndPasteTransfer cap = new CutAndPasteTransfer(); - cap.setForInput(); - Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); - } - - /* - * Exit the program - */ - public void quit() - { - jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + ""); - jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + ""); - jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + ""); - jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + ""); - System.exit(0); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void aboutMenuItem_actionPerformed(ActionEvent e) - { - StringBuffer message = new StringBuffer("JalView version " + - jalview.bin.Cache.getProperty( - "VERSION") + - "; last updated: " + - jalview.bin. - Cache.getDefault("BUILD_DATE", "unknown")); - - if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( - jalview.bin.Cache.getProperty("VERSION"))) - { - message.append("\n\n!! Jalview version " - + jalview.bin.Cache.getProperty("LATEST_VERSION") - + " is available for download from http://www.jalview.org !!\n"); - - } - - message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." + - "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." + - "\nFor all issues relating to Jalview, email help@jalview.org" + - "\n\nIf you use JalView, please cite:" + - "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" + - "\nBioinformatics, 2004 12;426-7."); - - JOptionPane.showInternalMessageDialog(Desktop.desktop, - - message.toString(), "About Jalview", - JOptionPane.INFORMATION_MESSAGE); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void documentationMenuItem_actionPerformed(ActionEvent e) - { - try - { - ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); - java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); - javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); - - javax.help.HelpBroker hb = hs.createHelpBroker(); - hb.setCurrentID("home"); - hb.setDisplayed(true); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - protected void preferences_actionPerformed(ActionEvent e) - { - new Preferences(); - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void saveState_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "jar" }, - new String[] { "Jalview Project" }, "Jalview Project"); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Save State"); - - int value = chooser.showSaveDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - java.io.File choice = chooser.getSelectedFile(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); - Jalview2XML.SaveState(choice); - } - } - - /** - * DOCUMENT ME! - * - * @param e DOCUMENT ME! - */ - public void loadState_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( - "LAST_DIRECTORY"), new String[] { "jar" }, - new String[] { "Jalview Project" }, "Jalview Project"); - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Restore state"); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - String choice = chooser.getSelectedFile().getAbsolutePath(); - jalview.bin.Cache.setProperty("LAST_DIRECTORY", - chooser.getSelectedFile().getParent()); - Jalview2XML.LoadJalviewAlign(choice); - } - } - - /* public void vamsasLoad_actionPerformed(ActionEvent e) - { - JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. - getProperty("LAST_DIRECTORY")); - - chooser.setFileView(new JalviewFileView()); - chooser.setDialogTitle("Load Vamsas file"); - chooser.setToolTipText("Import"); - - int value = chooser.showOpenDialog(this); - - if (value == JalviewFileChooser.APPROVE_OPTION) - { - jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null); - vs.load( - chooser.getSelectedFile().getAbsolutePath() - ); - } - - }*/ - - - public void inputSequence_actionPerformed(ActionEvent e) - { - SequenceFetcher sf = new SequenceFetcher(null); - } -} - +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation; either version 2 + * of the License, or (at your option) any later version. + * + * This program is distributed in the hope that it will be useful, + * but WITHOUT ANY WARRANTY; without even the implied warranty of + * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + * GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with this program; if not, write to the Free Software + * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ +package jalview.gui; + +import jalview.io.*; + +import java.awt.*; +import java.awt.datatransfer.*; +import java.awt.dnd.*; +import java.awt.event.*; + +import javax.swing.*; + + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Desktop extends jalview.jbgui.GDesktop + implements DropTargetListener +{ + /** DOCUMENT ME!! */ + public static JDesktopPane desktop; + static int openFrameCount = 0; + static final int xOffset = 30; + static final int yOffset = 30; + public static jalview.ws.Discoverer discoverer; + + public static Object [] jalviewClipboard; + + + /** + * Creates a new Desktop object. + */ + public Desktop() + { + Image image = null; + + + try + { + java.net.URL url = getClass().getResource("/images/logo.gif"); + + if (url != null) + { + image = java.awt.Toolkit.getDefaultToolkit().createImage(url); + + MediaTracker mt = new MediaTracker(this); + mt.addImage(image, 0); + mt.waitForID(0); + setIconImage(image); + } + } + catch (Exception ex) + { + } + + setTitle("Jalview "+jalview.bin.Cache.getProperty("VERSION")); + setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE); + desktop = new JDesktopPane(); + desktop.setBackground(Color.white); + setContentPane(desktop); + desktop.setDragMode(JDesktopPane.OUTLINE_DRAG_MODE); + + // This line prevents Windows Look&Feel resizing all new windows to maximum + // if previous window was maximised + desktop.setDesktopManager(new DefaultDesktopManager()); + + Dimension screenSize = Toolkit.getDefaultToolkit().getScreenSize(); + String x = jalview.bin.Cache.getProperty("SCREEN_X"); + String y = jalview.bin.Cache.getProperty("SCREEN_Y"); + String width = jalview.bin.Cache.getProperty("SCREEN_WIDTH"); + String height = jalview.bin.Cache.getProperty("SCREEN_HEIGHT"); + + if ((x != null) && (y != null) && (width != null) && (height != null)) + { + setBounds(Integer.parseInt(x), Integer.parseInt(y), + Integer.parseInt(width), Integer.parseInt(height)); + } + else + { + setBounds((int) (screenSize.width - 900) / 2, + (int) (screenSize.height - 650) / 2, 900, 650); + } + + this.addWindowListener(new WindowAdapter() + { + public void windowClosing(WindowEvent evt) + { + quit(); + } + }); + + this.setDropTarget(new java.awt.dnd.DropTarget(desktop, this)); + + /////////Add a splashscreen on startup + /////////Add a splashscreen on startup + JInternalFrame frame = new JInternalFrame(); + + SplashScreen splash = new SplashScreen(frame, image); + frame.setContentPane(splash); + frame.setLayer(JLayeredPane.PALETTE_LAYER); + frame.setLocation((int) ((getWidth() - 750) / 2), + (int) ((getHeight() - 160) / 2)); + + addInternalFrame(frame, "", 750, 160, false); + + discoverer=new jalview.ws.Discoverer(); // Only gets started if gui is displayed. + + } + + /** + * DOCUMENT ME! + * + * @param frame DOCUMENT ME! + * @param title DOCUMENT ME! + * @param w DOCUMENT ME! + * @param h DOCUMENT ME! + */ + public static synchronized void addInternalFrame(final JInternalFrame frame, + String title, int w, int h) + { + addInternalFrame(frame, title, w, h, true); + } + + /** + * DOCUMENT ME! + * + * @param frame DOCUMENT ME! + * @param title DOCUMENT ME! + * @param w DOCUMENT ME! + * @param h DOCUMENT ME! + * @param resizable DOCUMENT ME! + */ + public static synchronized void addInternalFrame(final JInternalFrame frame, + String title, int w, int h, boolean resizable) + { + + frame.setTitle(title); + if(frame.getWidth()<1 || frame.getHeight()<1) + { + frame.setSize(w, h); + } + // THIS IS A PUBLIC STATIC METHOD, SO IT MAY BE CALLED EVEN IN + // A HEADLESS STATE WHEN NO DESKTOP EXISTS. MUST RETURN + // IF JALVIEW IS RUNNING HEADLESS + ///////////////////////////////////////////////// + if (System.getProperty("java.awt.headless") != null + && System.getProperty("java.awt.headless").equals("true")) + { + return; + } + + + openFrameCount++; + + frame.setVisible(true); + frame.setClosable(true); + frame.setResizable(resizable); + frame.setMaximizable(resizable); + frame.setIconifiable(resizable); + frame.setFrameIcon(null); + + if (frame.getX()<1 && frame.getY()<1) + { + frame.setLocation(xOffset * openFrameCount, yOffset * ((openFrameCount-1)%10)+yOffset); + } + + final JMenuItem menuItem = new JMenuItem(title); + frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() + { + public void internalFrameActivated(javax.swing.event. + InternalFrameEvent evt) + { + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + itf.requestFocus(); + + } + + public void internalFrameClosed( + javax.swing.event.InternalFrameEvent evt) + { + openFrameCount--; + windowMenu.remove(menuItem); + JInternalFrame itf = desktop.getSelectedFrame(); + if (itf != null) + itf.requestFocus(); + } + ; + }); + + menuItem.addActionListener(new ActionListener() + { + public void actionPerformed(ActionEvent e) + { + try + { + frame.setSelected(true); + frame.setIcon(false); + } + catch (java.beans.PropertyVetoException ex) + { + + } + } + }); + + windowMenu.add(menuItem); + + desktop.add(frame); + frame.toFront(); + try{ + frame.setSelected(true); + frame.requestFocus(); + }catch(java.beans.PropertyVetoException ve) + {} + } + + public void dragEnter(DropTargetDragEvent evt) + {} + + public void dragExit(DropTargetEvent evt) + {} + + public void dragOver(DropTargetDragEvent evt) + {} + + public void dropActionChanged(DropTargetDragEvent evt) + {} + + /** + * DOCUMENT ME! + * + * @param evt DOCUMENT ME! + */ + public void drop(DropTargetDropEvent evt) + { + Transferable t = evt.getTransferable(); + java.util.List files = null; + + try + { + DataFlavor uriListFlavor = new DataFlavor("text/uri-list;class=java.lang.String"); + if (t.isDataFlavorSupported(DataFlavor.javaFileListFlavor)) + { + //Works on Windows and MacOSX + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + files = (java.util.List) t.getTransferData(DataFlavor.javaFileListFlavor); + } + else if (t.isDataFlavorSupported(uriListFlavor)) + { + // This is used by Unix drag system + evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE); + String data = (String) t.getTransferData(uriListFlavor); + files = new java.util.ArrayList(1); + for (java.util.StringTokenizer st = new java.util.StringTokenizer( + data, + "\r\n"); + st.hasMoreTokens(); ) + { + String s = st.nextToken(); + if (s.startsWith("#")) + { + // the line is a comment (as per the RFC 2483) + continue; + } + + java.net.URI uri = new java.net.URI(s); + java.io.File file = new java.io.File(uri); + files.add(file); + } + } + } + catch (Exception e) + { + e.printStackTrace(); + } + + if (files != null) + { + try + { + for (int i = 0; i < files.size(); i++) + { + String file = files.get(i).toString(); + String protocol = FormatAdapter.FILE; + String format = null; + + if (file.endsWith(".jar")) + { + format = "Jalview"; + + } + else + { + format = new IdentifyFile().Identify(file, + protocol); + } + LoadFile(file, protocol, format); + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputLocalFileMenuItem_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), + new String[] + { + "fa, fasta, fastq", "aln", "pfam", "msf", "pir", "blc", + "jar" + }, + new String[] + { + "Fasta", "Clustal", "PFAM", "MSF", "PIR", "BLC", "Jalview" + }, jalview.bin.Cache.getProperty("DEFAULT_FILE_FORMAT")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Open local file"); + chooser.setToolTipText("Open"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getPath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + + String format = null; + if (chooser.getSelectedFormat().equals("Jalview")) + { + format = "Jalview"; + } + else + { + format = new IdentifyFile().Identify(choice, FormatAdapter.FILE); + } + + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); + LoadFile(choice, FormatAdapter.FILE, format); + } + } + + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + * @param protocol DOCUMENT ME! + * @param format DOCUMENT ME! + */ + public void LoadFile(String file, String protocol, String format) + { + FileLoader fileLoader = new FileLoader(); + fileLoader.LoadFile(file, protocol, format); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputURLMenuItem_actionPerformed(ActionEvent e) + { + // This construct allows us to have a wider textfield + // for viewing + JLabel label = new JLabel("Enter URL of Input File"); + JTextField textinput = new JTextField("http://www.", 40); + JPanel panel = new JPanel(new BorderLayout()); + panel.add(label, BorderLayout.NORTH); + panel.add(textinput, BorderLayout.SOUTH); + + + int reply = JOptionPane.showInternalConfirmDialog(desktop, + panel, "Input Alignment From URL", + JOptionPane.OK_CANCEL_OPTION ); + + + if (reply != JOptionPane.OK_OPTION ) + { + return; + } + + String url = textinput.getText(); + + if (url.toLowerCase().endsWith(".jar")) + { + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalview"); + Jalview2XML.LoadJalviewAlign(url); + } + else + { + + String format = new IdentifyFile().Identify(url, FormatAdapter.URL); + + if (format.equals("URL NOT FOUND")) + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Couldn't locate " + url, + "URL not found", + JOptionPane.WARNING_MESSAGE); + + return; + } + + LoadFile(url, FormatAdapter.URL, format); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void inputTextboxMenuItem_actionPerformed(ActionEvent e) + { + CutAndPasteTransfer cap = new CutAndPasteTransfer(); + cap.setForInput(); + Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500); + } + + /* + * Exit the program + */ + public void quit() + { + jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x + ""); + jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y + ""); + jalview.bin.Cache.setProperty("SCREEN_WIDTH", getWidth() + ""); + jalview.bin.Cache.setProperty("SCREEN_HEIGHT", getHeight() + ""); + System.exit(0); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void aboutMenuItem_actionPerformed(ActionEvent e) + { + StringBuffer message = new StringBuffer("JalView version " + + jalview.bin.Cache.getProperty( + "VERSION") + + "; last updated: " + + jalview.bin. + Cache.getDefault("BUILD_DATE", "unknown")); + + if (!jalview.bin.Cache.getProperty("LATEST_VERSION").equals( + jalview.bin.Cache.getProperty("VERSION"))) + { + message.append("\n\n!! Jalview version " + + jalview.bin.Cache.getProperty("LATEST_VERSION") + + " is available for download from http://www.jalview.org !!\n"); + + } + + message.append( "\nAuthors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton." + + "\nCurrent development managed by Andrew Waterhouse; Barton Group, University of Dundee." + + "\nFor all issues relating to Jalview, email help@jalview.org" + + "\n\nIf you use JalView, please cite:" + + "\n\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"" + + "\nBioinformatics, 2004 12;426-7."); + + JOptionPane.showInternalMessageDialog(Desktop.desktop, + + message.toString(), "About Jalview", + JOptionPane.INFORMATION_MESSAGE); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void documentationMenuItem_actionPerformed(ActionEvent e) + { + try + { + ClassLoader cl = jalview.gui.Desktop.class.getClassLoader(); + java.net.URL url = javax.help.HelpSet.findHelpSet(cl, "help/help"); + javax.help.HelpSet hs = new javax.help.HelpSet(cl, url); + + javax.help.HelpBroker hb = hs.createHelpBroker(); + hb.setCurrentID("home"); + hb.setDisplayed(true); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + protected void preferences_actionPerformed(ActionEvent e) + { + new Preferences(); + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void saveState_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] { "jar" }, + new String[] { "Jalview Project" }, "Jalview Project"); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Save State"); + + int value = chooser.showSaveDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + java.io.File choice = chooser.getSelectedFile(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice.getParent()); + Jalview2XML.SaveState(choice); + } + } + + /** + * DOCUMENT ME! + * + * @param e DOCUMENT ME! + */ + public void loadState_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.getProperty( + "LAST_DIRECTORY"), new String[] { "jar" }, + new String[] { "Jalview Project" }, "Jalview Project"); + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Restore state"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + String choice = chooser.getSelectedFile().getAbsolutePath(); + jalview.bin.Cache.setProperty("LAST_DIRECTORY", + chooser.getSelectedFile().getParent()); + Jalview2XML.LoadJalviewAlign(choice); + } + } + + /* public void vamsasLoad_actionPerformed(ActionEvent e) + { + JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache. + getProperty("LAST_DIRECTORY")); + + chooser.setFileView(new JalviewFileView()); + chooser.setDialogTitle("Load Vamsas file"); + chooser.setToolTipText("Import"); + + int value = chooser.showOpenDialog(this); + + if (value == JalviewFileChooser.APPROVE_OPTION) + { + jalview.io.VamsasDatastore vs = new jalview.io.VamsasDatastore(null); + vs.load( + chooser.getSelectedFile().getAbsolutePath() + ); + } + + }*/ + + + public void inputSequence_actionPerformed(ActionEvent e) + { + SequenceFetcher sf = new SequenceFetcher(null); + } +} + diff --git a/src/jalview/gui/SequenceFetcher.java b/src/jalview/gui/SequenceFetcher.java index e3282d8..2e2456b 100755 --- a/src/jalview/gui/SequenceFetcher.java +++ b/src/jalview/gui/SequenceFetcher.java @@ -341,7 +341,7 @@ public class SequenceFetcher SequenceI[] parseResult(String result, String title) { - String format = IdentifyFile.Identify(result, "Paste"); + String format = new IdentifyFile().Identify(result, "Paste"); SequenceI[] sequences = null; if (FormatAdapter.formats.contains(format)) diff --git a/src/jalview/ws/JPredClient.java b/src/jalview/ws/JPredClient.java index 6fd0a4a..d353b51 100755 --- a/src/jalview/ws/JPredClient.java +++ b/src/jalview/ws/JPredClient.java @@ -399,7 +399,7 @@ public class JPredClient { jalview.bin.Cache.log.debug("Getting associated alignment."); // we ignore the returned alignment if we only predicted on a single sequence - String format = jalview.io.IdentifyFile.Identify(result.getAligfile(), + String format = new jalview.io.IdentifyFile().Identify(result.getAligfile(), "Paste"); if (jalview.io.FormatAdapter.formats.contains(format)) -- 1.7.10.2