-/********************\r
- * 2004 Jalview Reengineered\r
- * Barton Group\r
- * Dundee University\r
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2005 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 jalview.schemes.*;\r
-import javax.swing.*;\r
import java.awt.*;\r
+import java.awt.datatransfer.*;\r
+import java.awt.dnd.*;\r
import java.awt.event.*;\r
+import javax.swing.*;\r
\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
\r
-public class Desktop extends jalview.jbgui.GDesktop\r
+public class Desktop\r
+ extends jalview.jbgui.GDesktop implements DropTargetListener\r
{\r
public static JDesktopPane desktop;\r
static int openFrameCount = 0;\r
- static final int xOffset = 30, yOffset = 30;\r
+ static final int xOffset = 30;\r
+ static final int yOffset = 30;\r
\r
public Desktop()\r
{\r
- Image image =null;\r
- try{\r
- java.net.URL url = getClass().getResource("/images/BartonGroupBanner.gif");\r
- if(url!=null)\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
+ catch (Exception ex)\r
+ {\r
+ }\r
\r
setTitle("Jalview 2005");\r
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);\r
- setVisible(true);\r
desktop = new JDesktopPane();\r
desktop.setBackground(Color.white);\r
setContentPane(desktop);\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
+ 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
+ setBounds(Integer.parseInt(x), Integer.parseInt(y),\r
+ Integer.parseInt(width), Integer.parseInt(height));\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
+ {\r
+ setBounds( (int) (screenSize.width - 900) / 2,\r
+ (int) (screenSize.height - 650) / 2, 900, 650);\r
+ }\r
\r
-/////////Add a splashscreen on startup\r
+ this.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ jalview.bin.Cache.setProperty("SCREEN_X", getBounds().x +\r
+ "");\r
+ jalview.bin.Cache.setProperty("SCREEN_Y", getBounds().y +\r
+ "");\r
+ jalview.bin.Cache.setProperty("SCREEN_WIDTH",\r
+ getWidth() + "");\r
+ jalview.bin.Cache.setProperty("SCREEN_HEIGHT",\r
+ 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
+ /////////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),\r
+ (int) ( (getHeight() - 160) / 2));\r
+ }\r
+\r
+ public static void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h)\r
+ {\r
+ addInternalFrame(frame, title, w, h, true);\r
+ }\r
+\r
+ public static void addInternalFrame(final JInternalFrame frame,\r
+ String title, int w, int h,\r
+ boolean resizable)\r
+ {\r
desktop.add(frame);\r
- frame.setVisible(true);\r
openFrameCount++;\r
+\r
try\r
{\r
frame.setSelected(true);\r
}\r
catch (java.beans.PropertyVetoException e)\r
- {}\r
- frame.setResizable(true);\r
- frame.setSize(845, 200);\r
- frame.setLocation( (int)((getWidth()-845) /2), (int)((getHeight()-240) /2));\r
- frame.setClosable(false);\r
- frame.setIconifiable(false);\r
- frame.setMaximizable(false);\r
+ {\r
+ }\r
+\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
\r
- }\r
+ final JMenuItem menuItem = new JMenuItem(title);\r
+ frame.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
+ {\r
+ public void internalFrameClosed(\r
+ javax.swing.event.InternalFrameEvent evt)\r
+ {\r
+ openFrameCount--;\r
+ windowMenu.remove(menuItem);\r
+ }\r
+ ;\r
+ });\r
\r
- public static void addInternalFrame(final JInternalFrame frame, String title, int w, int h)\r
- {\r
- desktop.add(frame);\r
- frame.setVisible(true);\r
- openFrameCount++;\r
- try {\r
- frame.setSelected(true);\r
- } catch (java.beans.PropertyVetoException e) {}\r
- frame.setTitle(title);\r
- frame.setResizable(true);\r
- frame.setSize(w,h);\r
- frame.setClosable(true);\r
- frame.setMaximizable(true);\r
- frame.setIconifiable(true);\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
- { public void internalFrameClosed(javax.swing.event.InternalFrameEvent evt)\r
- {\r
- openFrameCount--;\r
- windowMenu.remove(menuItem);\r
- };\r
- });\r
-\r
- menuItem.addActionListener(new ActionListener()\r
+ menuItem.addActionListener(new ActionListener()\r
{\r
public void actionPerformed(ActionEvent e)\r
{\r
- try{ frame.setSelected(true); frame.setIcon(false); }\r
- catch(java.beans.PropertyVetoException ex){};\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
\r
- windowMenu.add(menuItem);\r
- }\r
-\r
-\r
-\r
- public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JFileChooser chooser = new JFileChooser(jalview.bin.Cache.getProperty("LAST_DIRECTORY"));\r
- chooser.setFileView(new JalviewFileView());\r
- chooser.setDialogTitle("Open local file");\r
- chooser.setToolTipText("Open");\r
- int value = chooser.showOpenDialog(this);\r
- if(value == JFileChooser.APPROVE_OPTION)\r
- {\r
- String choice = chooser.getSelectedFile().getPath();\r
- jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice);\r
- String format = IdentifyFile.Identify(choice, "File");\r
- LoadFile(choice, "File", format);\r
- }\r
- }\r
-\r
- public void LoadFile(String file, String protocol, String format)\r
- {\r
- SequenceI [] sequences = null;\r
-\r
- if (FormatProperties.contains(format))\r
- sequences = FormatAdapter.read(file, protocol, format);\r
-\r
- if (sequences != null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, file, 700, 500);\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\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 or PFAM"\r
- ,"Error loading file",\r
- JOptionPane.WARNING_MESSAGE);\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
- if (url == null)\r
- return;\r
-\r
- String format = IdentifyFile.Identify(url, "URL");\r
-\r
- System.out.println(format +" format");\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
+ frame.setVisible(true);\r
+ windowMenu.add(menuItem);\r
+ }\r
\r
- LoadFile(url, "URL", format);\r
- }\r
+ public void dragEnter(DropTargetDragEvent evt)\r
+ {\r
+ }\r
+\r
+ public void dragExit(DropTargetEvent evt)\r
+ {\r
+ }\r
\r
- public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true);\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
+ public void dragOver(DropTargetDragEvent evt)\r
+ {\r
+ }\r
\r
+ public void dropActionChanged(DropTargetDragEvent evt)\r
+ {\r
+ }\r
\r
- if(accept == JOptionPane.YES_OPTION)\r
+ public void drop(DropTargetDropEvent evt)\r
{\r
- String format = IdentifyFile.Identify(cap.getText(), "Paste");\r
- SequenceI [] sequences = null;\r
+ Transferable t = evt.getTransferable();\r
\r
- if (FormatProperties.contains( format ))\r
- sequences = FormatAdapter.read(cap.getText(), "Paste", format);\r
+ if (!t.isDataFlavorSupported(DataFlavor.javaFileListFlavor))\r
+ {\r
+ return;\r
+ }\r
+\r
+ evt.acceptDrop(DnDConstants.ACTION_COPY_OR_MOVE);\r
\r
+ try\r
+ {\r
+ java.util.List files = (java.util.List) t.getTransferData(DataFlavor.\r
+ javaFileListFlavor);\r
\r
- if(sequences!=null)\r
+ for (int i = 0; i < files.size(); i++)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- addInternalFrame(af, "Cut & Paste input - "+format, 700, 500);\r
- af.statusBar.setText("Successfully pasted alignment file");\r
+ String file = files.get(i).toString();\r
+ String protocol = "File";\r
+\r
+ if (file.endsWith(".jar"))\r
+ {\r
+ Jalview2XML.LoadJalviewAlign(file);\r
+ }\r
+ else\r
+ {\r
+ String format = jalview.io.IdentifyFile.Identify(file,\r
+ protocol);\r
+ LoadFile(file, protocol, format);\r
+ }\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ public void inputLocalFileMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ 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
+ if (chooser.getSelectedFormat().equals("Jalview"))\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", "Jalivew");\r
+ Jalview2XML.LoadJalviewAlign(choice);\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 or PFAM",\r
- "Error parsing text", JOptionPane.WARNING_MESSAGE);\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
- }\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
-/*\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
+ public void inputURLMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ String url = JOptionPane.showInternalInputDialog(Desktop.desktop,\r
+ "Enter url of input file", "Input alignment from URL",\r
+ JOptionPane.QUESTION_MESSAGE, null, null, "http://www.")\r
+ .toString();\r
+\r
+ if (url == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ String format = IdentifyFile.Identify(url, "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
+ LoadFile(url, "URL", format);\r
+ }\r
\r
+ public void inputTextboxMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer();\r
+ cap.setForInput();\r
+ Desktop.addInternalFrame(cap, "Cut & Paste Alignment File", 600, 500);\r
+ }\r
\r
- public void aboutMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "JalView 2005"\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: \"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
- "About Jalview",\r
- JOptionPane.INFORMATION_MESSAGE);\r
- }\r
+ /*\r
+ * Exit the program\r
+ */\r
+ public void quit_actionPerformed(ActionEvent e)\r
+ {\r
+ if (jalview.bin.Jalview.applet != null)\r
+ {\r
+ jalview.bin.Jalview.applet.destroy();\r
+ }\r
+ else\r
+ {\r
+ System.exit(0);\r
+ }\r
+ }\r
\r
- public void documentationMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
+ public void aboutMenuItem_actionPerformed(ActionEvent e)\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "JalView 2005 version " +\r
+ jalview.bin.Cache.VERSION +\r
+ "; last updated: " +\r
+ 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
+ "\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 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
+ 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.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
- static JInternalFrame conservationSlider;\r
- static JInternalFrame PIDSlider;\r
- public static int setConservationSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
- {\r
- SliderPanel sp = null;\r
-\r
- if(conservationSlider == null)\r
- {\r
- sp = new SliderPanel(ap, 30, true, cs);\r
- conservationSlider = new JInternalFrame();\r
- conservationSlider.setContentPane(sp);\r
- conservationSlider.setResizable(false);\r
- addInternalFrame(conservationSlider, "Conservation Colour Increment ("+source+")", 420, 90);\r
- conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
- {\r
- conservationSlider = null;\r
- }\r
- });\r
- }\r
- else\r
- {\r
- conservationSlider.setTitle("Conservation Colour Increment ("+source+")");\r
- sp = (SliderPanel)conservationSlider.getContentPane();\r
- sp.cs = cs;\r
- }\r
-\r
- if(ap.av.alignment.getGroups()!=null)\r
- sp.setAllGroupsCheckEnabled( true );\r
- else\r
- sp.setAllGroupsCheckEnabled( false);\r
-\r
- return sp.getValue();\r
-\r
- }\r
-\r
- public static void hideConservationSlider()\r
- {\r
- try{\r
- conservationSlider.setClosed(true);\r
- conservationSlider = null;\r
- }catch(Exception ex){}\r
-}\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(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jar"},\r
+ new String[]\r
+ {"Jalview Project"}, "Jalview Project");\r
\r
+ chooser.setFileView(new JalviewFileView());\r
+ chooser.setDialogTitle("Save State");\r
\r
- public static void hidePIDSlider()\r
- {\r
- try{\r
- PIDSlider.setClosed(true);\r
- PIDSlider = null;\r
- }catch(Exception ex){}\r
- }\r
-\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
- {\r
- SliderPanel pid = null;\r
- if(PIDSlider == null)\r
- {\r
- pid = new SliderPanel(ap, 50, false, cs);\r
- PIDSlider = new JInternalFrame();\r
- PIDSlider.setContentPane(pid);\r
- PIDSlider.setResizable(false);\r
- addInternalFrame(PIDSlider, "Percentage Identity Threshold ("+source+")", 420, 90);\r
- }\r
- else\r
- {\r
- PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
- pid = (SliderPanel)PIDSlider.getContentPane();\r
- pid.cs = cs;\r
- }\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- pid.setAllGroupsCheckEnabled(true);\r
- else\r
- pid.setAllGroupsCheckEnabled(false);\r
-\r
-\r
- return pid.getValue();\r
-\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
+ Jalview2XML.SaveState(choice);\r
+ }\r
+ }\r
+\r
+ public void loadState_actionPerformed(ActionEvent e)\r
+ {\r
+ JalviewFileChooser chooser = new JalviewFileChooser(jalview.bin.Cache.\r
+ getProperty(\r
+ "LAST_DIRECTORY"), new String[]\r
+ {"jar"},\r
+ new String[]\r
+ {"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
+ Jalview2XML.LoadJalviewAlign(choice);\r
+ }\r
+ }\r
\r
+ class LoadingThread\r
+ extends Thread\r
+ {\r
+ String file;\r
+ String protocol;\r
+ String 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
+\r
+ public void run()\r
+ {\r
+ SequenceI[] sequences = null;\r
+\r
+ if (FormatAdapter.formats.contains(format))\r
+ {\r
+ sequences = FormatAdapter.readFile(file, protocol, format);\r
+ }\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,\r
+ AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.currentFileFormat = format;\r
+ af.statusBar.setText("Successfully loaded file " + file);\r
+\r
+ try\r
+ {\r
+ af.setMaximum(Preferences.showFullscreen);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ }\r
+ }\r
+ else\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "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
git://source.jalview.org / jalview.git / blobdiff