-package jalview.io;\r
-\r
-import jalview.gui.AlignFrame;\r
-import jalview.gui.Jalview2XML;\r
-import javax.swing.JOptionPane;\r
-import jalview.datamodel.Alignment;\r
-import jalview.gui.Desktop;\r
-import jalview.datamodel.SequenceI;\r
-\r
-public class FileLoader\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
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,\r
- String format)\r
- {\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
- loader.start();\r
- while (loader.isAlive())\r
- {\r
- try\r
- {\r
- Thread.sleep(500);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
-\r
- return loader.af;\r
- }\r
-\r
-\r
- class LoadingThread\r
- extends Thread\r
-{\r
- String file;\r
- String protocol;\r
- String format;\r
- AlignFrame af;\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 (format.equalsIgnoreCase("Jalview"))\r
- {\r
- af = Jalview2XML.LoadJalviewAlign(file);\r
- }\r
- else\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
- af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- af.statusBar.setText("Successfully loaded file " + file);\r
-\r
- Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
-\r
-\r
- try\r
- {\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\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
-\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+
+package jalview.io;
+
+import jalview.gui.AlignFrame;
+import jalview.gui.Jalview2XML;
+import javax.swing.JOptionPane;
+
+import jalview.gui.*;
+import jalview.datamodel.*;
+import java.util.Vector;
+import java.util.StringTokenizer;
+
+public class FileLoader
+{
+ String file;
+ String protocol;
+ String format;
+ AlignViewport viewport;
+
+ public void LoadFile(AlignViewport viewport, String file, String protocol, String format)
+ {
+ this.viewport = viewport;
+ LoadFile(file, protocol, format);
+ }
+
+ public void LoadFile(String file, String protocol, String format)
+ {
+ this.file = file;
+ this.protocol = protocol;
+ this.format = format;
+
+ LoadingThread loader = new LoadingThread();
+ loader.start();
+ }
+
+ public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
+ String format)
+ {
+ this.file = file;
+ this.protocol = protocol;
+ this.format = format;
+
+ LoadingThread loader = new LoadingThread();
+ loader.start();
+ while (loader.isAlive())
+ {
+ try
+ {
+ Thread.sleep(500);
+ }
+ catch (Exception ex)
+ {}
+ }
+
+ return loader.af;
+ }
+
+
+
+ public void updateRecentlyOpened()
+ {
+ Vector recent = new Vector();
+
+ String type = protocol.equals(FormatAdapter.FILE)
+ ? "RECENT_FILE" : "RECENT_URL";
+
+ String historyItems = jalview.bin.Cache.getProperty(type);
+
+ StringTokenizer st;
+
+ if (historyItems != null)
+ {
+ st = new StringTokenizer(historyItems, "\t");
+
+ while (st.hasMoreTokens())
+ {
+ recent.addElement(st.nextElement().toString().trim());
+ }
+ }
+
+ if (recent.contains(file))
+ {
+ recent.remove(file);
+ }
+
+ StringBuffer newHistory = new StringBuffer(file);
+ for (int i = 0; i < recent.size() && i < 10; i++)
+ {
+ newHistory.append("\t");
+ newHistory.append(recent.elementAt(i));
+ }
+
+ jalview.bin.Cache.setProperty(type, newHistory.toString());
+
+ if(type.equals(FormatAdapter.FILE))
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+ }
+
+
+ class LoadingThread
+ extends Thread
+ {
+
+ AlignFrame af;
+
+
+
+ public void run()
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.startLoading(file);
+
+ SequenceI[] sequences = null;
+
+ if (format.equalsIgnoreCase("Jalview"))
+ {
+ af = new Jalview2XML().LoadJalviewAlign(file);
+ }
+ else
+ {
+ String error = AppletFormatAdapter.SUPPORTED_FORMATS;
+
+ if (FormatAdapter.isValidFormat(format))
+ {
+ try
+ {
+ sequences = new FormatAdapter().readFile(file, protocol, format);
+ }
+ catch (java.io.IOException ex)
+ {
+ error = ex.getMessage();
+ }
+ }
+
+ if ( (sequences != null) && (sequences.length > 0))
+ {
+ if(viewport!=null)
+ {
+ for(int i=0; i<sequences.length; i++)
+ viewport.getAlignment().addSequence(sequences[i]);
+
+ viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());
+ }
+ else
+ {
+ af = new AlignFrame(new Alignment(sequences));
+ af.currentFileFormat = format;
+ af.statusBar.setText("Successfully loaded file " + file);
+
+ Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,
+ AlignFrame.NEW_WINDOW_HEIGHT);
+
+ try
+ {
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ }
+ catch (java.beans.PropertyVetoException ex)
+ {
+ }
+ }
+ }
+ else
+ {
+ if (Desktop.instance != null)
+ Desktop.instance.stopLoading();
+
+ final String errorMessage = "Couldn't load file "+file+"\n"+error;
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ errorMessage,
+ "Error loading file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ }
+
+ if (af != null)
+ {
+ updateRecentlyOpened();
+ }
+
+ if (Desktop.instance != null)
+ Desktop.instance.stopLoading();
+
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff