+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\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
+\r
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
-import jalview.gui.Preferences;\r
+import java.util.*;\r
+\r
+import javax.swing.*;\r
+\r
+import jalview.datamodel.*;\r
+import jalview.gui.*;\r
\r
public class FileLoader\r
+ implements Runnable\r
{\r
+ String file;\r
+ String protocol;\r
+ String format;\r
+ AlignViewport viewport;\r
+ AlignFrame alignFrame;\r
+\r
+ public void LoadFile(AlignViewport viewport, String file, String protocol,\r
+ String format)\r
+ {\r
+ this.viewport = viewport;\r
+ LoadFile(file, protocol, format);\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
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
+\r
+ final Thread loader = new Thread(this);\r
+\r
+ SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ loader.start();\r
+ }\r
+ });\r
}\r
\r
public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,\r
- String format)\r
+ String format)\r
{\r
- LoadingThread loader = new LoadingThread(file, protocol, format);\r
+ this.file = file;\r
+ this.protocol = protocol;\r
+ this.format = format;\r
+\r
+ Thread loader = new Thread(this);\r
loader.start();\r
+\r
while (loader.isAlive())\r
{\r
try\r
{\r
- Thread.sleep(50);\r
+ Thread.sleep(500);\r
}\r
catch (Exception ex)\r
{}\r
}\r
\r
- return loader.af;\r
+ return alignFrame;\r
}\r
\r
+ public void updateRecentlyOpened()\r
+ {\r
+ Vector recent = new Vector();\r
\r
- class LoadingThread\r
- extends Thread\r
-{\r
- String file;\r
- String protocol;\r
- String format;\r
- AlignFrame af;\r
+ String type = protocol.equals(FormatAdapter.FILE)\r
+ ? "RECENT_FILE" : "RECENT_URL";\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
+ String historyItems = jalview.bin.Cache.getProperty(type);\r
\r
- public void run()\r
- {\r
- SequenceI[] sequences = null;\r
+ StringTokenizer st;\r
\r
- if (format.equalsIgnoreCase("Jalview"))\r
+ if (historyItems != null)\r
{\r
- af = Jalview2XML.LoadJalviewAlign(file);\r
+ st = new StringTokenizer(historyItems, "\t");\r
+\r
+ while (st.hasMoreTokens())\r
+ {\r
+ recent.addElement(st.nextElement().toString().trim());\r
+ }\r
}\r
- else\r
+\r
+ if (recent.contains(file))\r
{\r
- if (FormatAdapter.formats.contains(format))\r
+ recent.remove(file);\r
+ }\r
+\r
+ StringBuffer newHistory = new StringBuffer(file);\r
+ for (int i = 0; i < recent.size() && i < 10; i++)\r
+ {\r
+ newHistory.append("\t");\r
+ newHistory.append(recent.elementAt(i));\r
+ }\r
+\r
+ jalview.bin.Cache.setProperty(type, newHistory.toString());\r
+\r
+ if (type.equals(FormatAdapter.FILE))\r
+ {\r
+ jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);\r
+ }\r
+ }\r
+\r
+ public void run()\r
+ {\r
+ try\r
+ {\r
+ if (Desktop.instance != null)\r
{\r
- sequences = FormatAdapter.readFile(file, protocol, format);\r
+ Desktop.instance.startLoading(file);\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
+ Alignment al = null;\r
\r
- Desktop.addInternalFrame(af, file, AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ alignFrame = new Jalview2XML().LoadJalviewAlign(file);\r
+ }\r
+ else\r
+ {\r
+ String error = AppletFormatAdapter.SUPPORTED_FORMATS;\r
\r
+ if (FormatAdapter.isValidFormat(format))\r
+ {\r
+ try\r
+ {\r
+ al = new FormatAdapter().readFile(file, protocol, format);\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ error = ex.getMessage();\r
+ }\r
+ }\r
\r
- try\r
+ if ( (al != null) && (al.getHeight() > 0))\r
{\r
- af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
+ if (viewport != null)\r
+ {\r
+ for (int i = 0; i < al.getHeight(); i++)\r
+ {\r
+ viewport.getAlignment().addSequence(al.getSequenceAt(i));\r
+ }\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+\r
+ }\r
+ else\r
+ {\r
+ alignFrame = new AlignFrame(al,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ alignFrame.statusBar.setText("Successfully loaded file " + file);\r
+ alignFrame.setFileName(file, format);\r
+\r
+ Desktop.addInternalFrame(alignFrame, file,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+\r
+ try\r
+ {\r
+ alignFrame.setMaximum(jalview.bin.Cache.getDefault(\r
+ "SHOW_FULLSCREEN", false));\r
+ }\r
+ catch (java.beans.PropertyVetoException ex)\r
+ {\r
+ }\r
+ }\r
}\r
- catch (Exception ex)\r
+ else\r
{\r
+ if (Desktop.instance != null)\r
+ {\r
+ Desktop.instance.stopLoading();\r
+ }\r
+\r
+ final String errorMessage = "Couldn't load file " + file + "\n" +\r
+ error;\r
+\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ errorMessage,\r
+ "Error loading file",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
}\r
}\r
- else\r
+\r
+ updateRecentlyOpened();\r
+\r
+ }\r
+ catch (OutOfMemoryError er)\r
+ {\r
+\r
+ er.printStackTrace();\r
+ alignFrame = null;\r
+\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\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
+ public void run()\r
+ {\r
+ javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Out of memory loading file " + file + "!!"\r
+ +\r
+ "\nSee help files for increasing Java Virtual Machine memory."\r
+ , "Out of memory",\r
+ javax.swing.JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
}\r
+\r
+ System.gc();\r
+ if (Desktop.instance != null)\r
+ {\r
+ Desktop.instance.stopLoading();\r
+ }\r
+\r
}\r
-}\r
\r
}\r
git://source.jalview.org / jalview.git / blobdiff