X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=4ab9b3bf416b3b5a2bc9354a0d90b8204828cbcf;hb=8fa9d08c44b3ba0aaa357ab9ed41b893b904a63f;hp=38959a75633457b4d18756400b23b4ca3f58154c;hpb=8d3d3b4edf47e543b8b352c1b2c247cfc59122a4;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 38959a7..4ab9b3b 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,123 +1,211 @@ -/* -* 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.io; - -import jalview.gui.AlignFrame; -import jalview.gui.Jalview2XML; -import javax.swing.JOptionPane; -import jalview.datamodel.Alignment; -import jalview.gui.Desktop; -import jalview.datamodel.SequenceI; - -public class FileLoader -{ - public void LoadFile(String file, String protocol, String format) - { - LoadingThread loader = new LoadingThread(file, protocol, format); - loader.start(); - } - - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, - String format) - { - LoadingThread loader = new LoadingThread(file, protocol, format); - loader.start(); - while (loader.isAlive()) - { - try - { - Thread.sleep(500); - } - catch (Exception ex) - {} - } - - return loader.af; - } - - - class LoadingThread - extends Thread -{ - String file; - String protocol; - String format; - AlignFrame af; - - public LoadingThread(String file, String protocol, String format) - { - this.file = file; - this.protocol = protocol; - this.format = format; - } - - public void run() - { - SequenceI[] sequences = null; - - if (format.equalsIgnoreCase("Jalview")) - { - af = Jalview2XML.LoadJalviewAlign(file); - } - else - { - String errorMessage = AppletFormatAdapter.SUPPORTED_FORMATS; - - if (FormatAdapter.formats.contains(format)) - { - try{ - sequences = new FormatAdapter().readFile(file, protocol, format); - }catch(java.io.IOException ex) - { - errorMessage = ex.getMessage(); - } - } - - if ( (sequences != null) && (sequences.length > 0)) - { - 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 (Exception ex) - { - } - } - else - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't load file "+file+"\n" - +errorMessage, - "Error loading file", - JOptionPane.WARNING_MESSAGE); - } - } - } -} - -} +/* +* 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