From a4fca83856b96df2fe8701bb5cc14c8d1d0a6b09 Mon Sep 17 00:00:00 2001 From: jprocter Date: Wed, 31 Oct 2007 15:10:06 +0000 Subject: [PATCH] error message associated with an alignment file loading failure is passed back to user (finally!) --- src/jalview/io/FileLoader.java | 508 +++++++++++++++++++------------------- src/jalview/io/FileParse.java | 2 + src/jalview/io/IdentifyFile.java | 4 +- 3 files changed, 262 insertions(+), 252 deletions(-) diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 5f53579..6310cc4 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,251 +1,257 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2007 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 java.util.*; - -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.gui.*; - -public class FileLoader - implements Runnable -{ - String file; - String protocol; - String format; - AlignViewport viewport; - AlignFrame alignFrame; - - 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; - - final Thread loader = new Thread(this); - - SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - loader.start(); - } - }); - } - - public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, - String format) - { - this.file = file; - this.protocol = protocol; - this.format = format; - - Thread loader = new Thread(this); - loader.start(); - - while (loader.isAlive()) - { - try - { - Thread.sleep(500); - } - catch (Exception ex) - {} - } - - return alignFrame; - } - - 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 (protocol.equals(FormatAdapter.FILE)) - { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); - } - } - - public void run() - { - String title = protocol.equals(AppletFormatAdapter.PASTE) - ? "Copied From Clipboard" : file; - - try - { - if (Desktop.instance != null) - { - Desktop.instance.startLoading(file); - } - - Alignment al = null; - - if (format.equalsIgnoreCase("Jalview")) - { - alignFrame = new Jalview2XML().LoadJalviewAlign(file); - } - else - { - String error = AppletFormatAdapter.SUPPORTED_FORMATS; - - if (FormatAdapter.isValidFormat(format)) - { - try - { - al = new FormatAdapter().readFile(file, protocol, format); - } - catch (java.io.IOException ex) - { - error = ex.getMessage(); - } - } - - if ( (al != null) && (al.getHeight() > 0)) - { - if (viewport != null) - { - for (int i = 0; i < al.getHeight(); i++) - { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); - } - viewport.firePropertyChange("alignment", null, - viewport.getAlignment().getSequences()); - - } - else - { - alignFrame = new AlignFrame(al, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - - alignFrame.statusBar.setText("Successfully loaded file " + title); - - if (!protocol.equals(AppletFormatAdapter.PASTE)) - alignFrame.setFileName(file, format); - - Desktop.addInternalFrame(alignFrame, title, - AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - - try - { - alignFrame.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 " + title + "\n" + - error; - - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - JOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, - "Error loading file", - JOptionPane.WARNING_MESSAGE); - } - }); - } - } - - updateRecentlyOpened(); - - } - catch (OutOfMemoryError er) - { - - er.printStackTrace(); - alignFrame = null; - - javax.swing.SwingUtilities.invokeLater(new Runnable() - { - public void run() - { - javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Out of memory loading file " + file + "!!" - + - "\nSee help files for increasing Java Virtual Machine memory." - , "Out of memory", - javax.swing.JOptionPane.WARNING_MESSAGE); - } - }); - } - - System.gc(); - if (Desktop.instance != null) - { - Desktop.instance.stopLoading(); - } - - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer + * Copyright (C) 2007 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 java.util.*; + +import javax.swing.*; + +import jalview.datamodel.*; +import jalview.gui.*; + +public class FileLoader + implements Runnable +{ + String file; + String protocol; + String format; + AlignViewport viewport; + AlignFrame alignFrame; + + 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; + + final Thread loader = new Thread(this); + + SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + loader.start(); + } + }); + } + + public AlignFrame LoadFileWaitTillLoaded(String file, String protocol, + String format) + { + this.file = file; + this.protocol = protocol; + this.format = format; + + Thread loader = new Thread(this); + loader.start(); + + while (loader.isAlive()) + { + try + { + Thread.sleep(500); + } + catch (Exception ex) + {} + } + + return alignFrame; + } + + 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 (protocol.equals(FormatAdapter.FILE)) + { + jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); + } + } + + public void run() + { + String title = protocol.equals(AppletFormatAdapter.PASTE) + ? "Copied From Clipboard" : file; + + try + { + if (Desktop.instance != null) + { + Desktop.instance.startLoading(file); + } + + Alignment al = null; + + if (format.equalsIgnoreCase("Jalview")) + { + alignFrame = new Jalview2XML().LoadJalviewAlign(file); + } + else + { + String error = AppletFormatAdapter.SUPPORTED_FORMATS; + + if (FormatAdapter.isValidFormat(format)) + { + try + { + al = new FormatAdapter().readFile(file, protocol, format); + } + catch (java.io.IOException ex) + { + error = ex.getMessage(); + } + } else { + if (format!=null && format.length()>7) + { + // ad hoc message in format. + error = format +"\n"+error; + } + } + + if ( (al != null) && (al.getHeight() > 0)) + { + if (viewport != null) + { + for (int i = 0; i < al.getHeight(); i++) + { + viewport.getAlignment().addSequence(al.getSequenceAt(i)); + } + viewport.firePropertyChange("alignment", null, + viewport.getAlignment().getSequences()); + + } + else + { + alignFrame = new AlignFrame(al, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + alignFrame.statusBar.setText("Successfully loaded file " + title); + + if (!protocol.equals(AppletFormatAdapter.PASTE)) + alignFrame.setFileName(file, format); + + Desktop.addInternalFrame(alignFrame, title, + AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + + try + { + alignFrame.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 " + title + "\n" + + error; + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + errorMessage, + "Error loading file", + JOptionPane.WARNING_MESSAGE); + } + }); + } + } + + updateRecentlyOpened(); + + } + catch (OutOfMemoryError er) + { + + er.printStackTrace(); + alignFrame = null; + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + javax.swing.JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Out of memory loading file " + file + "!!" + + + "\nSee help files for increasing Java Virtual Machine memory." + , "Out of memory", + javax.swing.JOptionPane.WARNING_MESSAGE); + } + }); + } + + System.gc(); + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } + + } + +} diff --git a/src/jalview/io/FileParse.java b/src/jalview/io/FileParse.java index 9c05d5f..8a97e39 100755 --- a/src/jalview/io/FileParse.java +++ b/src/jalview/io/FileParse.java @@ -128,6 +128,7 @@ public class FileParse else if (type.equals(AppletFormatAdapter.URL)) { try { + try { checkURLSource(fileStr); if (suffixSeparator=='#') extractSuffix(fileStr); // URL lref is stored for later reference. @@ -146,6 +147,7 @@ public class FileParse } } } + } catch (Exception e) { errormessage = "CANNOT ACCESS DATA AT URL '"+fileStr+"' ("+e.getMessage()+")"; diff --git a/src/jalview/io/IdentifyFile.java b/src/jalview/io/IdentifyFile.java index 86036fd..86b04a8 100755 --- a/src/jalview/io/IdentifyFile.java +++ b/src/jalview/io/IdentifyFile.java @@ -40,6 +40,7 @@ public class IdentifyFile */ public String Identify(String file, String protocol) { + String emessage = "UNIDENTIFIED FILE PARSING ERROR"; FileParse parser = null; try { parser = new FileParse(file, protocol); @@ -49,10 +50,11 @@ public class IdentifyFile } catch (Exception e) { System.err.println("Error whilst identifying"); e.printStackTrace(System.err); + emessage = e.getMessage(); } if (parser!=null) return parser.errormessage; - return "UNIDENTIFIED FILE PARSING ERROR"; + return emessage; } public String Identify(FileParse source) { return Identify(source, true); // preserves original behaviour prior to version 2.3 -- 1.7.10.2