X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=2d59f2923d47c6e26de137919f486a8b7b3ebf99;hb=a9315b41e948f66f4632f7d419fda643bc0b9354;hp=584840e99274cb08e4e628d0194208f6f157aee4;hpb=9d8d94660cfba31f6dd39cd6a8a25e3e88284277;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 584840e..2d59f29 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,30 +1,34 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, G Barton, M Clamp, S Searle + * + * This file is part of Jalview. + * + * Jalview 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 3 of the License, or (at your option) any later version. + * + * Jalview 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 Jalview. If not, see . */ - package jalview.io; -import java.util.*; +import jalview.datamodel.AlignmentI; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.Desktop; +import jalview.gui.Jalview2XML; -import javax.swing.*; +import java.util.StringTokenizer; +import java.util.Vector; -import jalview.datamodel.*; -import jalview.gui.*; +import jalview.util.MessageManager; +import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; public class FileLoader implements Runnable { @@ -47,15 +51,20 @@ public class FileLoader implements Runnable long memused; boolean raiseGUI = true; + /** - * default constructor always raised errors in GUI dialog boxes + * default constructor always raised errors in GUI dialog boxes */ - public FileLoader() { + public FileLoader() + { this(true); } + /** - * construct a Fileloader that may raise errors non-interactively - * @param raiseGUI true if errors are to be raised as GUI dialog boxes + * construct a Fileloader that may raise errors non-interactively + * + * @param raiseGUI + * true if errors are to be raised as GUI dialog boxes */ public FileLoader(boolean raiseGUI) { @@ -169,7 +178,12 @@ public class FileLoader implements Runnable public void updateRecentlyOpened() { Vector recent = new Vector(); - + if (protocol.equals(FormatAdapter.PASTE)) + { + // do nothing if the file was pasted in as text... there is no filename to + // refer to it as. + return; + } String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE" : "RECENT_URL"; @@ -233,13 +247,18 @@ public class FileLoader implements Runnable format = new IdentifyFile().Identify(file, protocol); } } + // TODO: cache any stream datasources as a temporary file (eg. PDBs + // retrieved via URL) if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) { System.gc(); - memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free memory before load + memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free + // memory + // before + // load } loadtime = -System.currentTimeMillis(); - Alignment al = null; + AlignmentI al = null; if (format.equalsIgnoreCase("Jalview")) { @@ -285,11 +304,12 @@ public class FileLoader implements Runnable error = format + "\n" + error; } } - + if ((al != null) && (al.getHeight() > 0)) { if (viewport != null) { + // TODO: create undo object for this JAL-1101 for (int i = 0; i < al.getHeight(); i++) { viewport.getAlignment().addSequence(al.getSequenceAt(i)); @@ -308,9 +328,14 @@ public class FileLoader implements Runnable if (!protocol.equals(AppletFormatAdapter.PASTE)) alignFrame.setFileName(file, format); - - Desktop.addInternalFrame(alignFrame, title, - AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + if (raiseGUI) + { + // add the window to the GUI + // note - this actually should happen regardless of raiseGUI status in Jalview 3 + // TODO: define 'virtual desktop' for benefit of headless scripts that perform queries to find the 'current working alignment' + Desktop.addInternalFrame(alignFrame, title, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + } try { @@ -337,7 +362,7 @@ public class FileLoader implements Runnable public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, "Error loading file", + errorMessage, MessageManager.getString("label.error_loading_file"), JOptionPane.WARNING_MESSAGE); } }); @@ -351,10 +376,9 @@ public class FileLoader implements Runnable updateRecentlyOpened(); - } - catch (Exception er) + } catch (Exception er) { - System.err.println("Exception whilst opening file '"+file); + System.err.println("Exception whilst opening file '" + file); er.printStackTrace(); if (raiseGUI) { @@ -362,20 +386,15 @@ public class FileLoader implements Runnable { public void run() { - javax.swing.JOptionPane - .showInternalMessageDialog( - Desktop.desktop, - "Encountered problems opening " - + file - + "!!" - , "File open error", - javax.swing.JOptionPane.WARNING_MESSAGE); + javax.swing.JOptionPane.showInternalMessageDialog( + Desktop.desktop, MessageManager.formatMessage("label.problems_opening_file", new String[]{file}), + MessageManager.getString("label.file_open_error"), + javax.swing.JOptionPane.WARNING_MESSAGE); } }); } alignFrame = null; - } - catch (OutOfMemoryError er) + } catch (OutOfMemoryError er) { er.printStackTrace(); @@ -398,15 +417,19 @@ public class FileLoader implements Runnable } }); } - else - { - System.err.println("Out of memory loading file " + file + "!!"); - } + System.err.println("Out of memory loading file " + file + "!!"); + } loadtime += System.currentTimeMillis(); - + // TODO: Estimate percentage of memory used by a newly loaded alignment - + // warn if more memory will be needed to work with it // System.gc(); - memused = memused - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference in free memory after load + memused = memused + - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference + // in free + // memory + // after + // load if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) { if (alignFrame != null) @@ -417,11 +440,15 @@ public class FileLoader implements Runnable + (loadtime / 1000.0) + "s, took an additional " + (1.0 * memused / (1024.0 * 1024.0)) + " MB (" + al.getHeight() + " seqs by " + al.getWidth() + " cols)"); - } else { - // report that we didn't load anything probably due to an out of memory error - System.out.println("Failed to load '"+title+"' in " + } + else + { + // report that we didn't load anything probably due to an out of memory + // error + System.out.println("Failed to load '" + title + "' in " + (loadtime / 1000.0) + "s, took an additional " - + (1.0 * memused / (1024.0 * 1024.0)) + " MB (alignment is null)"); + + (1.0 * memused / (1024.0 * 1024.0)) + + " MB (alignment is null)"); } } // remove the visual delay indicator