X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fio%2FFileLoader.java;h=27b49441ff4951f3268a938c1b2ca1cda9161a03;hb=bb99cb8aa479dc7dd30b3678f183044247e25998;hp=3a77b7301e5f7754f7b08e7068dced0bc40c5238;hpb=b92eeace1b8b5237b3719a4d5b42e8a60af015e9;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 3a77b73..27b4944 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.Alignment; +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 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)); @@ -351,10 +371,9 @@ 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 +381,15 @@ 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, "Encountered problems opening " + file + + "!!", "File open error", + javax.swing.JOptionPane.WARNING_MESSAGE); } }); } alignFrame = null; - } - catch (OutOfMemoryError er) + } catch (OutOfMemoryError er) { er.printStackTrace(); @@ -398,22 +412,22 @@ public class FileLoader implements Runnable } }); } - else - { - System.err.println("Out of memory loading file " + file + "!!"); - } - } - loadtime += System.currentTimeMillis(); + System.err.println("Out of memory loading file " + file + "!!"); - if (Desktop.instance != null) - { - Desktop.instance.stopLoading(); } + 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 - if (alignFrame != null) + memused = memused + - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference + // in free + // memory + // after + // load + if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) { - if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) + if (alignFrame != null) { AlignmentI al = alignFrame.getViewport().getAlignment(); @@ -422,6 +436,20 @@ public class FileLoader implements Runnable + (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 " + + (loadtime / 1000.0) + "s, took an additional " + + (1.0 * memused / (1024.0 * 1024.0)) + + " MB (alignment is null)"); + } + } + // remove the visual delay indicator + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); } }