X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=fe31a407b32446248042015439c1b52caa3e74ed;hb=153dd62dc91da13ae732600e6ea55ddbe15eab39;hp=584840e99274cb08e4e628d0194208f6f157aee4;hpb=9d8d94660cfba31f6dd39cd6a8a25e3e88284277;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 584840e..fe31a40 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,22 +1,20 @@ /* - * 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 2.6) + * Copyright (C) 2010 J Procter, AM Waterhouse, 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.*; @@ -47,15 +45,20 @@ 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 +172,12 @@ 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"; @@ -233,10 +241,15 @@ 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; @@ -351,10 +364,9 @@ 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 +374,15 @@ 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(); @@ -398,15 +405,19 @@ 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 +428,15 @@ 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