X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1edf8320848eecf9aabd1f192ae0ca8fcbd75c2b;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=f53cd88f36d5326444393ef0c60ff458b58b1164;hpb=2de8acfae59aced665e4c37ad0f7dcc2ed68818e;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index f53cd88..1edf832 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,29 +1,46 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Development Version 2.4.1) - * Copyright (C) 2009 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * - * 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.io; -import java.util.*; - -import javax.swing.*; - -import jalview.datamodel.*; -import jalview.gui.*; +import jalview.api.ComplexAlignFile; +import jalview.api.FeaturesDisplayedI; +import jalview.bin.Cache; +import jalview.bin.Jalview; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.ColumnSelection; +import jalview.datamodel.PDBEntry; +import jalview.datamodel.SequenceI; +import jalview.gui.AlignFrame; +import jalview.gui.AlignViewport; +import jalview.gui.Desktop; +import jalview.gui.Jalview2XML; +import jalview.schemes.ColourSchemeI; +import jalview.structure.StructureSelectionManager; +import jalview.util.MessageManager; + +import java.util.StringTokenizer; +import java.util.Vector; + +import javax.swing.JOptionPane; +import javax.swing.SwingUtilities; public class FileLoader implements Runnable { @@ -59,7 +76,7 @@ public class FileLoader implements Runnable * construct a Fileloader that may raise errors non-interactively * * @param raiseGUI - * true if errors are to be raised as GUI dialog boxes + * true if errors are to be raised as GUI dialog boxes */ public FileLoader(boolean raiseGUI) { @@ -140,6 +157,7 @@ public class FileLoader implements Runnable public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format) { this.source = source; + file = source.getInFile(); protocol = source.type; this.format = format; @@ -173,11 +191,16 @@ 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"; - String historyItems = jalview.bin.Cache.getProperty(type); + String historyItems = Cache.getProperty(type); StringTokenizer st; @@ -203,11 +226,11 @@ public class FileLoader implements Runnable newHistory.append(recent.elementAt(i)); } - jalview.bin.Cache.setProperty(type, newHistory.toString()); + Cache.setProperty(type, newHistory.toString()); if (protocol.equals(FormatAdapter.FILE)) { - jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format); + Cache.setProperty("DEFAULT_FILE_FORMAT", format); } } @@ -236,17 +259,34 @@ public class FileLoader implements Runnable { format = new IdentifyFile().Identify(file, protocol); } + + } + + if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE")) + { + Desktop.instance.stopLoading(); + System.err.println("The input file \"" + file + + "\" has no data content!"); + if (!Jalview.isHeadlessMode()) + { + JOptionPane.showMessageDialog(null, "The input file \"" + + file + "\" has no data content!", "Empty data file", + JOptionPane.ERROR_MESSAGE); + } + return; } + // 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 + // memory + // before + // load } loadtime = -System.currentTimeMillis(); - Alignment al = null; + AlignmentI al = null; if (format.equalsIgnoreCase("Jalview")) { @@ -257,7 +297,7 @@ public class FileLoader implements Runnable .println("IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream."); // We read the data anyway - it might make sense. } - alignFrame = new Jalview2XML(raiseGUI).LoadJalviewAlign(file); + alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(file); } else { @@ -277,7 +317,8 @@ public class FileLoader implements Runnable // open a new source and read from it FormatAdapter fa = new FormatAdapter(); al = fa.readFile(file, protocol, format); - source = fa.afile; // keep reference for later if necessary. + source = fa.getAlignFile(); // keep reference for later if + // necessary. } } catch (java.io.IOException ex) { @@ -295,33 +336,83 @@ public class FileLoader implements Runnable if ((al != null) && (al.getHeight() > 0)) { - if (viewport != null) + // construct and register dataset sequences + for (SequenceI sq : al.getSequences()) { - for (int i = 0; i < al.getHeight(); i++) + while (sq.getDatasetSequence() != null) { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); + sq = sq.getDatasetSequence(); } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + if (sq.getPDBId() != null) + { + for (PDBEntry pdbe : sq.getPDBId()) + { + // register PDB entries with desktop's structure selection + // manager + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).registerPDBEntry(pdbe); + } + } + } + if (viewport != null) + { + // append to existing alignment + viewport.addAlignment(al, title); } else { - alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); - - alignFrame.statusBar.setText("Successfully loaded file " - + title); + // otherwise construct the alignFrame + if (source instanceof ComplexAlignFile) + { + ColumnSelection colSel = ((ComplexAlignFile) source) + .getColumnSelection(); + SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) + .getHiddenSequences(); + boolean showSeqFeatures = ((ComplexAlignFile) source) + .isShowSeqFeatures(); + ColourSchemeI cs = ((ComplexAlignFile) source) + .getColourScheme(); + FeaturesDisplayedI fd = ((ComplexAlignFile) source) + .getDisplayedFeatures(); + alignFrame = new AlignFrame(al, hiddenSeqs, colSel, + AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + + alignFrame.getViewport().setShowSequenceFeatures( + showSeqFeatures); + alignFrame.getViewport().setFeaturesDisplayed(fd); + alignFrame.changeColour(cs); + } + else + { + alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, + AlignFrame.DEFAULT_HEIGHT); + } + // add metadata and update ui if (!protocol.equals(AppletFormatAdapter.PASTE)) + { alignFrame.setFileName(file, format); + } + + alignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", new String[] + { title })); - 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 { - alignFrame.setMaximum(jalview.bin.Cache.getDefault( + alignFrame.setMaximum(Cache.getDefault( "SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { @@ -337,14 +428,17 @@ public class FileLoader implements Runnable final String errorMessage = "Couldn't load file " + title + "\n" + error; - if (raiseGUI) + // TODO: refactor FileLoader to be independent of Desktop / Applet GUI + // bits ? + if (raiseGUI && Desktop.desktop != null) { javax.swing.SwingUtilities.invokeLater(new Runnable() { public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, - errorMessage, "Error loading file", + errorMessage, MessageManager + .getString("label.error_loading_file"), JOptionPane.WARNING_MESSAGE); } }); @@ -369,8 +463,10 @@ public class FileLoader implements Runnable public void run() { javax.swing.JOptionPane.showInternalMessageDialog( - Desktop.desktop, "Encountered problems opening " + file - + "!!", "File open error", + Desktop.desktop, MessageManager.formatMessage( + "label.problems_opening_file", new String[] + { file }), MessageManager + .getString("label.file_open_error"), javax.swing.JOptionPane.WARNING_MESSAGE); } }); @@ -387,15 +483,12 @@ public class FileLoader implements 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); + javax.swing.JOptionPane.showInternalMessageDialog( + Desktop.desktop, MessageManager.formatMessage( + "warn.out_of_memory_loading_file", new String[] + { file }), MessageManager + .getString("label.out_of_memory"), + javax.swing.JOptionPane.WARNING_MESSAGE); } }); } @@ -408,10 +501,10 @@ public class FileLoader implements Runnable // System.gc(); memused = memused - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference - // in free - // memory - // after - // load + // in free + // memory + // after + // load if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage()) { if (alignFrame != null)