X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=c38718613af28aa1abc968a772aee8e189f9445a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=584840e99274cb08e4e628d0194208f6f157aee4;hpb=9d8d94660cfba31f6dd39cd6a8a25e3e88284277;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 584840e..c387186 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,30 +1,46 @@ /* - * 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 + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors + * + * 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. - * - * 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 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.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.json.binding.biojson.v1.ColourSchemeMapper; +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 { @@ -47,15 +63,20 @@ 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) { @@ -136,6 +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; @@ -169,7 +191,12 @@ 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"; @@ -232,14 +259,38 @@ 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 null or unidentifiable data content!"); + if (!Jalview.isHeadlessMode()) + { + javax.swing.JOptionPane.showInternalMessageDialog( + Desktop.desktop, + MessageManager.getString("label.couldnt_read_data") + + " in " + file + "\n" + + AppletFormatAdapter.SUPPORTED_FORMATS, + MessageManager.getString("label.couldnt_read_data"), + JOptionPane.WARNING_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 + memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free + // memory + // before + // load } loadtime = -System.currentTimeMillis(); - Alignment al = null; + AlignmentI al = null; if (format.equalsIgnoreCase("Jalview")) { @@ -250,7 +301,7 @@ 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 { @@ -270,7 +321,8 @@ 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) { @@ -286,31 +338,86 @@ public class FileLoader implements Runnable } } - if ((al != null) && (al.getHeight() > 0)) + if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { - 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.getAllPDBEntries() != null) + { + for (PDBEntry pdbe : sq.getAllPDBEntries()) + { + // 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(); + String colourSchemeName = ((ComplexAlignFile) source) + .getGlobalColourScheme(); + 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); + ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( + colourSchemeName, al); + if (cs != null) + { + 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 { @@ -328,16 +435,22 @@ public class FileLoader implements Runnable Desktop.instance.stopLoading(); } - final String errorMessage = "Couldn't load file " + title + "\n" - + error; - if (raiseGUI) + final String errorMessage = MessageManager + .getString("label.couldnt_load_file") + + " " + + title + + "\n" + error; + // 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); } }); @@ -351,10 +464,9 @@ 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 +474,17 @@ 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(); @@ -386,27 +495,28 @@ 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); } }); } - 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 +527,15 @@ 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