X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=1edf8320848eecf9aabd1f192ae0ca8fcbd75c2b;hb=67b3acb8df1438ef37a756c04e14f5a3b8406808;hp=82b94c3680d326a201c2a2304bd4eeca761a04c1;hpb=9c37999eb4b461a5c7a94e10ac39583c1c29200a;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 82b94c3..1edf832 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2) - * Copyright (C) 2014 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,17 +20,22 @@ */ package jalview.io; +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.List; import java.util.StringTokenizer; import java.util.Vector; @@ -152,6 +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; @@ -194,7 +200,7 @@ public class FileLoader implements Runnable String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE" : "RECENT_URL"; - String historyItems = jalview.bin.Cache.getProperty(type); + String historyItems = Cache.getProperty(type); StringTokenizer st; @@ -220,11 +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); } } @@ -253,6 +259,21 @@ 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) @@ -276,7 +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 { @@ -296,7 +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) { @@ -314,6 +336,7 @@ public class FileLoader implements Runnable if ((al != null) && (al.getHeight() > 0)) { + // construct and register dataset sequences for (SequenceI sq : al.getSequences()) { while (sq.getDatasetSequence() != null) @@ -322,36 +345,60 @@ public class FileLoader implements Runnable } if (sq.getPDBId() != null) { - for (PDBEntry pdbe : (List) sq.getPDBId()) + for (PDBEntry pdbe : sq.getPDBId()) { + // register PDB entries with desktop's structure selection + // manager StructureSelectionManager.getStructureSelectionManager( Desktop.instance).registerPDBEntry(pdbe); } } } + 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)); - } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + // append to existing alignment + viewport.addAlignment(al, title); } else { - alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, - AlignFrame.DEFAULT_HEIGHT); + // otherwise construct the alignFrame - alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new String[] - { title })); + 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 })); + if (raiseGUI) { // add the window to the GUI @@ -365,7 +412,7 @@ public class FileLoader implements Runnable try { - alignFrame.setMaximum(jalview.bin.Cache.getDefault( + alignFrame.setMaximum(Cache.getDefault( "SHOW_FULLSCREEN", false)); } catch (java.beans.PropertyVetoException ex) { @@ -381,7 +428,9 @@ 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() { @@ -434,12 +483,12 @@ public class FileLoader implements Runnable { public void run() { - 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); + 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); } }); }