X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=c38718613af28aa1abc968a772aee8e189f9445a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=1d9655bb3d9adb4813a9d6adecde4014020ffb0c;hpb=3325395b33ef3b52b4a62327621c5bddf12ee4e0;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 1d9655b..c387186 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 2.9.0b2) + * Copyright (C) 2015 The Jalview Authors * * This file is part of Jalview. * @@ -20,16 +20,25 @@ */ package jalview.io; +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 jalview.util.MessageManager; import javax.swing.JOptionPane; import javax.swing.SwingUtilities; @@ -148,6 +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; @@ -249,6 +259,25 @@ 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) @@ -272,7 +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 { @@ -292,7 +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) { @@ -308,31 +338,76 @@ 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()) { - // TODO: create undo object for this JAL-1101 - for (int i = 0; i < al.getHeight(); i++) + while (sq.getDatasetSequence() != null) + { + sq = sq.getDatasetSequence(); + } + if (sq.getAllPDBEntries() != null) { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); + for (PDBEntry pdbe : sq.getAllPDBEntries()) + { + // register PDB entries with desktop's structure selection + // manager + StructureSelectionManager.getStructureSelectionManager( + Desktop.instance).registerPDBEntry(pdbe); + } } - viewport.firePropertyChange("alignment", null, viewport - .getAlignment().getSequences()); + } + + if (viewport != null) + { + // 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(); + 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 })); + if (raiseGUI) { // add the window to the GUI @@ -360,9 +435,14 @@ 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() { @@ -396,8 +476,8 @@ public class FileLoader implements Runnable { javax.swing.JOptionPane.showInternalMessageDialog( Desktop.desktop, MessageManager.formatMessage( - "label.problems_opening_file", new String[] - { file }), MessageManager + "label.problems_opening_file", + new String[] { file }), MessageManager .getString("label.file_open_error"), javax.swing.JOptionPane.WARNING_MESSAGE); } @@ -415,12 +495,12 @@ 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); } }); }