X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b7dacd5a1f42d99aea6a649a32d3ee1c680d1ca9;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=0cd298713579df83ba113ffa73460e1ad5877e0d;hpb=e7543a7264d0cd505a7344b704ce669726c44afc;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 0cd2987..b7dacd5 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) - * Copyright (C) $$Year-Rel$$ 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. * @@ -21,6 +21,10 @@ package jalview.io; import jalview.api.ComplexAlignFile; +import jalview.api.FeatureSettingsModelI; +import jalview.api.FeaturesDisplayedI; +import jalview.api.FeaturesSourceI; +import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; @@ -29,6 +33,7 @@ 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; @@ -97,6 +102,7 @@ public class FileLoader implements Runnable SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -231,6 +237,7 @@ public class FileLoader implements Runnable } } + @Override public void run() { String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard" @@ -247,15 +254,34 @@ public class FileLoader implements Runnable // just in case the caller didn't identify the file for us if (source != null) { - format = new IdentifyFile().Identify(source, false); // identify + format = new IdentifyFile().identify(source, false); // identify // stream and // rewind rather // than close } else { - format = new IdentifyFile().Identify(file, protocol); + 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) @@ -299,7 +325,8 @@ 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.getAlignFile(); // keep reference for later if necessary. + source = fa.getAlignFile(); // keep reference for later if + // necessary. } } catch (java.io.IOException ex) { @@ -315,7 +342,7 @@ public class FileLoader implements Runnable } } - if ((al != null) && (al.getHeight() > 0)) + if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence()) { // construct and register dataset sequences for (SequenceI sq : al.getSequences()) @@ -324,9 +351,9 @@ public class FileLoader implements Runnable { sq = sq.getDatasetSequence(); } - if (sq.getPDBId() != null) + if (sq.getAllPDBEntries() != null) { - for (PDBEntry pdbe : sq.getPDBId()) + for (PDBEntry pdbe : sq.getAllPDBEntries()) { // register PDB entries with desktop's structure selection // manager @@ -336,8 +363,14 @@ public class FileLoader implements Runnable } } + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); if (viewport != null) { + if (proxyColourScheme != null) + { + viewport.applyFeaturesStyle(proxyColourScheme); + } // append to existing alignment viewport.addAlignment(al, title); } @@ -351,50 +384,63 @@ public class FileLoader implements Runnable .getColumnSelection(); SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) .getHiddenSequences(); - boolean showSeqFeatures = ((ComplexAlignFile) source) - .isShowSeqFeatures(); - ColourSchemeI cs = ((ComplexAlignFile) source) - .getColourScheme(); + String colourSchemeName = ((ComplexAlignFile) source) + .getGlobalColourScheme(); + FeaturesDisplayedI fd = ((ComplexAlignFile) source) + .getDisplayedFeatures(); alignFrame = new AlignFrame(al, hiddenSeqs, colSel, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); - + alignFrame.getViewport().setFeaturesDisplayed(fd); alignFrame.getViewport().setShowSequenceFeatures( - showSeqFeatures); - alignFrame.changeColour(cs); + ((ComplexAlignFile) source).isShowSeqFeatures()); + ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme( + colourSchemeName, al); + if (cs != null) + { + alignFrame.changeColour(cs); + } } else { alignFrame = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); + if (source instanceof FeaturesSourceI) + { + alignFrame.getViewport().setShowSequenceFeatures(true); + } } - } - // 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 })); + // add metadata and update ui + if (!protocol.equals(AppletFormatAdapter.PASTE)) + { + alignFrame.setFileName(file, format); + } + if (proxyColourScheme != null) + { + alignFrame.getViewport() + .applyFeaturesStyle(proxyColourScheme); + } + alignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", + new String[] { title })); - 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); - } + 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( - "SHOW_FULLSCREEN", false)); - } catch (java.beans.PropertyVetoException ex) - { + try + { + alignFrame.setMaximum(jalview.bin.Cache.getDefault( + "SHOW_FULLSCREEN", false)); + } catch (java.beans.PropertyVetoException ex) + { + } } } else @@ -404,12 +450,18 @@ 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() { + @Override public void run() { JOptionPane.showInternalMessageDialog(Desktop.desktop, @@ -436,12 +488,13 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { 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); } @@ -457,14 +510,15 @@ public class FileLoader implements Runnable { javax.swing.SwingUtilities.invokeLater(new Runnable() { + @Override 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); } }); } @@ -515,6 +569,7 @@ public class FileLoader implements Runnable * * @see java.lang.Object#finalize() */ + @Override protected void finalize() throws Throwable { source = null;