X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b449d19aba7692a4481264805f97c784584dd8f1;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=38033ff1a19542d495789270535d32b217483027;hpb=ad15cff29620f960119f80176f1fd443da9f6763;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 38033ff..b449d19 100755 --- a/src/jalview/io/FileLoader.java +++ b/src/jalview/io/FileLoader.java @@ -20,17 +20,24 @@ */ 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; 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.List; import java.util.StringTokenizer; import java.util.Vector; @@ -95,6 +102,7 @@ public class FileLoader implements Runnable SwingUtilities.invokeLater(new Runnable() { + @Override public void run() { loader.start(); @@ -229,6 +237,7 @@ public class FileLoader implements Runnable } } + @Override public void run() { String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard" @@ -245,15 +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) @@ -297,7 +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.afile; // keep reference for later if necessary. + source = fa.getAlignFile(); // keep reference for later if + // necessary. } } catch (java.io.IOException ex) { @@ -313,51 +342,87 @@ 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()) { while (sq.getDatasetSequence() != null) { sq = sq.getDatasetSequence(); } - if (sq.getPDBId() != null) + if (sq.getAllPDBEntries() != null) { - for (PDBEntry pdbe : (List) sq.getPDBId()) + for (PDBEntry pdbe : sq.getAllPDBEntries()) { + // register PDB entries with desktop's structure selection + // manager StructureSelectionManager.getStructureSelectionManager( Desktop.instance).registerPDBEntry(pdbe); } } } + + FeatureSettingsModelI proxyColourScheme = source + .getFeatureColourScheme(); if (viewport != null) { - // TODO: create undo object for this JAL-1101 - for (int i = 0; i < al.getHeight(); i++) + if (proxyColourScheme != null) { - viewport.getAlignment().addSequence(al.getSequenceAt(i)); + viewport.applyFeaturesStyle(proxyColourScheme); } - 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); - - alignFrame.statusBar.setText(MessageManager.formatMessage( - "label.successfully_loaded_file", new String[] - { title })); + // otherwise construct the alignFrame + if (source instanceof ComplexAlignFile) + { + ColumnSelection colSel = ((ComplexAlignFile) source) + .getColumnSelection(); + SequenceI[] hiddenSeqs = ((ComplexAlignFile) source) + .getHiddenSequences(); + 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( + ((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); } - if (source instanceof HtmlFile) + if (proxyColourScheme != null) { - ((HtmlFile) source).LoadAlignmentFeatures(alignFrame); - + alignFrame.getViewport() + .applyFeaturesStyle(proxyColourScheme); } + alignFrame.statusBar.setText(MessageManager.formatMessage( + "label.successfully_loaded_file", + new String[] { title })); + if (raiseGUI) { // add the window to the GUI @@ -385,12 +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, @@ -417,12 +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); } @@ -438,14 +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); } }); } @@ -496,6 +569,7 @@ public class FileLoader implements Runnable * * @see java.lang.Object#finalize() */ + @Override protected void finalize() throws Throwable { source = null;