X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=c38718613af28aa1abc968a772aee8e189f9445a;hb=c19d2a91ca05e052e3408bf5852d88eb5d0608f1;hp=76bd572aaefeb127794d7a4cee670b627611ab97;hpb=8f8e6868f55cfe6ab73b3fe82cfb360f3e71a025;p=jalview.git diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java index 76bd572..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 ($$Version-Rel$$) - * 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. * @@ -20,13 +20,9 @@ */ package jalview.io; -import java.util.StringTokenizer; -import java.util.Vector; - -import javax.swing.JOptionPane; -import javax.swing.SwingUtilities; - import jalview.api.ComplexAlignFile; +import jalview.api.FeaturesDisplayedI; +import jalview.bin.Jalview; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; @@ -35,10 +31,17 @@ 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 { String file; @@ -256,6 +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) @@ -299,7 +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.getAlignFile(); // keep reference for later if necessary. + source = fa.getAlignFile(); // keep reference for later if + // necessary. } } catch (java.io.IOException ex) { @@ -315,25 +338,30 @@ 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 : sq.getPDBId()) + 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 @@ -348,49 +376,56 @@ public class FileLoader implements Runnable .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.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT); alignFrame.getViewport().setShowSequenceFeatures( showSeqFeatures); - alignFrame.changeColour(cs); + 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); - } + // 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 })); + 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 @@ -400,9 +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() { @@ -436,8 +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); } @@ -455,12 +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); } }); }