X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=b7dacd5a1f42d99aea6a649a32d3ee1c680d1ca9;hb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;hp=9cc1e1664eb27b8da2bce9a138605a17a778b27e;hpb=cb5d856b1304448cae13a333cbd9017f81520d90;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 9cc1e16..b7dacd5 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,30 +1,48 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.0b1)
- * 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.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
-import java.util.*;
+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 javax.swing.*;
+import java.util.StringTokenizer;
+import java.util.Vector;
-import jalview.datamodel.*;
-import jalview.gui.*;
-import jalview.util.MessageManager;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
@@ -84,6 +102,7 @@ public class FileLoader implements Runnable
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
loader.start();
@@ -141,6 +160,7 @@ public class FileLoader implements Runnable
public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
{
this.source = source;
+
file = source.getInFile();
protocol = source.type;
this.format = format;
@@ -217,6 +237,7 @@ public class FileLoader implements Runnable
}
}
+ @Override
public void run()
{
String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
@@ -233,15 +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)
@@ -254,7 +294,7 @@ public class FileLoader implements Runnable
// load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
if (format.equalsIgnoreCase("Jalview"))
{
@@ -265,7 +305,7 @@ 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
{
@@ -285,7 +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)
{
@@ -301,33 +342,94 @@ 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)
{
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
+ sq = sq.getDatasetSequence();
}
- viewport.firePropertyChange("alignment", null, viewport
- .getAlignment().getSequences());
+ if (sq.getAllPDBEntries() != null)
+ {
+ 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)
+ {
+ if (proxyColourScheme != null)
+ {
+ viewport.applyFeaturesStyle(proxyColourScheme);
+ }
+ // 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 (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'
+ // 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);
}
@@ -348,16 +450,23 @@ 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,
- errorMessage, MessageManager.getString("label.error_loading_file"),
+ errorMessage, MessageManager
+ .getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
@@ -379,11 +488,14 @@ 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.getString("label.file_open_error"),
+ Desktop.desktop, MessageManager.formatMessage(
+ "label.problems_opening_file",
+ new String[] { file }), MessageManager
+ .getString("label.file_open_error"),
javax.swing.JOptionPane.WARNING_MESSAGE);
}
});
@@ -398,17 +510,15 @@ public class FileLoader implements Runnable
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
- javax.swing.JOptionPane
- .showInternalMessageDialog(
- Desktop.desktop,
- "Out of memory loading file "
- + file
- + "!!"
- + "\nSee help files for increasing Java Virtual Machine memory.",
- "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);
}
});
}
@@ -459,6 +569,7 @@ public class FileLoader implements Runnable
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
source = null;