X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=88f9ae5743f8895fc620859b529310ef3b9f0c18;hb=230fac58c5afe1843bf7177834fe1bd1d7e6f9d5;hp=cbdfc6ffae9a3ffdfe80e920441194187d794276;hpb=a45774ee31d9f35d4eff46d54d7deab719afb092;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index cbdfc6f..88f9ae5 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,38 +1,59 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ 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 javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.gui.*;
+import jalview.api.ComplexAlignFile;
+import jalview.api.FeatureSettingsModelI;
+import jalview.api.FeaturesDisplayedI;
+import jalview.api.FeaturesSourceI;
+import jalview.bin.Cache;
+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 javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
String file;
- String protocol;
+ DataSourceType protocol;
- String format;
+ FileFormatI format;
- FileParse source = null; // alternative specification of where data comes
+ AlignmentFileI source = null; // alternative specification of where data comes
// from
@@ -66,13 +87,14 @@ public class FileLoader implements Runnable
}
public void LoadFile(AlignViewport viewport, String file,
- String protocol, String format)
+ DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
LoadFile(file, protocol, format);
}
- public void LoadFile(String file, String protocol, String format)
+ public void LoadFile(String file, DataSourceType protocol,
+ FileFormatI format)
{
this.file = file;
this.protocol = protocol;
@@ -82,6 +104,7 @@ public class FileLoader implements Runnable
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
loader.start();
@@ -95,7 +118,7 @@ public class FileLoader implements Runnable
* @param file
* @param protocol
*/
- public void LoadFile(String file, String protocol)
+ public void LoadFile(String file, DataSourceType protocol)
{
LoadFile(file, protocol, null);
}
@@ -104,27 +127,28 @@ public class FileLoader implements Runnable
* Load alignment from (file, protocol) and wait till loaded
*
* @param file
- * @param protocol
+ * @param sourceType
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType)
{
- return LoadFileWaitTillLoaded(file, protocol, null);
+ return LoadFileWaitTillLoaded(file, sourceType, null);
}
/**
* Load alignment from (file, protocol) of type format and wait till loaded
*
* @param file
- * @param protocol
+ * @param sourceType
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
- String format)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType, FileFormatI format)
{
this.file = file;
- this.protocol = protocol;
+ this.protocol = sourceType;
this.format = format;
return _LoadFileWaitTillLoaded();
}
@@ -136,11 +160,13 @@ public class FileLoader implements Runnable
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
+ public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+ FileFormatI format)
{
this.source = source;
+
file = source.getInFile();
- protocol = source.type;
+ protocol = source.getDataSourceType();
this.format = format;
return _LoadFileWaitTillLoaded();
}
@@ -172,13 +198,13 @@ public class FileLoader implements Runnable
public void updateRecentlyOpened()
{
Vector recent = new Vector();
- if (protocol.equals(FormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
// refer to it as.
return;
}
- String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+ String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
String historyItems = jalview.bin.Cache.getProperty(type);
@@ -207,17 +233,18 @@ public class FileLoader implements Runnable
newHistory.append(recent.elementAt(i));
}
- jalview.bin.Cache.setProperty(type, newHistory.toString());
+ Cache.setProperty(type, newHistory.toString());
- if (protocol.equals(FormatAdapter.FILE))
+ if (protocol == DataSourceType.FILE)
{
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
}
}
+ @Override
public void run()
{
- String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+ String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
try
@@ -231,15 +258,32 @@ 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
- // stream and
- // rewind rather
- // than close
+ 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)
+ {
+ 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)
@@ -252,9 +296,9 @@ public class FileLoader implements Runnable
// load
}
loadtime = -System.currentTimeMillis();
- Alignment al = null;
+ AlignmentI al = null;
- if (format.equalsIgnoreCase("Jalview"))
+ if (format == FileFormat.Jalview)
{
if (source != null)
{
@@ -263,13 +307,11 @@ 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
{
String error = AppletFormatAdapter.SUPPORTED_FORMATS;
- if (FormatAdapter.isValidFormat(format))
- {
try
{
if (source != null)
@@ -283,47 +325,105 @@ 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)
{
error = ex.getMessage();
}
- }
- else
+
+ if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
{
- if (format != null && format.length() > 7)
+ // construct and register dataset sequences
+ for (SequenceI sq : al.getSequences())
{
- // ad hoc message in format.
- error = format + "\n" + error;
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getAllPDBEntries() != null)
+ {
+ for (PDBEntry pdbe : sq.getAllPDBEntries())
+ {
+ // register PDB entries with desktop's structure selection
+ // manager
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance).registerPDBEntry(pdbe);
+ }
+ }
}
- }
- if ((al != null) && (al.getHeight() > 0))
- {
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
if (viewport != null)
{
- 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("Successfully loaded file "
- + title);
+ // otherwise construct the alignFrame
- if (!protocol.equals(AppletFormatAdapter.PASTE))
+ 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 == DataSourceType.PASTE))
+ {
alignFrame.setFileName(file, format);
+ }
+ if (proxyColourScheme != null)
+ {
+ alignFrame.getViewport()
+ .applyFeaturesStyle(proxyColourScheme);
+ }
+ alignFrame.statusBar.setText(MessageManager.formatMessage(
+ "label.successfully_loaded_file",
+ new String[] { title }));
- 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
{
@@ -341,16 +441,23 @@ 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, "Error loading file",
+ errorMessage, MessageManager
+ .getString("label.error_loading_file"),
JOptionPane.WARNING_MESSAGE);
}
});
@@ -372,11 +479,14 @@ public class FileLoader implements Runnable
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
javax.swing.JOptionPane.showInternalMessageDialog(
- Desktop.desktop, "Encountered problems opening " + file
- + "!!", "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);
}
});
@@ -391,17 +501,15 @@ 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);
}
});
}
@@ -452,6 +560,7 @@ public class FileLoader implements Runnable
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
source = null;