X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=cbdfc6ffae9a3ffdfe80e920441194187d794276;hb=232fd33251ad898065d090e99efa717b56cbc5e8;hp=6310cc456573b37a7ddc8aa70c6f9ea932daf965;hpb=a4fca83856b96df2fe8701bb5cc14c8d1d0a6b09;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 6310cc4..c7c1d71 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -1,48 +1,110 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
+ * 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.
- *
- * This program 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
-
package jalview.io;
-import java.util.*;
+import java.io.File;
+import java.io.IOException;
+import java.util.StringTokenizer;
+import java.util.Vector;
+
+import javax.swing.SwingUtilities;
+
+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.HiddenColumns;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignFrame;
+import jalview.gui.AlignViewport;
+import jalview.gui.Desktop;
+import jalview.gui.JvOptionPane;
+import jalview.json.binding.biojson.v1.ColourSchemeMapper;
+import jalview.project.Jalview2XML;
+import jalview.schemes.ColourSchemeI;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.MessageManager;
+import jalview.ws.utils.UrlDownloadClient;
+
+public class FileLoader implements Runnable
+{
+ String file;
-import javax.swing.*;
+ DataSourceType protocol;
-import jalview.datamodel.*;
-import jalview.gui.*;
+ FileFormatI format;
+
+ AlignmentFileReaderI source = null; // alternative specification of where data
+ // comes
+
+ // from
-public class FileLoader
- implements Runnable
-{
- String file;
- String protocol;
- String format;
AlignViewport viewport;
+
AlignFrame alignFrame;
- public void LoadFile(AlignViewport viewport, String file, String protocol,
- String format)
+ long loadtime;
+
+ long memused;
+
+ boolean raiseGUI = true;
+
+ private File selectedFile;
+
+ /**
+ * default constructor always raised errors in GUI dialog boxes
+ */
+ public FileLoader()
+ {
+ this(true);
+ }
+
+ /**
+ * construct a Fileloader that may raise errors non-interactively
+ *
+ * @param raiseGUI
+ * true if errors are to be raised as GUI dialog boxes
+ */
+ public FileLoader(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ public void LoadFile(AlignViewport viewport, Object file,
+ DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
- LoadFile(file, protocol, format);
+ if (file instanceof File) {
+ this.selectedFile = (File) file;
+ file = selectedFile.getPath();
+ }
+ LoadFile(file.toString(), 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;
@@ -52,6 +114,7 @@ public class FileLoader
SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
loader.start();
@@ -59,37 +122,115 @@ public class FileLoader
});
}
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
- String format)
+ /**
+ * Load a (file, protocol) source of unknown type
+ *
+ * @param file
+ * @param protocol
+ */
+ public void LoadFile(String file, DataSourceType protocol)
+ {
+ LoadFile(file, protocol, null);
+ }
+
+ /**
+ * Load alignment from (file, protocol) and wait till loaded
+ *
+ * @param file
+ * @param sourceType
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType)
+ {
+ return LoadFileWaitTillLoaded(file, sourceType, null);
+ }
+
+ /**
+ * Load alignment from (file, protocol) of type format and wait till loaded
+ *
+ * @param file
+ * @param sourceType
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType, FileFormatI format)
{
this.file = file;
- this.protocol = protocol;
+ this.protocol = sourceType;
this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
- Thread loader = new Thread(this);
- loader.start();
+ /**
+ * Load alignment from (file, protocol) of type format and wait till loaded
+ *
+ * @param file
+ * @param sourceType
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(File file,
+ DataSourceType sourceType, FileFormatI format)
+ {
+ this.selectedFile = file;
+ this.file = file.getPath();
+ this.protocol = sourceType;
+ this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
- while (loader.isAlive())
- {
- try
- {
- Thread.sleep(500);
- }
- catch (Exception ex)
- {}
- }
+ /**
+ * Load alignment from FileParse source of type format and wait till loaded
+ *
+ * @param source
+ * @param format
+ * @return alignFrame constructed from file contents
+ */
+ public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
+ FileFormatI format)
+ {
+ this.source = source;
+
+ file = source.getInFile();
+ protocol = source.getDataSourceType();
+ this.format = format;
+ return _LoadFileWaitTillLoaded();
+ }
+
+ /**
+ * runs the 'run' method (in this thread), then return the alignFrame that's
+ * (hopefully) been read
+ *
+ * @return
+ */
+ protected AlignFrame _LoadFileWaitTillLoaded()
+ {
+ this.run();
return alignFrame;
}
public void updateRecentlyOpened()
{
- Vector recent = new Vector();
-
- String type = protocol.equals(FormatAdapter.FILE)
- ? "RECENT_FILE" : "RECENT_URL";
+ Vector recent = new Vector<>();
+ if (protocol == DataSourceType.PASTE)
+ {
+ // do nothing if the file was pasted in as text... there is no filename to
+ // refer to it as.
+ return;
+ }
+ if (file != null
+ && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+ {
+ // ignore files loaded from the system's temporary directory
+ return;
+ }
+ String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
+ : "RECENT_URL";
- String historyItems = jalview.bin.Cache.getProperty(type);
+ String historyItems = Cache.getProperty(type);
StringTokenizer st;
@@ -99,7 +240,7 @@ public class FileLoader
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ recent.addElement(st.nextToken().trim());
}
}
@@ -115,87 +256,236 @@ public class FileLoader
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.getName());
}
}
+ @Override
public void run()
{
- String title = protocol.equals(AppletFormatAdapter.PASTE)
- ? "Copied From Clipboard" : file;
-
+ String title = protocol == DataSourceType.PASTE
+ ? "Copied From Clipboard"
+ : file;
+ Runtime rt = Runtime.getRuntime();
try
{
if (Desktop.instance != null)
{
Desktop.instance.startLoading(file);
}
+ if (format == null)
+ {
+ // 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
+ }
+ else if (selectedFile != null) {
+ format = new IdentifyFile().identify(selectedFile, protocol);
+ }
+ else
+ {
+ format = new IdentifyFile().identify(file, protocol);
+ }
- Alignment al = null;
+ }
- if (format.equalsIgnoreCase("Jalview"))
+ if (format == null)
{
- alignFrame = new Jalview2XML().LoadJalviewAlign(file);
+ Desktop.instance.stopLoading();
+ System.err.println("The input file \"" + file
+ + "\" has null or unidentifiable data content!");
+ if (!Jalview.isHeadlessMode())
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.getString("label.couldnt_read_data")
+ + " in " + file + "\n"
+ + AppletFormatAdapter.getSupportedFormats(),
+ MessageManager.getString("label.couldnt_read_data"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ return;
}
- else
+ // TODO: cache any stream datasources as a temporary file (eg. PDBs
+ // retrieved via URL)
+ if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
{
- String error = AppletFormatAdapter.SUPPORTED_FORMATS;
+ System.gc();
+ memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
+ // memory
+ // before
+ // load
+ }
+ loadtime = -System.currentTimeMillis();
+ AlignmentI al = null;
- if (FormatAdapter.isValidFormat(format))
+ if (FileFormat.Jalview.equals(format))
+ {
+ if (source != null)
{
- try
- {
- al = new FormatAdapter().readFile(file, protocol, format);
- }
- catch (java.io.IOException ex)
+ // Tell the user (developer?) that this is going to cause a problem
+ System.err.println(
+ "IMPLEMENTATION ERROR: Cannot read consecutive Jalview XML projects from a stream.");
+ // We read the data anyway - it might make sense.
+ }
+ // BH 2018 switch to File object here instead of filename
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+ }
+ else
+ {
+ String error = AppletFormatAdapter.getSupportedFormats();
+ try
+ {
+ if (source != null)
{
- error = ex.getMessage();
+ // read from the provided source
+ al = new FormatAdapter().readFromFile(source, format);
}
- } else {
- if (format!=null && format.length()>7)
+ else
{
- // ad hoc message in format.
- error = format +"\n"+error;
+
+ // open a new source and read from it
+ FormatAdapter fa = new FormatAdapter();
+ boolean downloadStructureFile = format.isStructureFile()
+ && protocol.equals(DataSourceType.URL);
+ if (downloadStructureFile)
+ {
+ String structExt = format.getExtensions().split(",")[0];
+ String urlLeafName = file.substring(
+ file.lastIndexOf(
+ System.getProperty("file.separator")),
+ file.lastIndexOf("."));
+ String tempStructureFileStr = createNamedJvTempFile(
+ urlLeafName, structExt);
+
+ // BH - switching to File object here so as to hold
+ // ._bytes array directly
+ File tempFile = new File(tempStructureFileStr);
+ UrlDownloadClient.download(file, tempFile);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE,
+ format);
+ source = fa.getAlignFile();
+ }
+ else
+ {
+ if (selectedFile == null) {
+ al = fa.readFile(file, protocol, format);
+
+ } else {
+ al = fa.readFile(selectedFile, protocol, format);
+ }
+ source = fa.getAlignFile(); // keep reference for later if
+
+ // necessary.
+ }
}
+ } catch (java.io.IOException ex)
+ {
+ error = ex.getMessage();
}
- 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())
{
- for (int i = 0; i < al.getHeight(); i++)
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ if (sq.getAllPDBEntries() != null)
{
- viewport.getAlignment().addSequence(al.getSequenceAt(i));
+ for (PDBEntry pdbe : sq.getAllPDBEntries())
+ {
+ // register PDB entries with desktop's structure selection
+ // manager
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(pdbe);
+ }
}
- viewport.firePropertyChange("alignment", null,
- viewport.getAlignment().getSequences());
+ }
+ FeatureSettingsModelI proxyColourScheme = source
+ .getFeatureColourScheme();
+ if (viewport != null)
+ {
+ // append to existing alignment
+ viewport.addAlignment(al, title);
+ viewport.applyFeaturesStyle(proxyColourScheme);
}
else
{
- alignFrame = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
+ // otherwise construct the alignFrame
- alignFrame.statusBar.setText("Successfully loaded file " + title);
-
- if (!protocol.equals(AppletFormatAdapter.PASTE))
+ if (source instanceof ComplexAlignFile)
+ {
+ HiddenColumns colSel = ((ComplexAlignFile) source)
+ .getHiddenColumns();
+ 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);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+ }
+ if (proxyColourScheme != null)
+ {
+ alignFrame.getViewport()
+ .applyFeaturesStyle(proxyColourScheme);
+ }
+ alignFrame.setStatus(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
{
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
- }
- catch (java.beans.PropertyVetoException ex)
+ alignFrame.setMaximum(jalview.bin.Cache
+ .getDefault("SHOW_FULLSCREEN", false));
+ } catch (java.beans.PropertyVetoException ex)
{
}
}
@@ -207,46 +497,111 @@ public class FileLoader
Desktop.instance.stopLoading();
}
- final String errorMessage = "Couldn't load file " + title + "\n" +
- error;
-
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ 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)
{
- public void run()
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage,
- "Error loading file",
- JOptionPane.WARNING_MESSAGE);
- }
- });
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ errorMessage,
+ MessageManager
+ .getString("label.error_loading_file"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println(errorMessage);
+ }
}
}
updateRecentlyOpened();
- }
- catch (OutOfMemoryError er)
+ } catch (Exception er)
{
-
+ System.err.println("Exception whilst opening file '" + file);
er.printStackTrace();
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "label.problems_opening_file", new String[]
+ { file }),
+ MessageManager.getString("label.file_open_error"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
alignFrame = null;
+ } catch (OutOfMemoryError er)
+ {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
+ er.printStackTrace();
+ alignFrame = null;
+ if (raiseGUI)
{
- public void run()
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
{
- 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);
- }
- });
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ MessageManager.formatMessage(
+ "warn.out_of_memory_loading_file", new String[]
+ { file }),
+ MessageManager.getString("label.out_of_memory"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ System.err.println("Out of memory loading file " + file + "!!");
+
}
+ loadtime += System.currentTimeMillis();
+ // TODO: Estimate percentage of memory used by a newly loaded alignment -
+ // warn if more memory will be needed to work with it
+ // System.gc();
+ memused = memused
+ - (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // difference
+ // in free
+ // memory
+ // after
+ // load
+ if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ {
+ if (alignFrame != null)
+ {
+ AlignmentI al = alignFrame.getViewport().getAlignment();
- System.gc();
+ System.out.println("Loaded '" + title + "' in "
+ + (loadtime / 1000.0) + "s, took an additional "
+ + (1.0 * memused / (1024.0 * 1024.0)) + " MB ("
+ + al.getHeight() + " seqs by " + al.getWidth() + " cols)");
+ }
+ else
+ {
+ // report that we didn't load anything probably due to an out of memory
+ // error
+ System.out.println("Failed to load '" + title + "' in "
+ + (loadtime / 1000.0) + "s, took an additional "
+ + (1.0 * memused / (1024.0 * 1024.0))
+ + " MB (alignment is null)");
+ }
+ }
+ // remove the visual delay indicator
if (Desktop.instance != null)
{
Desktop.instance.stopLoading();
@@ -254,4 +609,27 @@ public class FileLoader
}
+ /**
+ * This method creates the file -
+ * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+ * file name and extension
+ *
+ * @param fileName
+ * the name of the temp file to be created
+ * @param extension
+ * the extension of the temp file to be created
+ * @return
+ */
+ private static String createNamedJvTempFile(String fileName,
+ String extension) throws IOException
+ {
+ String seprator = System.getProperty("file.separator");
+ String jvTempDir = System.getProperty("java.io.tmpdir") + "jalview"
+ + seprator + System.currentTimeMillis();
+ File tempStructFile = new File(
+ jvTempDir + seprator + fileName + "." + extension);
+ tempStructFile.mkdirs();
+ return tempStructFile.toString();
+ }
+
}