X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=a64582dc1a9eaca84d8125bbaae2c19629cf1052;hb=b87512d6e28a2a93ea2f08dcfbee320856c5c8de;hp=3ad74c71ff2bed320f08579b9f1081459f15751f;hpb=483e7163b1fb8d4bcb9393014816c944befce328;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3ad74c7..a64582d 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -27,35 +27,57 @@ import jalview.api.FeaturesSourceI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.ColumnSelection;
+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.Jalview2XML;
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 java.util.StringTokenizer;
-import java.util.Vector;
+import jalview.util.Platform;
+import jalview.ws.utils.UrlDownloadClient;
+
+import java.awt.Dimension;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.util.ArrayList;
+import java.util.List;
import javax.swing.SwingUtilities;
public class FileLoader implements Runnable
{
+ private static final String DEFAULT_FILE_FORMAT_PROPERTY = "DEFAULT_FILE_FORMAT";
+
+ private static final String RECENT_URL_PROPERTY = "RECENT_URL";
+
+ private static final String RECENT_FILE_PROPERTY = "RECENT_FILE";
+
+ private static final String TAB = "\t";
+
+ /*
+ * maximum number of items in file/url history lists;
+ * pseudo-constant (not final) so amendable by Groovy if wanted
+ */
+ private static int MAX_HISTORY = 11;
+
String file;
DataSourceType protocol;
FileFormatI format;
- AlignmentFileI source = null; // alternative specification of where data comes
-
- // from
+ AlignmentFileReaderI source; // alternative specification of where data
+ // comes from
AlignViewport viewport;
@@ -67,6 +89,8 @@ public class FileLoader implements Runnable
boolean raiseGUI = true;
+ private File selectedFile;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
@@ -86,16 +110,90 @@ public class FileLoader implements Runnable
this.raiseGUI = raiseGUI;
}
+ /**
+ * It is critical that all these fields are set, as this instance is reused.
+ *
+ * @param source
+ * @param file
+ * @param inFile
+ * @param dataSourceType
+ * @param format
+ */
+ private void setFileFields(AlignmentFileReaderI source, File file,
+ String inFile, DataSourceType dataSourceType, FileFormatI format)
+ {
+ this.source = source;
+ this.file = inFile;
+ this.selectedFile = file;
+ this.protocol = dataSourceType;
+ this.format = format;
+ }
+
+
+ /**
+ * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+ * JavaScript
+ *
+ * @param viewport
+ * @param file
+ * @param protocol
+ * @param format
+ */
+ @Deprecated
public void LoadFile(AlignViewport viewport, String file,
DataSourceType protocol, FileFormatI format)
{
- this.viewport = viewport;
- LoadFile(file, protocol, format);
+ if (viewport != null)
+ {
+ this.viewport = viewport;
+ }
+ loadFile(file, protocol, format);
}
+ public void LoadFile(AlignViewport viewport, File file,
+ DataSourceType protocol, FileFormatI format)
+ {
+ loadFile(viewport, file, protocol, format);
+ }
+
+ /**
+ * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+ * JavaScript
+ *
+ * @param file
+ * @param protocol
+ * @param format
+ */
+ @Deprecated
public void LoadFile(String file, DataSourceType protocol,
FileFormatI format)
{
+ loadFile(file, protocol, format);
+ }
+
+ /**
+ * necessary to use Object here in order to pass the file data
+ *
+ * @param viewport
+ * @param file
+ * File preferably to String
+ * @param protocol
+ * @param format
+ */
+ public void loadFile(AlignViewport viewport, File file,
+ DataSourceType protocol, FileFormatI format)
+ {
+ if (viewport != null)
+ {
+ this.viewport = viewport;
+ }
+ this.selectedFile = file;
+ loadFile(selectedFile.getPath(), protocol, format);
+ }
+
+ private void loadFile(String file, DataSourceType protocol,
+ FileFormatI format)
+ {
this.file = file;
this.protocol = protocol;
this.format = format;
@@ -113,23 +211,13 @@ public class FileLoader implements Runnable
}
/**
- * 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
*/
+ @Deprecated
public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType)
{
@@ -144,80 +232,84 @@ public class FileLoader implements Runnable
* @param format
* @return alignFrame constructed from file contents
*/
+ @Deprecated
public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType, FileFormatI format)
{
- this.file = file;
- this.protocol = sourceType;
- this.format = format;
- return _LoadFileWaitTillLoaded();
+ setFileFields(null, null, file, sourceType, format);
+ return _loadFileWaitTillLoaded();
}
/**
- * Load alignment from FileParse source of type format and wait till loaded
+ * Load alignment from (file, protocol) of type format and wait till loaded
*
- * @param source
+ * @param fileObject
+ * @param sourceType
* @param format
* @return alignFrame constructed from file contents
+ * @throws NullPointerException
+ * if {@code file} is null
*/
- public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
- FileFormatI format)
+ public AlignFrame loadFileWaitTillLoaded(File fileObject,
+ DataSourceType sourceType, FileFormatI format)
{
- this.source = source;
-
- file = source.getInFile();
- protocol = source.getDataSourceType();
- this.format = format;
- return _LoadFileWaitTillLoaded();
+ setFileFields(null, fileObject, fileObject.getPath(), sourceType, format);
+ return _loadFileWaitTillLoaded();
}
/**
- * start thread and wait until finished, then return the alignFrame that's
- * (hopefully) been read.
+ * Runs the 'run' method (in this thread), then returns the alignFrame that
+ * (hopefully) has been constructed
*
* @return
*/
- protected AlignFrame _LoadFileWaitTillLoaded()
+ private AlignFrame _loadFileWaitTillLoaded()
{
- Thread loader = new Thread(this);
- loader.start();
-
- while (loader.isAlive())
- {
- try
- {
- Thread.sleep(500);
- } catch (Exception ex)
- {
- }
- }
-
+ this.run();
return alignFrame;
}
+ /**
+ * Updates the Jalview properties file to add the last file or URL read to the
+ * tab-separated list in property RECENT_FILE or RECENT_URL respectively. The
+ * property is created if it does not already exist. The new entry is added as
+ * the first item (without duplication). If the list exceeds some maximum
+ * length (currently 10 entries), the oldest (last) entry is dropped.
+ *
+ * Files read from the temporary file directory are not added to the property.
+ *
+ * Property DEFAULT_FILE_FORMAT (e.g. "Fasta" etc) is also set if currently
+ * reading from file.
+ */
public void updateRecentlyOpened()
{
- Vector recent = new Vector();
+ List recent = new ArrayList<>();
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 == DataSourceType.FILE ? "RECENT_FILE"
- : "RECENT_URL";
-
- String historyItems = jalview.bin.Cache.getProperty(type);
+ // BH logic change here just includes ignoring file==null
+ 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_PROPERTY
+ : RECENT_URL_PROPERTY;
- StringTokenizer st;
+ String historyItems = Cache.getProperty(type);
+ // BH simpler coding
if (historyItems != null)
{
- st = new StringTokenizer(historyItems, "\t");
+ String[] tokens = historyItems.split("\\t");
- while (st.hasMoreTokens())
+ for (String token : tokens)
{
- recent.addElement(st.nextElement().toString().trim());
+ recent.add(token.trim());
}
}
@@ -226,32 +318,33 @@ public class FileLoader implements Runnable
recent.remove(file);
}
- StringBuffer newHistory = new StringBuffer(file);
- for (int i = 0; i < recent.size() && i < 10; i++)
+ StringBuilder newHistory = new StringBuilder(file);
+ for (int i = 0; i < recent.size() && i < MAX_HISTORY - 1; i++)
{
- newHistory.append("\t");
- newHistory.append(recent.elementAt(i));
+ newHistory.append(TAB);
+ newHistory.append(recent.get(i));
}
Cache.setProperty(type, newHistory.toString());
if (protocol == DataSourceType.FILE)
{
- Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
+ Cache.setProperty(DEFAULT_FILE_FORMAT_PROPERTY, format.getName());
}
}
@Override
public void run()
{
- String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
+ String title = protocol == DataSourceType.PASTE
+ ? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
try
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.startLoading(file);
+ Desktop.getInstance().startLoading(file);
}
if (format == null)
{
@@ -261,6 +354,9 @@ public class FileLoader implements Runnable
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);
@@ -270,16 +366,15 @@ public class FileLoader implements Runnable
if (format == null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
System.err.println("The input file \"" + file
+ "\" has null or unidentifiable data content!");
if (!Jalview.isHeadlessMode())
{
- JvOptionPane.showInternalMessageDialog(
- Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.getString("label.couldnt_read_data")
+ " in " + file + "\n"
- + AppletFormatAdapter.SUPPORTED_FORMATS,
+ + AppletFormatAdapter.getSupportedFormats(),
MessageManager.getString("label.couldnt_read_data"),
JvOptionPane.WARNING_MESSAGE);
}
@@ -287,7 +382,7 @@ public class FileLoader implements Runnable
}
// TODO: cache any stream datasources as a temporary file (eg. PDBs
// retrieved via URL)
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
System.gc();
memused = (rt.maxMemory() - rt.totalMemory() + rt.freeMemory()); // free
@@ -303,35 +398,69 @@ public class FileLoader implements Runnable
if (source != null)
{
// 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.");
+ System.err.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);
+ // BH 2018 switch to File object here instead of filename
+ Platform.timeCheck(null, Platform.TIME_MARK);
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
+ Platform.timeCheck("JVP loaded", Platform.TIME_MARK);
+
}
else
{
- String error = AppletFormatAdapter.SUPPORTED_FORMATS;
- try
+ String error = AppletFormatAdapter.getSupportedFormats();
+ try
+ {
+ if (source != null)
{
- if (source != null)
- {
- // read from the provided source
+ // read from the provided source
al = new FormatAdapter().readFromFile(source, format);
+ }
+ else
+ {
+
+ // 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];
+ int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+ : System.getProperty("file.separator"));
+ String urlLeafName = file.substring(pt,
+ file.lastIndexOf("."));
+ String tempStructureFileStr = createNamedJvTempFile(
+ urlLeafName, structExt);
+
+ // BH - switching to File object here so as to hold on to the
+ // bytes array directly
+ File tempFile = new File(tempStructureFileStr);
+ UrlDownloadClient.download(file, tempFile);
+
+ al = fa.readFile(tempFile, DataSourceType.FILE,
+ format);
+ source = fa.getAlignFile();
}
else
{
-
- // open a new source and read from it
- FormatAdapter fa = new FormatAdapter();
- al = fa.readFile(file, protocol, format);
+ 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();
}
+ } catch (java.io.IOException ex)
+ {
+ error = ex.getMessage();
+ }
if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
{
@@ -348,8 +477,8 @@ public class FileLoader implements Runnable
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(pdbe);
+ Desktop.getStructureSelectionManager()
+ .registerPDBEntry(pdbe);
}
}
}
@@ -371,8 +500,8 @@ public class FileLoader implements Runnable
if (source instanceof ComplexAlignFile)
{
- ColumnSelection colSel = ((ComplexAlignFile) source)
- .getColumnSelection();
+ HiddenColumns colSel = ((ComplexAlignFile) source)
+ .getHiddenColumns();
SequenceI[] hiddenSeqs = ((ComplexAlignFile) source)
.getHiddenSequences();
String colourSchemeName = ((ComplexAlignFile) source)
@@ -384,8 +513,8 @@ public class FileLoader implements Runnable
alignFrame.getViewport().setFeaturesDisplayed(fd);
alignFrame.getViewport().setShowSequenceFeatures(
((ComplexAlignFile) source).isShowSeqFeatures());
- ColourSchemeI cs = ColourSchemeMapper.getJalviewColourScheme(
- colourSchemeName, al);
+ ColourSchemeI cs = ColourSchemeMapper
+ .getJalviewColourScheme(colourSchemeName, al);
if (cs != null)
{
alignFrame.changeColour(cs);
@@ -404,15 +533,16 @@ public class FileLoader implements Runnable
if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
}
if (proxyColourScheme != null)
{
alignFrame.getViewport()
.applyFeaturesStyle(proxyColourScheme);
}
- alignFrame.statusBar.setText(MessageManager.formatMessage(
- "label.successfully_loaded_file",
- new String[] { title }));
+ alignFrame.setStatus(MessageManager.formatMessage(
+ "label.successfully_loaded_file", new String[]
+ { title }));
if (raiseGUI)
{
@@ -421,14 +551,19 @@ public class FileLoader implements Runnable
// 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,
+
+
+ Dimension dim = Platform.getDimIfEmbedded(alignFrame,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+ alignFrame.setSize(dim);
+ Desktop.addInternalFrame(alignFrame, title, dim.width,
+ dim.height);
}
try
{
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ alignFrame.setMaximum(jalview.bin.Cache
+ .getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
@@ -436,27 +571,25 @@ public class FileLoader implements Runnable
}
else
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
- final String errorMessage = MessageManager
- .getString("label.couldnt_load_file")
- + " "
- + title
- + "\n" + error;
+ 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)
+ if (raiseGUI && Desktop.getDesktopPane() != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
- errorMessage, MessageManager
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ errorMessage,
+ MessageManager
.getString("label.error_loading_file"),
JvOptionPane.WARNING_MESSAGE);
}
@@ -482,11 +615,11 @@ public class FileLoader implements 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.showInternalMessageDialog(Desktop.getDesktopPane(),
+ MessageManager.formatMessage(
+ "label.problems_opening_file", new String[]
+ { file }),
+ MessageManager.getString("label.file_open_error"),
JvOptionPane.WARNING_MESSAGE);
}
});
@@ -504,11 +637,11 @@ public class FileLoader implements Runnable
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(
- Desktop.desktop, MessageManager.formatMessage(
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
- { file }), MessageManager
- .getString("label.out_of_memory"),
+ { file }),
+ MessageManager.getString("label.out_of_memory"),
JvOptionPane.WARNING_MESSAGE);
}
});
@@ -526,7 +659,7 @@ public class FileLoader implements Runnable
// memory
// after
// load
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
if (alignFrame != null)
{
@@ -548,25 +681,53 @@ public class FileLoader implements Runnable
}
}
// remove the visual delay indicator
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
}
- /*
- * (non-Javadoc)
+ /**
+ * This method creates the file -
+ * {tmpdir}/jalview/{current_timestamp}/fileName.exetnsion using the supplied
+ * file name and extension
*
- * @see java.lang.Object#finalize()
+ * @param fileName
+ * the name of the temp file to be created
+ * @param extension
+ * the extension of the temp file to be created
+ * @return
*/
- @Override
- protected void finalize() throws Throwable
+ private static String createNamedJvTempFile(String fileName,
+ String extension) throws IOException
{
- source = null;
- alignFrame = null;
- viewport = null;
- super.finalize();
+ 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();
+ }
+
+ /**
+ *
+ * @param file a File, or a String which is a name of a file
+ * @return
+ * @throws FileNotFoundException
+ */
+ public static BufferedReader getBufferedReader(Object file) throws FileNotFoundException {
+ if (file instanceof String)
+ {
+ return new BufferedReader(new FileReader((String) file));
+ }
+ byte[] bytes = Platform.getFileBytes((File) file);
+ if (bytes != null)
+ {
+ return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
+ }
+ return new BufferedReader(new FileReader((File) file));
}
}