X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2FFileLoader.java;h=a64582dc1a9eaca84d8125bbaae2c19629cf1052;hb=b87512d6e28a2a93ea2f08dcfbee320856c5c8de;hp=3afbaad0a296e227f23b998ff0796efd50f208a0;hpb=994a386819147f73fa47f3c29ba6c438f0e4b15a;p=jalview.git
diff --git a/src/jalview/io/FileLoader.java b/src/jalview/io/FileLoader.java
index 3afbaad..a64582d 100755
--- a/src/jalview/io/FileLoader.java
+++ b/src/jalview/io/FileLoader.java
@@ -37,29 +37,47 @@ 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.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.util.StringTokenizer;
-import java.util.Vector;
+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;
- AlignmentFileReaderI source = null; // alternative specification of where data
- // comes
-
- // from
+ AlignmentFileReaderI source; // alternative specification of where data
+ // comes from
AlignViewport viewport;
@@ -71,6 +89,8 @@ public class FileLoader implements Runnable
boolean raiseGUI = true;
+ private File selectedFile;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
@@ -90,16 +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;
@@ -117,23 +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)
{
@@ -148,89 +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(AlignmentFileReaderI 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)
- {
- System.out.println(
- "Exception caught while waiting for FileLoader thread");
- ex.printStackTrace();
- }
- }
-
+ 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;
}
- if (file != null
- && file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
+ // 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"
- : "RECENT_URL";
-
- String historyItems = jalview.bin.Cache.getProperty(type);
+ 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());
}
}
@@ -239,18 +318,18 @@ 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.getName());
+ Cache.setProperty(DEFAULT_FILE_FORMAT_PROPERTY, format.getName());
}
}
@@ -263,9 +342,9 @@ public class FileLoader implements Runnable
Runtime rt = Runtime.getRuntime();
try
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.startLoading(file);
+ Desktop.getInstance().startLoading(file);
}
if (format == null)
{
@@ -275,6 +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);
@@ -284,12 +366,12 @@ 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.getSupportedFormats(),
@@ -300,7 +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
@@ -320,7 +402,11 @@ public class FileLoader implements Runnable
"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
{
@@ -342,21 +428,32 @@ public class FileLoader implements Runnable
if (downloadStructureFile)
{
String structExt = format.getExtensions().split(",")[0];
- String urlLeafName = file.substring(
- file.lastIndexOf(
- System.getProperty("file.separator")),
+ int pt = file.lastIndexOf(file.indexOf('/') >= 0 ? "/"
+ : System.getProperty("file.separator"));
+ String urlLeafName = file.substring(pt,
file.lastIndexOf("."));
String tempStructureFileStr = createNamedJvTempFile(
urlLeafName, structExt);
- UrlDownloadClient.download(file, tempStructureFileStr);
- al = fa.readFile(tempStructureFileStr, DataSourceType.FILE,
+
+ // 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
{
- 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.
}
}
@@ -380,8 +477,7 @@ public class FileLoader implements Runnable
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(pdbe);
}
}
@@ -437,6 +533,7 @@ public class FileLoader implements Runnable
if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
}
if (proxyColourScheme != null)
{
@@ -454,8 +551,13 @@ 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
@@ -469,23 +571,23 @@ 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;
// 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,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
errorMessage,
MessageManager
.getString("label.error_loading_file"),
@@ -513,7 +615,7 @@ public class FileLoader implements Runnable
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.problems_opening_file", new String[]
{ file }),
@@ -535,7 +637,7 @@ public class FileLoader implements Runnable
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }),
@@ -557,7 +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)
{
@@ -579,9 +681,9 @@ public class FileLoader implements Runnable
}
}
// remove the visual delay indicator
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
}
@@ -609,4 +711,23 @@ public class FileLoader implements Runnable
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));
+ }
+
}