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 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.StringTokenizer;
import java.util.Vector;
public class FileLoader implements Runnable
{
+ private File selectedFile;
+
String file;
DataSourceType protocol;
FileFormatI format;
- AlignmentFileReaderI source = null; // alternative specification of where data
- // comes
+ AlignmentFileReaderI source; // alternative specification of where data
+ // comes from
- // from
+ /**
+ * 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;
+ }
AlignViewport viewport;
this.raiseGUI = raiseGUI;
}
- public void LoadFile(AlignViewport viewport, String file,
+ 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, DataSourceType protocol,
+ public void loadFile(String file, DataSourceType protocol,
FileFormatI format)
{
this.file = file;
*/
public void LoadFile(String file, DataSourceType protocol)
{
- LoadFile(file, protocol, null);
+ loadFile(file, protocol, null);
}
/**
public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType)
{
- return LoadFileWaitTillLoaded(file, sourceType, null);
+ return loadFileWaitTillLoaded(file, sourceType, null);
}
/**
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file,
+ 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 (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)
+ {
+ setFileFields(null, file, null, sourceType, format);
+ return _loadFileWaitTillLoaded();
}
/**
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(AlignmentFileReaderI source,
+ public AlignFrame loadFileWaitTillLoaded(AlignmentFileReaderI source,
FileFormatI format)
{
- this.source = source;
-
- file = source.getInFile();
- protocol = source.getDataSourceType();
- this.format = format;
- return _LoadFileWaitTillLoaded();
+ setFileFields(source, null, source.getInFile(),
+ source.getDataSourceType(), 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 return the alignFrame that's
+ * (hopefully) been read
*
* @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;
}
public void updateRecentlyOpened()
{
- Vector recent = new Vector();
+ Vector<String> recent = new Vector<>();
if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
- String historyItems = jalview.bin.Cache.getProperty(type);
+ String historyItems = Cache.getProperty(type);
StringTokenizer st;
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ recent.addElement(st.nextToken().trim());
}
}
Runtime rt = Runtime.getRuntime();
try
{
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.startLoading(file);
+ Desktop.getInstance().startLoading(file);
}
if (format == 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);
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(),
}
// 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
"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
{
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
+ // .秘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.
}
}
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager
- .getStructureSelectionManager(Desktop.instance)
+ Desktop.getStructureSelectionManager()
.registerPDBEntry(pdbe);
}
}
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(
+ alignFrame.setStatus(MessageManager.formatMessage(
"label.successfully_loaded_file", new String[]
{ title }));
// 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
}
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"),
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"label.problems_opening_file", new String[]
{ file }),
@Override
public void run()
{
- JvOptionPane.showInternalMessageDialog(Desktop.desktop,
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
MessageManager.formatMessage(
"warn.out_of_memory_loading_file", new String[]
{ file }),
// memory
// after
// load
- if (Desktop.desktop != null && Desktop.desktop.isShowMemoryUsage())
+ if (Desktop.getDesktopPane() != null && Desktop.getDesktopPane().isShowMemoryUsage())
{
if (alignFrame != null)
{
}
}
// remove the visual delay indicator
- if (Desktop.instance != null)
+ if (Desktop.getInstance() != null)
{
- Desktop.instance.stopLoading();
+ Desktop.getInstance().stopLoading();
}
}
return tempStructFile.toString();
}
- /*
- * (non-Javadoc)
+ /**
*
- * @see java.lang.Object#finalize()
+ * @param file a File, or a String which is a name of a file
+ * @return
+ * @throws FileNotFoundException
*/
- @Override
- protected void finalize() throws Throwable
- {
- source = null;
- alignFrame = null;
- viewport = null;
- super.finalize();
+ 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));
}
}
git://source.jalview.org / jalview.git / blobdiff