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.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;
boolean raiseGUI = true;
+ private File selectedFile;
+
/**
* default constructor always raised errors in GUI dialog boxes
*/
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,
}
/**
+ * 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();
+ }
+
+ /**
* Load alignment from FileParse source of type format and wait till loaded
*
* @param source
}
/**
- * 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()
{
- 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
// 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;
while (st.hasMoreTokens())
{
- recent.addElement(st.nextElement().toString().trim());
+ recent.addElement(st.nextToken().trim());
}
}
@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)
{
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
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
+ alignFrame = new Jalview2XML(raiseGUI).loadJalviewAlign(selectedFile == null ? file : selectedFile);
}
else
{
// open a new source and read from it
FormatAdapter fa = new FormatAdapter();
- al = fa.readFile(file, protocol, format);
- source = fa.getAlignFile(); // keep reference for later if
- // necessary.
+ 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)
{
{
// register PDB entries with desktop's structure selection
// manager
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(pdbe);
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.getInstance())
+ .registerPDBEntry(pdbe);
}
}
}
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);
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)
{
try
{
- alignFrame.setMaximum(jalview.bin.Cache.getDefault(
- "SHOW_FULLSCREEN", false));
+ alignFrame.setMaximum(jalview.bin.Cache
+ .getDefault("SHOW_FULLSCREEN", false));
} catch (java.beans.PropertyVetoException ex)
{
}
}
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);
}
@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);
}
});
@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);
}
});
// 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();
}
}
- /*
- * (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));
}
}