import jalview.util.MessageManager;
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.InputStream;
+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
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());
}
}
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);
}
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.
}
}
if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
+ alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
}
if (proxyColourScheme != null)
{
return tempStructFile.toString();
}
+ /**
+ *
+ * @param file a File, or a String which is a name of a file
+ * @return
+ * @throws FileNotFoundException
+ */
+ @SuppressWarnings("unused")
+ public static BufferedReader getBuffereReader(Object file) throws FileNotFoundException {
+ if (file instanceof String)
+ return new BufferedReader(new FileReader((String) file));
+
+ byte[] bytes = /** @j2sNative file._bytes || */ null;
+ if (bytes != null)
+ return new BufferedReader(new InputStreamReader(new ByteArrayInputStream(bytes)));
+ return new BufferedReader(new FileReader((File) file));
+ }
+
}