*/
private static int MAX_HISTORY = 11;
- private File selectedFile;
-
String file;
DataSourceType protocol;
AlignmentFileReaderI source; // alternative specification of where data
// comes from
+ AlignViewport viewport;
+
+ AlignFrame alignFrame;
+
+ long loadtime;
+
+ long memused;
+
+ boolean raiseGUI = true;
+
+ private File selectedFile;
+
+ /**
+ * default constructor always raised errors in GUI dialog boxes
+ */
+ public FileLoader()
+ {
+ this(true);
+ }
+
+ /**
+ * construct a Fileloader that may raise errors non-interactively
+ *
+ * @param raiseGUI
+ * true if errors are to be raised as GUI dialog boxes
+ */
+ public FileLoader(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
/**
* It is critical that all these fields are set, as this instance is reused.
*
this.format = format;
}
- AlignViewport viewport;
-
- AlignFrame alignFrame;
-
- long loadtime;
-
- long memused;
-
- boolean raiseGUI = true;
/**
- * default constructor always raised errors in GUI dialog boxes
+ * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+ * JavaScript
+ *
+ * @param viewport
+ * @param file
+ * @param protocol
+ * @param format
*/
- public FileLoader()
+ @Deprecated
+ public void LoadFile(AlignViewport viewport, String file,
+ DataSourceType protocol, FileFormatI format)
{
- this(true);
+ 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);
}
/**
- * construct a Fileloader that may raise errors non-interactively
+ * Uppercase LoadFile is deprecated because it does not pass byte[] data to
+ * JavaScript
*
- * @param raiseGUI
- * true if errors are to be raised as GUI dialog boxes
+ * @param file
+ * @param protocol
+ * @param format
*/
- public FileLoader(boolean raiseGUI)
+ @Deprecated
+ public void LoadFile(String file, DataSourceType protocol,
+ FileFormatI format)
{
- this.raiseGUI = raiseGUI;
+ loadFile(file, protocol, format);
}
- public void loadFile(AlignViewport viewport, Object file,
+ /**
+ * 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)
{
- this.viewport = viewport;
- if (file instanceof File) {
- this.selectedFile = (File) file;
- file = selectedFile.getPath();
+ if (viewport != null)
+ {
+ this.viewport = viewport;
}
- loadFile(file.toString(), protocol, format);
+ this.selectedFile = file;
+ loadFile(selectedFile.getPath(), protocol, format);
}
- public void loadFile(String file, DataSourceType protocol,
+ private void loadFile(String file, DataSourceType protocol,
FileFormatI format)
{
this.file = file;
* @param sourceType
* @return alignFrame constructed from file contents
*/
+ @Deprecated
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,
+ @Deprecated
+ public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType, FileFormatI format)
{
setFileFields(null, null, file, sourceType, format);
// refer to it as.
return;
}
+ // BH logic change here just includes ignoring file==null
if (file == null
|| file.indexOf(System.getProperty("java.io.tmpdir")) > -1)
{
String historyItems = Cache.getProperty(type);
+ // BH simpler coding
if (historyItems != null)
{
String[] tokens = historyItems.split("\\t");