import jalview.api.FeatureSettingsModelI;
import jalview.api.FeaturesDisplayedI;
import jalview.api.FeaturesSourceI;
+import jalview.bin.Cache;
import jalview.bin.Jalview;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
{
String file;
- String protocol;
+ DataSourceType protocol;
- String format;
+ FileFormatI format;
- FileParse source = null; // alternative specification of where data comes
+ AlignmentFileI source = null; // alternative specification of where data comes
// from
}
public void LoadFile(AlignViewport viewport, String file,
- String protocol, String format)
+ DataSourceType protocol, FileFormatI format)
{
this.viewport = viewport;
LoadFile(file, protocol, format);
}
- public void LoadFile(String file, String protocol, String format)
+ public void LoadFile(String file, DataSourceType protocol,
+ FileFormatI format)
{
this.file = file;
this.protocol = protocol;
* @param file
* @param protocol
*/
- public void LoadFile(String file, String protocol)
+ public void LoadFile(String file, DataSourceType protocol)
{
LoadFile(file, protocol, null);
}
* Load alignment from (file, protocol) and wait till loaded
*
* @param file
- * @param protocol
+ * @param sourceType
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType)
{
- return LoadFileWaitTillLoaded(file, protocol, null);
+ return LoadFileWaitTillLoaded(file, sourceType, null);
}
/**
* Load alignment from (file, protocol) of type format and wait till loaded
*
* @param file
- * @param protocol
+ * @param sourceType
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(String file, String protocol,
- String format)
+ public AlignFrame LoadFileWaitTillLoaded(String file,
+ DataSourceType sourceType, FileFormatI format)
{
this.file = file;
- this.protocol = protocol;
+ this.protocol = sourceType;
this.format = format;
return _LoadFileWaitTillLoaded();
}
* @param format
* @return alignFrame constructed from file contents
*/
- public AlignFrame LoadFileWaitTillLoaded(FileParse source, String format)
+ public AlignFrame LoadFileWaitTillLoaded(AlignmentFileI source,
+ FileFormatI format)
{
this.source = source;
file = source.getInFile();
- protocol = source.type;
+ protocol = source.getDataSourceType();
this.format = format;
return _LoadFileWaitTillLoaded();
}
public void updateRecentlyOpened()
{
Vector recent = new Vector();
- if (protocol.equals(FormatAdapter.PASTE))
+ if (protocol == DataSourceType.PASTE)
{
// do nothing if the file was pasted in as text... there is no filename to
// refer to it as.
return;
}
- String type = protocol.equals(FormatAdapter.FILE) ? "RECENT_FILE"
+ String type = protocol == DataSourceType.FILE ? "RECENT_FILE"
: "RECENT_URL";
String historyItems = jalview.bin.Cache.getProperty(type);
newHistory.append(recent.elementAt(i));
}
- jalview.bin.Cache.setProperty(type, newHistory.toString());
+ Cache.setProperty(type, newHistory.toString());
- if (protocol.equals(FormatAdapter.FILE))
+ if (protocol == DataSourceType.FILE)
{
- jalview.bin.Cache.setProperty("DEFAULT_FILE_FORMAT", format);
+ Cache.setProperty("DEFAULT_FILE_FORMAT", format.toString());
}
}
@Override
public void run()
{
- String title = protocol.equals(AppletFormatAdapter.PASTE) ? "Copied From Clipboard"
+ String title = protocol == DataSourceType.PASTE ? "Copied From Clipboard"
: file;
Runtime rt = Runtime.getRuntime();
try
// just in case the caller didn't identify the file for us
if (source != null)
{
- format = new IdentifyFile().identify(source, false); // identify
- // stream and
- // rewind rather
- // than close
+ format = new IdentifyFile().identify(source, false);
+ // identify stream and rewind rather than close
}
else
{
}
- if (format == null || format.equalsIgnoreCase("EMPTY DATA FILE"))
+ if (format == null)
{
Desktop.instance.stopLoading();
System.err.println("The input file \"" + file
loadtime = -System.currentTimeMillis();
AlignmentI al = null;
- if (format.equalsIgnoreCase("Jalview"))
+ if (FileFormat.Jalview.equals(format))
{
if (source != null)
{
else
{
String error = AppletFormatAdapter.SUPPORTED_FORMATS;
- if (FormatAdapter.isValidFormat(format))
- {
try
{
if (source != null)
{
// read from the provided source
- al = new FormatAdapter().readFromFile(source, format);
+ al = new FormatAdapter().readFromFile(source, format);
}
else
{
{
error = ex.getMessage();
}
- }
- else
- {
- if (format != null && format.length() > 7)
- {
- // ad hoc message in format.
- error = format + "\n" + error;
- }
- }
if ((al != null) && (al.getHeight() > 0) && al.hasValidSequence())
{
}
}
// add metadata and update ui
- if (!protocol.equals(AppletFormatAdapter.PASTE))
+ if (!(protocol == DataSourceType.PASTE))
{
alignFrame.setFileName(file, format);
}