import jalview.api.FeaturesSourceI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.AlignmentAnnotation.TFType;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
private File selectedFile;
- private AlignmentAnnotation.TFType temperatureFactorType = null;
-
/**
* default constructor always raised errors in GUI dialog boxes
*/
public AlignFrame LoadFileWaitTillLoaded(String file,
DataSourceType sourceType, FileFormatI format)
{
- return LoadFileWaitTillLoaded(file, sourceType, format, null);
- }
-
- /**
- * Load alignment from (file, protocol) of type format with specified
- * temperature factor type and wait till loaded
- *
- * @param file
- * @param sourceType
- * @param format
- * @param tempfacType
- * @return alignFrame constructed from file contents
- */
- public AlignFrame LoadFileWaitTillLoaded(String file,
- DataSourceType sourceType, FileFormatI format, AlignmentAnnotation.TFType tempfacType)
- {
this.file = file;
this.protocol = sourceType;
this.format = format;
- this.temperatureFactorType = tempfacType;
return _LoadFileWaitTillLoaded();
}
{
if (selectedFile == null)
{
- al = fa.readFile(null, file, protocol, format,
- temperatureFactorType);
+ al = fa.readFile(null, file, protocol, format);
}
else
{
- al = fa.readFile(selectedFile, null, protocol, format,
- temperatureFactorType);
+ al = fa.readFile(selectedFile, null, protocol, format);
}
source = fa.getAlignFile(); // keep reference for later if
{
alignFrame.setFileName(file, format);
alignFrame.setFileObject(selectedFile); // BH 2018 SwingJS
+ alignFrame.getViewport().setSavedUpToDate(true);
}
if (proxyColourScheme != null)
{
// that perform queries to find the 'current working alignment'
Desktop.addInternalFrame(alignFrame, title,
AlignFrame.DEFAULT_WIDTH, AlignFrame.DEFAULT_HEIGHT);
+
+ /*
+ * for an Overview automatically opened with alignment,
+ * set its title now alignFrame title has been set
+ */
+ alignFrame.alignPanel.setOverviewTitle(alignFrame);
}
try