*/
package jalview.io.packed;
+import jalview.api.FeatureColourI;
import jalview.datamodel.AlignmentI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FileFormatI;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
FileParse src = dta.getDataSource();
if (dta.getType().equals(DataProvider.JvDataType.ALIGNMENT))
{
- String fmt = null;
+ FileFormatI fmt = null;
try
{
fmt = new IdentifyFile().identify(src, false);
if (fmt != null)
{
- if (!FormatAdapter.isValidIOFormat(fmt, false))
+ // parse the alignment
+ AlignmentI al = null;
+ try
{
- errmsg = fmt;
- exerror = null;
+ al = new FormatAdapter().readFromFile(src, fmt);
+ } catch (Exception e)
+ {
+ errmsg = "Failed to parse alignment from result set";
+ exerror = e;
}
- else
+ if (al != null)
{
- // parse the alignment
- AlignmentI al = null;
- try
- {
- al = new FormatAdapter().readFromFile(src, fmt);
- } catch (Exception e)
- {
- errmsg = "Failed to parse alignment from result set";
- exerror = e;
- }
- if (al != null)
- {
- // deuniquify and construct/merge additional dataset entries if
- // necessary.
- context.addAlignment(al);
- context.updateSetModified(true);
- rslt.add(al);
- deuniquify = true;
- }
+ // deuniquify and construct/merge additional dataset entries if
+ // necessary.
+ context.addAlignment(al);
+ context.updateSetModified(true);
+ rslt.add(al);
+ deuniquify = true;
}
}
}
// if not, create one.
if (context.featureColours == null)
{
- context.featureColours = new HashMap<String, Object>();
+ context.featureColours = new HashMap<String, FeatureColourI>();
}
try
{