package jalview.io.packed;
import jalview.datamodel.AlignmentI;
+import jalview.io.AnnotationFile;
import jalview.io.AppletFormatAdapter;
+import jalview.io.FeaturesFile;
import jalview.io.FileParse;
import jalview.io.FormatAdapter;
import jalview.io.IdentifyFile;
+import jalview.io.NewickFile;
import jalview.io.packed.DataProvider.JvDataType;
import java.io.BufferedReader;
br = new BufferedReader(src.getReader());
}
// TODO: add columnSelection to context
- if (new jalview.io.AnnotationFile().parseAnnotationFrom(
+ if (new AnnotationFile().parseAnnotationFrom(
context.getLastAlignment(), null, br))
{
context.updateSetModified(true);
}
try
{
- jalview.io.FeaturesFile ff = new jalview.io.FeaturesFile(src);
+ FeaturesFile ff = new FeaturesFile(src);
context.updateSetModified(ff.parse(context.getLastAlignment(),
context.featureColours, false, context.relaxedIdMatching));
} catch (Exception e)
{
try
{
- jalview.io.NewickFile nf = new jalview.io.NewickFile(src);
+ NewickFile nf = new NewickFile(src);
if (!nf.isValid())
{
nf.close();