*/
package jalview.io;
+import java.io.IOException;
+
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
-import java.io.IOException;
-
/**
* DOCUMENT ME!
*
public FastaFile(FileParse source) throws IOException
{
- super(source);
+ this(source, true);
+ }
+
+ public FastaFile(FileParse source, boolean closeData) throws IOException
+ {
+ super(true, source, closeData);
}
public FastaFile(SequenceI[] seqs)
anots[i] = new Annotation("" + cn, null, ' ', Float.NaN);
}
}
- AlignmentAnnotation aa = new AlignmentAnnotation(seq.getName()
- .substring(2), seq.getDescription(), anots);
+ AlignmentAnnotation aa = new AlignmentAnnotation(
+ seq.getName().substring(2), seq.getDescription(), anots);
return aa;
}
addProperties(al);
for (int i = 0; i < annotations.size(); i++)
{
- AlignmentAnnotation aa = annotations
- .elementAt(i);
+ AlignmentAnnotation aa = annotations.elementAt(i);
aa.setPadGaps(true, al.getGapCharacter());
al.addAnnotation(aa);
}