*/
package jalview.analysis;
-import java.util.Enumeration;
-import java.util.Hashtable;
-import java.util.Vector;
-
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.util.Comparison;
+
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.Vector;
public class SeqsetUtils
{
sqinfo.put("Description", seq.getDescription());
}
Vector sfeat = new Vector();
- jalview.datamodel.SequenceFeature[] sfarray = seq.getSequenceFeatures();
+ SequenceFeature[] sfarray = seq.getSequenceFeatures();
if (sfarray != null && sfarray.length > 0)
{
for (int i = 0; i < sfarray.length; i++)
public static boolean deuniquify(Hashtable map, SequenceI[] sequences,
boolean quiet)
{
- jalview.analysis.SequenceIdMatcher matcher = new SequenceIdMatcher(
- sequences);
+ SequenceIdMatcher matcher = new SequenceIdMatcher(sequences);
SequenceI msq = null;
Enumeration keys = map.keys();
Vector unmatched = new Vector();
int msflen = 0;
for (int i = 0, j = sequences.length; i < j; i++)
{
- String tempseq = jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
+ String tempseq = AlignSeq.extractGaps(Comparison.GapChars,
sequences[i].getSequenceAsString());
if (tempseq.length() == 0)