import java.util.BitSet;
import java.util.Collections;
import java.util.Enumeration;
+import java.util.HashMap;
import java.util.HashSet;
import java.util.Hashtable;
import java.util.Iterator;
for (int i = 0; i < sequences.size(); i++)
{
- if (getSequenceAt(i).getLength() > maxLength)
- {
- maxLength = getSequenceAt(i).getLength();
- }
+ maxLength = Math.max(maxLength, getSequenceAt(i).getLength());
}
-
return maxLength;
}
}
}
+ /**
+ * Returns a map from sequence to position (0, 1,...) in the alignment
+ */
+ @Override
+ public Map<SequenceI, Integer> getSequencePositions()
+ {
+ Map<SequenceI, Integer> map = new HashMap<>();
+
+ synchronized (sequences)
+ {
+ int i = sequences.size();
+ for (int j = 0; j < i; j++)
+ {
+ map.put(sequences.get(j), Integer.valueOf(j));
+ }
+ }
+ return map;
+ }
+
}