*/
package jalview.io;
-import jalview.bin.Cache;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceI;
import jalview.util.Comparison;
import java.io.IOException;
+import java.util.Vector;
public class PIRFile extends AlignFile
{
- // Vector words = new Vector(); // Stores the words in a line after splitting
+ public static boolean useModellerOutput = false;
+
+ Vector words = new Vector(); // Stores the words in a line after splitting
public PIRFile()
{
StringBuffer out = new StringBuffer();
int i = 0;
ModellerDescription md;
- boolean useModellerOutput = Cache.getDefault("PIR_MODELLER", false);
+
while ((i < s.length) && (s[i] != null))
{
String seq = s[i].getSequenceAsString();
}
else
{
+
if (useModellerOutput)
{
out.append(">P1;" + s[i].getName());