*/\r
package jalview.analysis;\r
\r
-import java.util.*;\r
-\r
import jalview.datamodel.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+\r
+import jalview.io.NewickFile;\r
+\r
+import jalview.schemes.ResidueProperties;\r
+\r
import jalview.util.*;\r
\r
+import java.util.*;\r
+\r
\r
/**\r
* DOCUMENT ME!\r
int start;\r
int end;\r
boolean hasDistances = true; // normal case for jalview trees\r
- boolean hasBootstrap = false; // normal case for jalview trees\r
+ boolean hasBootstrap = false; // normal case for jalview trees\r
\r
- private boolean hasRootDistance = true;\r
+ private boolean hasRootDistance = true;\r
\r
/**\r
* Creates a new NJTree object.\r
AlignSeq as = new AlignSeq(sequence[i], sequence[j], "pep");\r
as.calcScoreMatrix();\r
as.traceAlignment();\r
- as.printAlignment();\r
+ as.printAlignment(System.out);\r
distance[i][j] = (float) as.maxscore;\r
\r
if (max < distance[i][j])\r