public static BSTree createTree(Protein[] p) {
int l = p.length;
BSTree[] protree = new BSTree[l];
for (int i = 0; i < l; ++i) protree[i] = p[i].treeify();
while (l > 0) {
System.out.println(l + " generalized leaf node" + (l > 1 ? "s" : "") + " left.");
System.out.println(prettyPrint(protree));
if (l == 1) break;
int maxReward = Integer.MIN_VALUE;
int maxPos = -1;
Protein maxCestor = null;
for (int i = 0; i < l - 1; ++i) {
Protein thisCestor =
((Protein) (protree[i].root().data()))
.findMLAncestor((Protein) (protree[i + 1].root().data()));
int thisReward = thisCestor.weight();
if (maxReward < thisReward) {
maxReward = thisReward;
maxPos = i;
maxCestor = thisCestor;
}
}
// System.out.println ("We're joining \"" + ((Protein)(protree[maxPos].root().data())).desc()
// + "\"(" + maxPos + ") and \"" + ((Protein)(protree[maxPos+1].root().data())).desc() + "\"("
// + (maxPos + 1) + ") with a reward of " + maxReward + ".");
BSTree[] protree_new = new BSTree[l - 1];
BSTree tree_merged =
maxCestor.treeify().merge(protree[maxPos], protree[maxPos + 1], maxReward);
for (int i = 0; i < l - 1; ++i) {
protree_new[i] = (i < maxPos ? protree[i] : i == maxPos ? tree_merged : protree[i + 1]);
}
protree = protree_new;
// System.out.println ("Suddenly, " + (l-1) + " element" + (l-1==1?" is":"s are") + " left.");
--l;
}
return protree[0];
}
public static IProtein processProtein(final String line) {
String peptide = XMLUtil.extractAttribute(line, "protein_descr");
if (peptide == null) throw new IllegalArgumentException("bad line " + line);
return Protein.getProtein(peptide, "", "", null);
}