/**
*
* @brief Creates a UPGMA guide tree. This is a frontend function to
* the ported Muscle UPGMA code ().
*
* @param[out] tree
* created upgma tree. will be allocated here. use FreeMuscleTree()
* to free
* @param[in] labels
* pointer to nseq sequence names
* @param[in] distmat
* distance matrix
* @param[in] ftree
* optional: if non-NULL, tree will be written to this files
*
* @see FreeMuscleTree()
* @see MuscleUpgma2()
*
*/
void
GuideTreeUpgma(tree_t **tree, char **labels,
symmatrix_t *distmat, char *ftree)
{
linkage_t linkage = LINKAGE_AVG;
FILE *fp = NULL;
if (NULL != ftree) {
if (NULL == (fp=fopen(ftree, "w"))) {
Log(&rLog, LOG_ERROR, "Couldn't open tree-file '%s' for writing. Skipping", ftree);
}
/* fp NULL is handled later */
}
(*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t));
MuscleUpgma2((*tree), distmat, linkage, labels);
if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
Log(&rLog, LOG_DEBUG, "tree logging...");
LogTree((*tree), LogGetFP(&rLog, LOG_DEBUG));
}
if (NULL != fp) {
MuscleTreeToFile(fp, (*tree));
Log(&rLog, LOG_INFO, "Guide tree written to %s", ftree);
fclose(fp);
}
}
/**
*
* @brief
*
* @param[out] tree
* created upgma tree. will be allocated here. use FreeMuscleTree()
* to free
* @param[in] mseq
* @param[in] ftree
*
* @return non-zero on error
*
*/
int
GuideTreeFromFile(tree_t **tree, mseq_t *mseq, char *ftree)
{
int iNodeCount;
int iNodeIndex;
(*tree) = (tree_t *) CKMALLOC(1 * sizeof(tree_t));
if (MuscleTreeFromFile((*tree), ftree)!=0) {
Log(&rLog, LOG_ERROR, "%s", "MuscleTreeFromFile failed");
return -1;
}
/* Make sure tree is rooted */
if (!IsRooted((*tree))) {
Log(&rLog, LOG_ERROR, "User tree must be rooted");
return -1;
}
if ((int)GetLeafCount((*tree)) != mseq->nseqs) {
Log(&rLog, LOG_ERROR, "User tree does not match input sequences");
return -1;
}
/* compare tree labels and sequence names and set leaf-ids */
iNodeCount = GetNodeCount((*tree));
for (iNodeIndex = 0; iNodeIndex < iNodeCount; ++iNodeIndex) {
char *LeafName;
int iSeqIndex;
if (!IsLeaf(iNodeIndex, (*tree)))
continue;
LeafName = GetLeafName(iNodeIndex, (*tree));
if ((iSeqIndex=FindSeqName(LeafName, mseq))==-1) {
Log(&rLog, LOG_ERROR, "Label '%s' in tree could not be found in sequence names", LeafName);
return -1;
}
SetLeafId((*tree), iNodeIndex, iSeqIndex);
}
if (rLog.iLogLevelEnabled <= LOG_DEBUG) {
Log(&rLog, LOG_DEBUG, "tree logging...");
LogTree((*tree), LogGetFP(&rLog, LOG_DEBUG));
}
return 0;
}
// Copy the board config (piece locations and captured pieces for each player)
// from "ptree" to "board".
static void FillBoard(const char* label,
JNIEnv* env,
tree_t* ptree, /* source */
jobject board /* dest */) {
LogTree(label, ptree);
jclass boardClass = (*env)->GetObjectClass(env, board);
jfieldID fid = (*env)->GetFieldID(env, boardClass, "mSquares", "[I");
jintArray jarray = (jintArray)((*env)->GetObjectField(env, board, fid));
jint tmp[nsquare];
for (int i = 0; i < nsquare; ++i) {
tmp[i] = BOARD[i];
}
(*env)->SetIntArrayRegion(env, jarray, 0, nsquare, tmp);
fid = (*env)->GetFieldID(env, boardClass, "mCapturedBlack", "I");
(*env)->SetIntField(env, board, fid, ptree->posi.hand_black);
fid = (*env)->GetFieldID(env, boardClass, "mCapturedWhite", "I");
(*env)->SetIntField(env, board, fid, ptree->posi.hand_white);
}