ebc480f8ae9aec1de1422c08ccb10a180e818c62 kent Thu May 3 10:22:04 2012 -0700 Refactoring to get rid of rbTrees, and replace with simple children lists. diff --git src/kehayden/alphaChain/alphaChain.c src/kehayden/alphaChain/alphaChain.c index 6d9b8b3..8864b3d 100644 --- src/kehayden/alphaChain/alphaChain.c +++ src/kehayden/alphaChain/alphaChain.c @@ -1,508 +1,483 @@ /* alphaChain - Predicts faux centromere sequences using a probablistic model. */ #include "common.h" #include "linefile.h" #include "hash.h" -#include "localmem.h" #include "options.h" #include "dlist.h" -#include "rbTree.h" /* Global vars - all of which can be set by command line options. */ int maxChainSize = 3; int outSize = 10000; int minUse = 1; -boolean lower = FALSE; -boolean unpunc = FALSE; boolean fullOnly = FALSE; void usage() /* Explain usage and exit. */ { errAbort( "alphaChain - create a linear projection of alpha satellite arrays using the probablistic model\n" "of HuRef satellite graphs\n" "usage:\n" " alphaChain alphaMonFile.fa significant_output.txt\n" "options:\n" " -size=N - Set max chain size, default %d\n" " -chain=fileName - Write out word chain to file\n" " -outSize=N - Output this many words.\n" " -fullOnly - Only output chains of size\n" " -minUse=N - Set minimum use in output chain, default %d\n" , maxChainSize, minUse ); } /* Command line validation table. */ static struct optionSpec options[] = { {"size", OPTION_INT}, {"minUse", OPTION_INT}, {"chain", OPTION_STRING}, {"fullOnly", OPTION_BOOLEAN}, {"outSize", OPTION_INT}, {NULL, 0}, }; /* The wordTree structure below is the central data structure for this program. It is * used to build up a tree that contains all observed N-word-long sequences observed in * the text, where N corresponds to the "size" command line option which defaults to 3, * an option that in turn is stored in the maxChainSize variable. At this chain size the * text * this is the black dog and the black cat * would have the chains * this is the * is the black * the black dog * black dog and * dog and the * and the black * the black cat * and turn into the tree * this * is * the * is * the * black * the * black * dog * cat * black * dog * and * dog * and * the * and * the * black * Note how the tree is able to compress the two chains "the black dog" and "the black cat." * * A node in the tree can have as many children as it needs to at each node. The depth of * the tree is the same as the chain size, by default 3. At each node in the tree you get * a word, and a list of all words that are observed in the text to follow that word. * * Once the program has build up the wordTree, it can output it in a couple of fashions. */ struct wordTree /* A node in a tree of words. The head of the tree is a node with word value the empty string. */ { - struct rbTree *following; /* Contains words (as struct wordTree) that follow us. */ + struct wordTree *next; /* Next sibling */ + struct wordTree *children; /* Children in list. */ struct wordTree *parent; /* Parent of this node or NULL for root. */ char *word; /* The word itself including comma, period etc. */ int useCount; /* Number of times word used in input. */ int outTarget; /* Number of times want to output word. */ int outCount; /* Number of times output. */ double normVal; /* value to place the normalization value */ }; struct wordTree *wordTreeNew(char *word) /* Create and return new wordTree element. */ { struct wordTree *wt; AllocVar(wt); wt->word = cloneString(word); return wt; } -int wordTreeCmpWord(void *va, void *vb) -/* Compare two wordTree. */ +int wordTreeCmpWord(const void *va, const void *vb) +/* Compare two wordTree for slSort. */ { -struct wordTree *a = va, *b = vb; +const struct wordTree *a = *((struct wordTree **)va); +const struct wordTree *b = *((struct wordTree **)vb); return strcmp(a->word, b->word); } -struct wordTree *wordTreeAddFollowing(struct wordTree *wt, char *word, - struct lm *lm, struct rbTreeNode **stack) +struct wordTree *wordTreeFindInList(struct wordTree *list, char *word) +/* Return wordTree element in list that has given word, or NULL if none. */ +{ +struct wordTree *wt; +for (wt = list; wt != NULL; wt = wt->next) + if (sameString(wt->word, word)) + break; +return wt; +} + +struct wordTree *wordTreeAddFollowing(struct wordTree *wt, char *word) /* Make word follow wt in tree. If word already exists among followers * return it and bump use count. Otherwise create new one. */ { -struct wordTree *w; /* Points to following element if any */ -if (wt->following == NULL) +struct wordTree *child = wordTreeFindInList(wt->children, word); +if (child == NULL) { - /* Allocate new if you've never seen it before. */ - wt->following = rbTreeNewDetailed(wordTreeCmpWord, lm, stack); - w = NULL; + child = wordTreeNew(word); + child->parent = wt; + slAddHead(&wt->children, child); } -else - { - /* Find word in existing tree */ - struct wordTree key; - key.word = word; - w = rbTreeFind(wt->following, &key); +child->useCount += 1; +return child; } -if (w == NULL) + +int wordTreeSumUseCounts(struct wordTree *list) +/* Sum up useCounts in list */ { - w = wordTreeNew(word); - w->parent = wt; - rbTreeAdd(wt->following, w); - } -w->useCount += 1; -return w; +int total = 0; +struct wordTree *wt; +for (wt = list; wt != NULL; wt = wt->next) + total += wt->useCount; +return total; } int wordTreeChildrenUseCount(struct wordTree *wt) /* Return sum of useCounts of all children */ { -struct rbTree *following = wt->following; -if (following == NULL) - return 0; -struct slRef *childList = rbTreeItems(following); -struct slRef *childRef; -int total = 0; -for (childRef = childList; childRef != NULL; childRef = childRef->next) - { - struct wordTree *child = childRef->val; - total += child->useCount; +return wordTreeSumUseCounts(wt->children); } -slFreeList(&childList); + +int wordTreeSumOutTargets(struct wordTree *list) +/* Sum up useCounts in list */ +{ +int total = 0; +struct wordTree *wt; +for (wt = list; wt != NULL; wt = wt->next) + total += wt->outTarget; return total; } -void addChainToTree(struct wordTree *wt, struct dlList *chain, - struct lm *lm, struct rbTreeNode **stack) +void addChainToTree(struct wordTree *wt, struct dlList *chain) /* Add chain of words to tree. */ { struct dlNode *node; wt->useCount += 1; for (node = chain->head; !dlEnd(node); node = node->next) { char *word = node->val; verbose(2, " %s\n", word); - wt = wordTreeAddFollowing(wt, word, lm, stack); + wt = wordTreeAddFollowing(wt, word); } } void wordTreeNormalize(struct wordTree *wt, double outTarget, double normVal) /* Recursively set wt->normVal and wt->outTarget so each branch gets its share */ { wt->normVal = normVal; wt->outTarget = outTarget; -if (wt->following != NULL) - { int totalChildUses = wordTreeChildrenUseCount(wt); - struct slRef *list = rbTreeItems(wt->following); - struct slRef *ref; - for (ref = list; ref !=NULL; ref = ref->next) +struct wordTree *child; +for (child = wt->children; child != NULL; child = child->next) { - struct wordTree *child = ref->val; double childRatio = (double)child->useCount / totalChildUses; wordTreeNormalize(child, childRatio*outTarget, childRatio*normVal); } - slFreeList(&list); - } } void wordTreeDump(int level, struct wordTree *wt, FILE *f) /* Write out wordTree to file. */ { static char *words[64]; -struct slRef *list, *ref; int i; assert(level < ArraySize(words)); words[level] = wt->word; if (wt->useCount >= minUse) { if (!fullOnly || level == maxChainSize) { fprintf(f, "%d\t%d\t%d\t%d\t%f\t", level, wt->useCount, wt->outTarget, wt->outCount, wt->normVal); for (i=1; i<=level; ++i) { spaceOut(f, level*2); fprintf(f, "%s ", words[i]); } fprintf(f, "\n"); } } -if (wt->following != NULL) - { - list = rbTreeItems(wt->following); - for (ref = list; ref != NULL; ref = ref->next) - wordTreeDump(level+1, ref->val, f); - slFreeList(&list); - } +struct wordTree *child; +for (child = wt->children; child != NULL; child = child->next) + wordTreeDump(level+1, child, f); } -int totalUses = 0; -int curUses = 0; -int useThreshold = 0; -struct wordTree *pickedNode; +int totUseZeroCount; // debugging aid -int totUseZeroCount = 0; +struct wordTree *pickRandomOnOutTarget(struct wordTree *list) +/* Pick word from list randomly, but so that words more + * commonly seen are picked more often. */ +{ +struct wordTree *picked = NULL; -void addUse(void *v) -/* Add up to total uses. */ +/* Figure out total number of outputs left, and a random number between 0 and that total. */ +int total = wordTreeSumOutTargets(list); +if (total > 0) { -struct wordTree *wt = v; -totalUses += wt->outTarget; -} + int threshold = rand() % total; -void pickIfInThreshold(void *v) -/* See if inside threshold, and if so store it in pickedNode. */ + /* Loop through list returning selection corresponding to random threshold. */ + int binStart = 0; + struct wordTree *wt; + for (wt = list; wt != NULL; wt = wt->next) { -if (pickedNode == NULL) + int size = wt->outTarget; + int binEnd = binStart + size; + if (threshold < binEnd) { - struct wordTree *wt = v; - int top = curUses + wt->outTarget; - if (useThreshold < top) - pickedNode = wt; - curUses = top; + picked = wt; + break; } + binStart = binEnd; } - -void pickAny(void *v) -/* Force it to pick something - first thing as it turns out. */ -{ -if (pickedNode == NULL) - pickedNode = v; } -struct wordTree *pickRandom(struct rbTree *rbTree) -/* Pick word from list randomly, but so that words more - * commonly seen are picked more often. */ -{ -pickedNode = NULL; -curUses = 0; -totalUses = 0; -rbTreeTraverse(rbTree, addUse); -if (totalUses > 0) - { - useThreshold = rand() % totalUses; - rbTreeTraverse(rbTree, pickIfInThreshold); - } -if (pickedNode == NULL) +/* If did not find anything, that's ok. It can happen on legitimate input due to unevenness + * of read coverage. In this case we just return an arbitrary element. */ +if (picked == NULL) { - ++totUseZeroCount; - rbTreeTraverse(rbTree, pickAny); + picked = list; + totUseZeroCount += 1; } -assert(pickedNode != NULL); -return pickedNode; +return picked; } struct wordTree *predictNextFromAllPredecessors(struct wordTree *wt, struct dlNode *list) /* Predict next word given tree and recently used word list. If tree doesn't * have statistics for what comes next given the words in list, then it returns * NULL. */ { struct dlNode *node; for (node = list; !dlEnd(node); node = node->next) { char *word = node->val; - struct wordTree key; - key.word = word; - wt = rbTreeFind(wt->following, &key); - if (wt == NULL || wt->following == NULL) + wt = wordTreeFindInList(wt->children, word); + if (wt == NULL || wt->children == NULL) break; } struct wordTree *result = NULL; -if (wt != NULL && wt->following != NULL) - result = pickRandom(wt->following); +if (wt != NULL && wt->children != NULL) + result = pickRandomOnOutTarget(wt->children); return result; } struct wordTree *predictNext(struct wordTree *wt, struct dlList *recent) /* Predict next word given tree and recently used word list. Will use all words in * recent list if can, but if there is not data in tree, will back off, and use * progressively less previous words until ultimately it just picks a random * word. */ { struct dlNode *node; for (node = recent->head; !dlEnd(node); node = node->next) { struct wordTree *result = predictNextFromAllPredecessors(wt, node); if (result != NULL) return result; } -return pickRandom(wt->following); +return pickRandomOnOutTarget(wt->children); } void decrementOutputCounts(struct wordTree *wt) /* Decrement output count of self and parents. */ { while (wt != NULL) { wt->outTarget -= 1; wt->outCount += 1; wt = wt->parent; } } static void wordTreeGenerateFaux(struct wordTree *wt, int maxSize, struct wordTree *firstWord, int maxOutputWords, char *fileName) /* Go spew out a bunch of words according to probabilities in tree. */ { FILE *f = mustOpen(fileName, "w"); struct dlList *ll = dlListNew(); int listSize = 0; int outputWords = 0; for (;;) { if (++outputWords > maxOutputWords) break; struct dlNode *node; struct wordTree *picked; /* Get next predicted word. */ if (listSize == 0) { AllocVar(node); ++listSize; picked = firstWord; } else if (listSize >= maxSize) { node = dlPopHead(ll); picked = predictNext(wt, ll); // decrementOutputCounts(picked); // ugly placement? } else { picked = predictNext(wt, ll); AllocVar(node); ++listSize; } if (picked == NULL) break; /* Add word from whatever level we fetched back to our chain of up to maxChainSize. */ node->val = picked->word; dlAddTail(ll, node); fprintf(f, "%s\n", picked->word); decrementOutputCounts(picked); } dlListFree(&ll); carefulClose(&f); } -struct wordTree *wordTreeForChainsInFile(char *fileName, int chainSize, struct lm *lm) +static void wordTreeSort(struct wordTree *wt) +/* Sort all children lists in tree. */ +{ +slSort(&wt->children, wordTreeCmpWord); +struct wordTree *child; +for (child = wt->children; child != NULL; child = child->next) + wordTreeSort(child); +} + +struct wordTree *wordTreeForChainsInFile(char *fileName, int chainSize) /* Return a wordTree of all chains-of-words of length chainSize seen in file. * Allocate the structure in local memory pool lm. */ { /* Stuff for processing file a line at a time. */ struct lineFile *lf = lineFileOpen(fileName, TRUE); char *line, *word; /* We'll build up the tree starting with an empty root node. */ struct wordTree *wt = wordTreeNew(""); -/* Save time/space by sharing stack between all "following" rbTrees. */ -struct rbTreeNode **stack; -lmAllocArray(lm, stack, 256); - -/* Loop through each line of input file, lowercasing the whole line, and then - * looping through each word of line, stripping out special chars, and finally - * processing each word. */ +/* Loop through each line of file, treating it as a separate read. There's + * special cases at the beginning and end of line, and for short lines. In the + * main case we'll be maintaining a chain (doubly linked list) of maxChainSize words, + * popping off one word from the start, and adding one word to the end for each + * new word we encounter. This list is added to the tree each iteration. */ while (lineFileNext(lf, &line, NULL)) { - /* KEH NOTES: change 3/14/12: before process beginning and end of a file, now happens at the beginning and end of each line */ /* We'll keep a chain of three or so words in a doubly linked list. */ struct dlNode *node; struct dlList *chain = dlListNew(); int curSize = 0; int wordCount = 0; /* skipping the first word which is the read id */ word = nextWord(&line); while ((word = nextWord(&line)) != NULL) { - /* We come to this point in the code for each word in the file. - * Here we want to maintain a chain of sequential words up to - * chainSize long. We do this with a doubly-linked list structure. - * For the first few words in the file we'll just build up the list, + /* For the first few words in the file after ID, we'll just build up the chain, * only adding it to the tree when we finally do get to the desired * chain size. Once past the initial section of the file we'll be * getting rid of the first link in the chain as well as adding a new * last link in the chain with each new word we see. */ if (curSize < chainSize) { dlAddValTail(chain, cloneString(word)); ++curSize; if (curSize == chainSize) - addChainToTree(wt, chain, lm, stack); + addChainToTree(wt, chain); } else { /* Reuse doubly-linked-list node, but give it a new value, as we move * it from head to tail of list. */ node = dlPopHead(chain); freeMem(node->val); node->val = cloneString(word); dlAddTail(chain, node); - addChainToTree(wt, chain, lm, stack); + addChainToTree(wt, chain); } ++wordCount; } /* Handle last few words in line, where can't make a chain of full size. Also handles * lines that have fewer than chain size words. */ if (curSize < chainSize) - addChainToTree(wt, chain, lm, stack); + addChainToTree(wt, chain); while ((node = dlPopHead(chain)) != NULL) { if (!dlEmpty(chain)) - addChainToTree(wt, chain, lm, stack); + addChainToTree(wt, chain); freeMem(node->val); freeMem(node); } dlListFree(&chain); } lineFileClose(&lf); +wordTreeSort(wt); // ugly debug + return wt; } void wordTreeWrite(struct wordTree *wt, char *fileName) /* Write out tree to file */ { FILE *f = mustOpen(fileName, "w"); fprintf(f, "#level\tuseCount\toutTarget\toutCount\tnormVal\tmonomers\n"); wordTreeDump(0, wt, f); carefulClose(&f); } void alphaChain(char *inFile, char *outFile) /* alphaChain - Create Markov chain of words and optionally output chain in two formats. */ { -struct lm *lm = lmInit(0); -struct wordTree *wt = wordTreeForChainsInFile(inFile, maxChainSize, lm); +struct wordTree *wt = wordTreeForChainsInFile(inFile, maxChainSize); wordTreeNormalize(wt, outSize, 1.0); if (optionExists("chain")) { char *fileName = optionVal("chain", NULL); wordTreeWrite(wt, fileName); } -wordTreeGenerateFaux(wt, maxChainSize, pickRandom(wt->following), outSize, outFile); +wordTreeGenerateFaux(wt, maxChainSize, pickRandomOnOutTarget(wt->children), outSize, outFile); uglyf("totUseZeroCount = %d\n", totUseZeroCount); wordTreeWrite(wt, "ugly.chain"); - -lmCleanup(&lm); // Not really needed since we're just going to exit. } int main(int argc, char *argv[]) /* Process command line. */ { #ifdef SOON +/* Seed random number generator with time, so it doesn't always generate same sequence of #s */ srand( (unsigned)time(0) ); #endif /* SOON */ optionInit(&argc, argv, options); if (argc != 3) usage(); maxChainSize = optionInt("size", maxChainSize); minUse = optionInt("minUse", minUse); outSize = optionInt("outSize", outSize); fullOnly = optionExists("fullOnly"); alphaChain(argv[1], argv[2]); return 0; }