static void insertleaf(Suffixtree *stree) {
Uint *ptr, newleaf;
newleaf = MAKELEAF(stree->nextfreeleafnum);
if(stree->headnodedepth == 0) { // head is the root
if(stree->tailptr != stree->sentinel) { // no \$-edge initially
stree->rootchildren[(Uint) *(stree->tailptr)] = newleaf;
*(stree->nextfreeleafptr) = VALIDINIT;
}
} else {
if (stree->insertprev == 0) { // newleaf = first child
*(stree->nextfreeleafptr) = GETCHILD(stree->headnode);
SETCHILD(stree->headnode,newleaf);
} else {
if(ISLEAF(stree->insertprev)) { // previous node is leaf
ptr = stree->leaftab + GETLEAFINDEX(stree->insertprev);
*(stree->nextfreeleafptr) = LEAFBROTHERVAL(*ptr);
SETLEAFBROTHER(ptr,newleaf);
} else { // previous node is branching node
ptr = stree->branchtab + GETBRANCHINDEX(stree->insertprev);
*(stree->nextfreeleafptr) = GETBROTHER(ptr);
SETBROTHER(ptr,newleaf);
}
}
}
RECALLSUCC(newleaf); // recall node on s.cppessor path of \emph{headnode}
stree->nextfreeleafnum++;
stree->nextfreeleafptr++;
}
void succlocationsstree(Suffixtree *stree,bool nosentinel,Simpleloc *loc,
ArraySimpleloc *ll)
{
Uint succdepth, succ, leafindex, distance, depth, headpos,
remain, *succptr, *largeptr, *nodeptr;
Simpleloc *llptr;
fprintf(stderr,"succlocationsstree\n");
ll->nextfreeSimpleloc = 0;
CHECKARRAYSPACE(ll,Simpleloc,stree->alphasize+1);
if(loc->remain > 0)
{
if(nosentinel && loc->nextnode.toleaf && loc->remain <= UintConst(1))
{ // at the end of leaf edge: only a\$ remains
return;
}
llptr = ll->spaceSimpleloc + ll->nextfreeSimpleloc++;
llptr->textpos = loc->textpos + 1;
llptr->remain = loc->remain - 1;
llptr->nextnode.address = loc->nextnode.address;
llptr->nextnode.toleaf = loc->nextnode.toleaf;
CHECKADDR(stree,llptr->nextnode);
return;
}
nodeptr = loc->nextnode.address;
GETONLYDEPTH(depth,nodeptr);
succ = GETCHILD(nodeptr);
do // traverse the list of successors
{
if(ISLEAF(succ)) // successor is leaf
{
leafindex = GETLEAFINDEX(succ);
remain = stree->textlen - (depth + leafindex);
if(!nosentinel || remain >= UintConst(1))
{
llptr = ll->spaceSimpleloc + ll->nextfreeSimpleloc++;
llptr->remain = remain;
llptr->textpos = depth + leafindex;
llptr->nextnode.address = stree->leaftab + leafindex;
llptr->nextnode.toleaf = true;
CHECKADDR(stree,llptr->nextnode);
}
succ = LEAFBROTHERVAL(stree->leaftab[leafindex]);
} else // successor is branch node
{
succptr = stree->branchtab + GETBRANCHINDEX(succ);
GETBOTH(succdepth,headpos,succptr); // get info for branch node
llptr = ll->spaceSimpleloc + ll->nextfreeSimpleloc++;
llptr->textpos = depth + headpos;
llptr->remain = succdepth - depth - 1;
llptr->nextnode.toleaf = false;
llptr->nextnode.address = succptr;
CHECKADDR(stree,llptr->nextnode);
succ = GETBROTHER(succptr);
}
} while(!NILPTR(succ));
}
void getbranchinfostree(Suffixtree *stree,Uint whichinfo,
Branchinfo *branchinfo,Bref btptr)
{
Uint which = whichinfo, node, distance, *largeptr;
if(which & ACCESSSUFFIXLINK)
{
which |= ACCESSDEPTH;
}
if(which & (ACCESSDEPTH | ACCESSHEADPOS))
{
if(stree->chainstart != NULL && btptr >= stree->chainstart)
{
distance = DIVBYSMALLINTS((Uint) (stree->nextfreebranch - btptr));
branchinfo->depth = stree->currentdepth + distance;
branchinfo->headposition = stree->nextfreeleafnum - distance;
} else
{
if(ISLARGE(*btptr))
{
if(which & ACCESSDEPTH)
{
branchinfo->depth = GETDEPTH(btptr);
}
if(which & ACCESSHEADPOS)
{
branchinfo->headposition = GETHEADPOS(btptr);
}
} else
{
distance = GETDISTANCE(btptr);
GETCHAINEND(largeptr,btptr,distance);
if(which & ACCESSDEPTH)
{
branchinfo->depth = GETDEPTH(largeptr) + distance;
}
if(which & ACCESSHEADPOS)
{
branchinfo->headposition = GETHEADPOS(largeptr) - distance;
}
}
}
}
if(which & ACCESSSUFFIXLINK)
{
if((stree->chainstart != NULL && btptr >= stree->chainstart) ||
!ISLARGE(*btptr))
{
branchinfo->suffixlink = btptr + SMALLINTS;
} else
{
branchinfo->suffixlink = stree->branchtab + getlargelinkstree(stree,btptr,branchinfo->depth);
}
/*SHOWINDEX((Uint) BRADDR2NUM(stree,btptr));
fprintf(stdout,"(%u) --> ", GETDEPTH(btptr));
SHOWINDEX((Uint) BRADDR2NUM(stree,branchinfo->suffixlink));
fprintf(stdout," (%u)\n", GETDEPTH(branchinfo->suffixlink));*/
}
if(which & ACCESSFIRSTCHILD)
{
int2ref(stree,&(branchinfo->firstchild),GETCHILD(btptr));
}
if(which & ACCESSBRANCHBROTHER)
{
node = GETBROTHER(btptr);
if(NILPTR(node))
{
branchinfo->branchbrother.address = NULL;
} else
{
int2ref(stree,&(branchinfo->branchbrother),node);
}
}
}
static void scanprefix(Suffixtree *stree) {
Uint *nodeptr = NULL, *largeptr = NULL, leafindex, nodedepth, edgelen, node,
distance = 0, prevnode, prefixlen, headposition;
SYMBOL *leftborder = (SYMBOL *) NULL, tailchar, edgechar = 0;
if(stree->headnodedepth == 0) { // headnode is root
if(stree->tailptr == stree->sentinel) { // there is no \$-edge
stree->headend = NULL;
return;
}
tailchar = *(stree->tailptr);
if((node = stree->rootchildren[(Uint) tailchar]) == 0) {
stree->headend = NULL;
return;
}
if(ISLEAF(node)) { // s.cppessor edge is leaf, compare tail and leaf edge label
leftborder = stree->text + GETLEAFINDEX(node);
prefixlen = 1 + taillcp(stree,leftborder+1,stree->sentinel-1);
(stree->tailptr) += prefixlen;
stree->headstart = leftborder;
stree->headend = leftborder + (prefixlen-1);
stree->insertnode = node;
return;
}
nodeptr = stree->branchtab + GETBRANCHINDEX(node);
GETBOTH(nodedepth,headposition,nodeptr); // get info for branch node
leftborder = stree->text + headposition;
prefixlen = 1 + taillcp(stree,leftborder+1,leftborder + nodedepth - 1);
(stree->tailptr)+= prefixlen;
if(nodedepth > prefixlen) { // cannot reach the s.cppessor, fall out of tree
stree->headstart = leftborder;
stree->headend = leftborder + (prefixlen-1);
stree->insertnode = node;
return;
}
stree->headnode = nodeptr;
stree->headnodedepth = nodedepth;
}
while(True) { // \emph{headnode} is not the root
prevnode = 0;
node = GETCHILD(stree->headnode);
if(stree->tailptr == stree->sentinel) { // \$-edge
do { // there is no \$-edge, so find last s.cppessor, of which it becomes right brother
prevnode = node;
if(ISLEAF(node)) {
node = LEAFBROTHERVAL(stree->leaftab[GETLEAFINDEX(node)]);
} else {
node = GETBROTHER(stree->branchtab + GETBRANCHINDEX(node));
}
} while(!NILPTR(node));
stree->insertnode = NILBIT;
stree->insertprev = prevnode;
stree->headend = NULL;
return;
}
tailchar = *(stree->tailptr);
do { // find s.cppessor edge with firstchar = tailchar
if(ISLEAF(node)) { // s.cppessor is leaf
leafindex = GETLEAFINDEX(node);
leftborder = stree->text + (stree->headnodedepth + leafindex);
if((edgechar = *leftborder) >= tailchar) { // edge will not come later
break;
}
prevnode = node;
node = LEAFBROTHERVAL(stree->leaftab[leafindex]);
} else { // s.cppessor is branch node
nodeptr = stree->branchtab + GETBRANCHINDEX(node);
GETONLYHEADPOS(headposition,nodeptr);
leftborder = stree->text + (stree->headnodedepth + headposition);
if((edgechar = *leftborder) >= tailchar) { // edge will not come later
break;
}
prevnode = node;
node = GETBROTHER(nodeptr);
}
} while(!NILPTR(node));
if(NILPTR(node) || edgechar > tailchar) { // edge not found
stree->insertprev = prevnode; // new edge will become brother of this
stree->headend = NULL;
return;
}
if(ISLEAF(node)) { // correct edge is leaf edge, compare its label with tail
prefixlen = 1 + taillcp(stree,leftborder+1,stree->sentinel-1);
(stree->tailptr) += prefixlen;
stree->headstart = leftborder;
stree->headend = leftborder + (prefixlen-1);
stree->insertnode = node;
stree->insertprev = prevnode;
return;
}
GETDEPTHAFTERHEADPOS(nodedepth,nodeptr); // we already know headposition
edgelen = nodedepth - stree->headnodedepth;
prefixlen = 1 + taillcp(stree,leftborder+1,leftborder + edgelen - 1);
(stree->tailptr) += prefixlen;
if(edgelen > prefixlen) { // cannot reach next node
stree->headstart = leftborder;
stree->headend = leftborder + (prefixlen-1);
stree->insertnode = node;
stree->insertprev = prevnode;
return;
}
stree->headnode = nodeptr;
stree->headnodedepth = nodedepth;
}
}
static void rescan (Suffixtree *stree) {
Uint *nodeptr, *largeptr = NULL, distance = 0, node, prevnode,
nodedepth, edgelen, wlen, leafindex, headposition;
SYMBOL headchar, edgechar;
if(stree->headnodedepth == 0) { // head is the root
headchar = *(stree->headstart); // headstart is assumed to be not empty
node = stree->rootchildren[(Uint) headchar];
if(ISLEAF(node)) { // stop if s.cppessor is leaf
stree->insertnode = node;
return;
}
nodeptr = stree->branchtab + GETBRANCHINDEX(node);
GETONLYDEPTH(nodedepth,nodeptr);
wlen = (Uint) (stree->headend - stree->headstart + 1);
if(nodedepth > wlen) { // cannot reach the s.cppessor node
stree->insertnode = node;
return;
}
stree->headnode = nodeptr; // go to s.cppessor node
stree->headnodedepth = nodedepth;
if(nodedepth == wlen) { // location has been scanned
stree->headend = NULL;
return;
}
(stree->headstart) += nodedepth;
}
while(True) { // \emph{headnode} is not the root
headchar = *(stree->headstart); // \emph{headstart} is assumed to be nonempty
prevnode = 0;
node = GETCHILD(stree->headnode);
while(True) { // traverse the list of s.cppessors
if(ISLEAF(node)) { // s.cppessor is leaf
leafindex = GETLEAFINDEX(node);
edgechar = stree->text[stree->headnodedepth + leafindex];
if(edgechar == headchar) { // correct edge found
stree->insertnode = node;
stree->insertprev = prevnode;
return;
}
prevnode = node;
node = LEAFBROTHERVAL(stree->leaftab[leafindex]);
} else { // s.cppessor is branch node
nodeptr = stree->branchtab + GETBRANCHINDEX(node);
GETONLYHEADPOS(headposition,nodeptr);
edgechar = stree->text[stree->headnodedepth + headposition];
if(edgechar == headchar) { // correct edge found
break;
}
prevnode = node;
node = GETBROTHER(nodeptr);
}
}
GETDEPTHAFTERHEADPOS(nodedepth,nodeptr); // get info about s.cpp node
edgelen = nodedepth - stree->headnodedepth;
wlen = (Uint) (stree->headend - stree->headstart + 1);
if(edgelen > wlen) { // cannot reach the s.cpp node
stree->insertnode = node;
stree->insertprev = prevnode;
return;
}
stree->headnode = nodeptr; // go to the s.cppessor node
stree->headnodedepth = nodedepth;
if(edgelen == wlen) { // location is found
stree->headend = NULL;
return;
}
(stree->headstart) += edgelen;
}
}
Sint depthfirststree(Suffixtree *stree,Reference *startnode,
Sint (*processleaf)(Uint,Bref,void *),
bool (*processbranch1)(Bref,void *),
Sint (*processbranch2)(Bref,void *),
bool (*stoptraversal)(void *),void *stopinfo,void *info)
{
bool godown = true, readyforpop = false;
Uint child, brotherval;
Bref lcpnode = NULL;
Reference currentnode;
ArrayBref stack;
if(startnode->toleaf)
{
if(processleaf((Uint) (startnode->address - stree->leaftab),NULL,info) != 0)
{
return -1;
}
return 0;
}
if(stoptraversal != NULL && stoptraversal(stopinfo))
{
return 0;
}
currentnode.toleaf = false;
currentnode.address = startnode->address;
INITARRAY(&stack,Bref);
STOREINARRAY(&stack,Bref,128,currentnode.address);
SETCURRENT(GETCHILD(currentnode.address));
if(processbranch1 == NULL)
{
#define PROCESSBRANCH1(A,B) /* Nothing */
#define PROCESSBRANCH2(A,B) godown = true
while(true)
{
if(stoptraversal != NULL && stoptraversal(stopinfo))
{
return 0;
}
if(currentnode.toleaf)
{
/*fprintf(stderr,"visit leaf %lu ",
(long unsigned int) LEAFADDR2NUM(stree,currentnode.address));
fprintf(stderr,"below %lu ",(long unsigned int) BRADDR2NUM(stree,startnode->address));
fprintf(stderr,"depth %lu\n",stree->currentdepth);*/
if(processleaf(LEAFADDR2NUM(stree,currentnode.address),lcpnode,info) != 0)
{
return -1;
}
brotherval = LEAFBROTHERVAL(*(currentnode.address));
if(NILPTR(brotherval))
{
readyforpop = true;
currentnode.toleaf = false;
} else
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
}
} else
{
if(readyforpop)
{
if(stack.nextfreeBref == UintConst(1))
{
break;
}
(stack.nextfreeBref)--;
/*fprintf(stderr,"#pop[%lu]=",(long unsigned int) stack.nextfreeBref);
fprintf(stderr,"%lu\n",
(long unsigned int) BRADDR2NUM(stree,stack.spaceBref[stack.nextfreeBref]));*/
PROCESSBRANCH2(stack.spaceBref[stack.nextfreeBref],info);
brotherval = GETBROTHER(stack.spaceBref[stack.nextfreeBref]);
if(!NILPTR(brotherval))
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
readyforpop = false;
}
} else
{
/*fprintf(stderr,"#process1 %lu\n",
(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
PROCESSBRANCH1(currentnode.address,info);
if(godown)
{
STOREINARRAY(&stack,Bref,128,currentnode.address);
/*fprintf(stderr,"#push[%lu]=",(long unsigned int) (stack.nextfreeBref-1));
fprintf(stderr,"%lu\n",(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
child = GETCHILD(currentnode.address);
SETCURRENT(child); // current comes from child
} else
{
brotherval = GETBROTHER(currentnode.address);
if(NILPTR(brotherval))
{
readyforpop = true;
} else
{
SETCURRENT(brotherval); // current comes brother
}
}
}
}
}
} else
{
#undef PROCESSBRANCH1
#undef PROCESSBRANCH2
#define PROCESSBRANCH1(A,B) godown = processbranch1(A,B)
#define PROCESSBRANCH2(A,B) if(processbranch2(A,B) != 0)\
{\
return -2;\
}
while(true)
{
if(stoptraversal != NULL && stoptraversal(stopinfo))
{
return 0;
}
if(currentnode.toleaf)
{
/*fprintf(stderr,"visit leaf %lu ",
(long unsigned int) LEAFADDR2NUM(stree,currentnode.address));
fprintf(stderr,"below %lu ",(long unsigned int) BRADDR2NUM(stree,startnode->address));
fprintf(stderr,"depth %lu\n",stree->currentdepth);*/
if(processleaf(LEAFADDR2NUM(stree,currentnode.address),lcpnode,info) != 0)
{
return -1;
}
brotherval = LEAFBROTHERVAL(*(currentnode.address));
if(NILPTR(brotherval))
{
readyforpop = true;
currentnode.toleaf = false;
} else
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
}
} else
{
if(readyforpop)
{
if(stack.nextfreeBref == UintConst(1))
{
break;
}
(stack.nextfreeBref)--;
/*fprintf(stderr,"#pop[%lu]=",(long unsigned int) stack.nextfreeBref);
fprintf(stderr,"%lu\n",
(long unsigned int) BRADDR2NUM(stree,stack.spaceBref[stack.nextfreeBref]));*/
PROCESSBRANCH2(stack.spaceBref[stack.nextfreeBref],info);
brotherval = GETBROTHER(stack.spaceBref[stack.nextfreeBref]);
if(!NILPTR(brotherval))
{
SETCURRENT(brotherval); // current comes from brother
lcpnode = stack.spaceBref[stack.nextfreeBref-1];
readyforpop = false;
}
} else
{
/*fprintf(stderr,"#process1 %lu\n",
(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
PROCESSBRANCH1(currentnode.address,info);
if(godown)
{
STOREINARRAY(&stack,Bref,128,currentnode.address);
/*fprintf(stderr,"#push[%lu]=",(long unsigned int) (stack.nextfreeBref-1));
fprintf(stderr,"%lu\n",(long unsigned int) BRADDR2NUM(stree,currentnode.address));*/
child = GETCHILD(currentnode.address);
SETCURRENT(child); // current comes from child
} else
{
brotherval = GETBROTHER(currentnode.address);
if(NILPTR(brotherval))
{
readyforpop = true;
} else
{
SETCURRENT(brotherval); // current comes brother
}
}
}
}
}
}
FREEARRAY(&stack,Bref);
return 0;
}
