1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
|
/*
* KSeg
* Copyright (C) 1999-2006 Ilya Baran
*
* This program is free software; you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
* the Free Software Foundation; either version 2 of the License, or
* (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 675 Mass Ave, Cambridge, MA 02139, USA.
*
* Send comments and/or bug reports to:
* ibaran@mit.edu
*/
#include "G_ref.H"
#include "G_refs.H"
#include "G_refSearcher.H"
#include "my_hash_set.H"
struct topSortState
{
topSortState(G_ref *e, int c) : element(e), child(c) {}
G_ref *element;
int child;
};
G_refs::G_refs()
{
mHoldingRemovals = false; mToBeRemoved = NULL;
}
G_refs::~G_refs()
{
ASSERT(!mHoldingRemovals);
}
void G_refs::appendUnique(G_ref *r)
{
if(findRef(r) == -1) append(r);
}
void G_refs::update(bool fromLocus)
{
//if fromLocus is true, formulas are not reparsed.
int i;
for(i = 0; i < (int)count(); i++) at(i)->update(fromLocus);
}
void G_refs::removeRef(G_ref *r)
{
if(mHoldingRemovals) mToBeRemoved->insert(r);
else remove(find(r));
}
bool G_refs::operator==(G_refs &r)
{
if(count() != r.count()) return false;
int i;
for(i = 0; i < (int)count(); i++) if(at(i) != r.at(i)) return false;
return true;
}
void G_refs::holdRemovals()
{
ASSERT(!mHoldingRemovals);
mHoldingRemovals = true;
mToBeRemoved = new hash_set<G_ref *>();
}
void G_refs::commitRemovals()
{
ASSERT(mHoldingRemovals);
int i;
int offs = 0;
for(i = 0; i < (int)count(); i++) {
(*this)[i - offs] = at(i);
if(mToBeRemoved->count(at(i))) offs++;
}
erase(end() - offs, end());
mHoldingRemovals = false;
delete mToBeRemoved;
mToBeRemoved = NULL;
}
void G_refs::topologicalSort(G_refs toBeAdded, const G_ref *target)
{
//this function creates a list such that every object comes after all its parents.
//all children of objects in toBeAdded will be inserted into the list.
//uses a hash table to keep track of what's been added.
//target is when only a certain object needs to be updated (like for loci). It's NULL by default.
int i;
clear();
hash_set<G_ref *> added;
vector<topSortState> stateStack;
AncestorSearcher *as = NULL;
if(target) as = new AncestorSearcher(target);
//loops are separate:
G_refs loops;
for(i = 0; i < (int)toBeAdded.count(); ++i) {
if(toBeAdded[i]->getType() == G_LOOP) {
loops.push_back(toBeAdded[i]);
}
}
//main loop:
for(i = 0; i < (int)toBeAdded.count(); ++i) {
if(added.count(toBeAdded[i])) continue;
added.insert(toBeAdded[i]);
stateStack.push_back(topSortState(toBeAdded[i], 0));
while(stateStack.size()) {
topSortState &state = stateStack.back();
if(state.child >= (int)state.element->getChildrenConst().count()) {
//finished!
if(state.element->getType() == G_LOOP) {
loops.appendUnique(state.element);
}
else {
append(state.element);
}
stateStack.pop_back();
continue;
}
G_ref *newRef = state.element->getChildrenConst()[state.child];
state.child++;
if(added.count(newRef)) continue;
if(target && !as->search(newRef)) continue;
added.insert(newRef);
stateStack.push_back(topSortState(newRef, 0));
}
}
reverse(begin(), end());
vector<G_ref *>::insert(end(), loops.begin(), loops.end());
if(target) delete as;
}
|
