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Viewing changes to src/pal/treesearch/FreeInternalNode.java

  • Committer: Package Import Robot
  • Author(s): Andreas Tille
  • Date: 2012-01-27 13:57:54 UTC
  • Revision ID: package-import@ubuntu.com-20120127135754-d63l3581f65fw9pk
Tags: upstream-1.5.1
Import upstream version 1.5.1

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src/pal/treesearch/FreeInternalNode.java
 
1
// FreeInternalNode.java
 
2
//
 
3
// (c) 1999-2004 PAL Development Core Team
 
4
//
 
5
// This package may be distributed under the
 
6
// terms of the Lesser GNU General Public License (LGPL)
 
7
 
 
8
package pal.treesearch;
 
9
 
 
10
/**
 
11
 * <p>Title: FreeInternalNode </p>
 
12
 * <p>Description: A free internal node has three FreeBranches connected to it. </p>
 
13
 * @author Matthew Goode
 
14
 * @version 1.0
 
15
 */
 
16
import java.util.*;
 
17
 
 
18
import pal.eval.*;
 
19
import pal.tree.*;
 
20
 
 
21
public class FreeInternalNode implements FreeNode {
 
22
        private final FreeBranch[] connections_ = new FreeBranch[3];
 
23
        private final FreeBranch[] markConnections_ = new FreeBranch[3];
 
24
 
 
25
        private final PatternInfo[] patternInfos_;
 
26
        private final boolean[] patternsValid_;
 
27
 
 
28
        private static final int[] LEFT_LOOKUP = {      1 , 0, 0        };
 
29
        private static final int[] RIGHT_LOOKUP = {     2 , 2, 1        };
 
30
 
 
31
//      private final int index_;
 
32
        private final UnconstrainedLikelihoodModel.Internal calculator_;
 
33
        private boolean topologyChangedSinceLastFlat_ = true;
 
34
        private boolean topologyChangedSincleLastExtended_ = true;
 
35
 
 
36
 
 
37
        public FreeInternalNode(Node i, FreeBranch parentFreeBranch, GeneralConstructionTool tool, GeneralConstraintGroupManager.Store store) {
 
38
                this.connections_[0] = parentFreeBranch;
 
39
                this.connections_[1] = new FreeBranch(i.getChild(0),this, tool,store);
 
40
                this.connections_[2] = new FreeBranch(i.getChild(1),this, tool,store);
 
41
                this.patternsValid_ = new boolean[] { false, false, false};
 
42
 
 
43
                this.calculator_ = tool.allocateNewFreeInternalCalculator();
 
44
                final int numberOfSites = tool.getNumberOfSites();
 
45
                this.patternInfos_ = new PatternInfo[] {
 
46
                                                                                         new PatternInfo( numberOfSites, true ),
 
47
                                                                                         new PatternInfo( numberOfSites, true ),
 
48
                                                                                         new PatternInfo( numberOfSites, true )
 
49
                        };
 
50
 
 
51
        }
 
52
 
 
53
 
 
54
 
 
55
        public void mark() {
 
56
                markConnections_[0] = connections_[0];
 
57
                markConnections_[1] = connections_[1];
 
58
                markConnections_[2] = connections_[2];
 
59
        }
 
60
        public void undoToMark() {
 
61
                connections_[0] = markConnections_[0];
 
62
                connections_[1] = markConnections_[1];
 
63
                connections_[2] = markConnections_[2];
 
64
                topologyChanged();
 
65
        }
 
66
        private final void topologyChanged() {
 
67
                this.topologyChangedSinceLastFlat_ = true;
 
68
                this.topologyChangedSincleLastExtended_ = true;
 
69
        }
 
70
        public boolean hasDirectConnection(FreeBranch c) {
 
71
                for(int i = 0 ; i < connections_.length ; i++) {
 
72
                                if(connections_[i]==c) {        return true;    }
 
73
                        }
 
74
                        return false;
 
75
 
 
76
        }
 
77
        public boolean hasConnection(FreeBranch c, FreeBranch caller) {
 
78
                for(int i = 0 ; i < connections_.length ; i++) {
 
79
                        if((connections_[i]==c)||(connections_[i]!=caller&&connections_[i].hasConnection(c,this))) {
 
80
                                return true;
 
81
                        }
 
82
                }
 
83
                return false;
 
84
        }
 
85
 
 
86
//      public final int getIndex() { return index_; }
 
87
        public void testLikelihood(FreeBranch caller, GeneralConstructionTool tool) {
 
88
                for(int i = 0 ; i < connections_.length ; i++) {
 
89
                        if(connections_[i]!=caller) {
 
90
                                connections_[i].testLikelihood(this,tool);
 
91
                        }
 
92
                }
 
93
        }
 
94
        public void setConnectingBranches(FreeBranch[] store, int number){
 
95
                if(number!=3) {
 
96
                        throw new IllegalArgumentException("Must be three connections not:"+number);
 
97
                }
 
98
                System.arraycopy(store,0,connections_,0,3);
 
99
                topologyChanged();
 
100
        }
 
101
        //Interchange related
 
102
        public FreeBranch getLeftBranch(FreeBranch caller) {
 
103
                return connections_[LEFT_LOOKUP[getCallerIndex(caller)]];
 
104
        }
 
105
 
 
106
        public FreeBranch getRightBranch(FreeBranch caller) {
 
107
                return connections_[RIGHT_LOOKUP[getCallerIndex(caller)]];
 
108
        }
 
109
        public FreeBranch extract(FreeBranch caller) {
 
110
                int callerIndex = getCallerIndex(caller);
 
111
                FreeBranch left = connections_[LEFT_LOOKUP[callerIndex]];
 
112
                FreeBranch right = connections_[RIGHT_LOOKUP[callerIndex]];
 
113
                FreeNode rightNode = right.getOther(this);
 
114
                left.swapNode(this,rightNode);
 
115
                rightNode.swapConnection(right,left);
 
116
                topologyChanged();
 
117
                return right;
 
118
        }
 
119
        public void swapConnection(FreeBranch original, FreeNode nodeToReplace, FreeBranch newConnection) {
 
120
                int index = getCallerIndex(original);
 
121
                connections_[index] = newConnection;
 
122
                newConnection.swapNode(nodeToReplace,this);
 
123
                original.swapNode(this,nodeToReplace);
 
124
 
 
125
                nodeToReplace.swapConnection(newConnection,original);
 
126
                topologyChanged();
 
127
        }
 
128
        public void swapConnection(FreeBranch original,FreeBranch newConnection) {
 
129
                int index = getCallerIndex(original);
 
130
                connections_[index] = newConnection;
 
131
                topologyChanged();
 
132
        }
 
133
        public PatternInfo getPatternInfo(GeneralConstructionTool tool, FreeBranch caller) {
 
134
          return getPatternInfo( tool, getCallerIndex(caller));
 
135
        }
 
136
 
 
137
        private final PatternInfo getPatternInfo(final GeneralConstructionTool tool, final int callerIndex) {
 
138
 
 
139
                if(!patternsValid_[callerIndex]) {
 
140
                        //Need to rebuild
 
141
                        final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
142
                        final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
143
                  final FreeNode left = leftConnection.getOther(this);
 
144
                  final FreeNode right = rightConnection.getOther(this);
 
145
                  final PatternInfo leftPattern= left.getPatternInfo(tool,leftConnection);
 
146
                  final PatternInfo rightPattern= right.getPatternInfo(tool,rightConnection);
 
147
                        tool.build(patternInfos_[callerIndex],leftPattern, rightPattern);
 
148
                  patternsValid_[callerIndex] = true;
 
149
                }
 
150
                return patternInfos_[callerIndex];
 
151
        }
 
152
 
 
153
        public Node buildPALNodeES(double branchLength, FreeBranch caller) {
 
154
                final int callerIndex = getCallerIndex(caller);
 
155
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
156
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
157
                Node[] children = new Node[] {
 
158
                        leftConnection.buildPALNodeES(this), rightConnection.buildPALNodeES(this)
 
159
                };
 
160
                return NodeFactory.createNodeBranchLength(branchLength,children);
 
161
        }
 
162
        public Node buildPALNodeBase(double branchLength, FreeBranch caller) {
 
163
                final int callerIndex = getCallerIndex(caller);
 
164
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
165
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
166
                Node[] children = new Node[] {
 
167
                        leftConnection.buildPALNodeBase(this), rightConnection.buildPALNodeBase(this)
 
168
                };
 
169
                return NodeFactory.createNodeBranchLength(branchLength,children);
 
170
        }
 
171
 
 
172
        public String toString(FreeBranch caller) {
 
173
                StringBuffer sb = new StringBuffer();
 
174
                boolean printed = false;
 
175
                for(int i = 0 ; i < connections_.length ; i++) {
 
176
                        if(connections_[i]!=caller) {
 
177
                                if(printed) {
 
178
                                        sb.append(", ");
 
179
                                }
 
180
                                printed = true;
 
181
                                sb.append(connections_[i].toString(this));
 
182
                        }
 
183
                }
 
184
                return sb.toString();
 
185
        }
 
186
// ==============
 
187
        public void getAllComponents(ArrayList store, Class componentType) {
 
188
                getAllComponents(store, componentType, null);
 
189
        }
 
190
        public void getAllComponents(ArrayList store, Class componentType, FreeBranch caller) {
 
191
                if(componentType.isAssignableFrom(getClass())) { store.add(this); }
 
192
                for(int i = 0 ; i < connections_.length ; i++) {
 
193
                        if(connections_[i]!=caller) {
 
194
                                connections_[i].getAllComponents(store,componentType, this);
 
195
                        }
 
196
                }
 
197
        }
 
198
 
 
199
 
 
200
// ==============
 
201
 
 
202
        private final int getCallerIndex(FreeBranch caller) {
 
203
                if(caller==null) {
 
204
                        throw new IllegalArgumentException("getCallerIndex() called on null object");
 
205
                }
 
206
                if(caller==connections_[0]) { return 0; }
 
207
                if(caller==connections_[1]) { return 1; }
 
208
                if(caller==connections_[2]) { return 2; }
 
209
                throw new IllegalArgumentException("Unknown caller");
 
210
        }
 
211
 
 
212
 
 
213
 
 
214
        public ConditionalProbabilityStore getLeftExtendedConditionalProbabilities( FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) {
 
215
                final int callerIndex = getCallerIndex(callingConnection);
 
216
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
217
                return leftConnection.getExtendedConditionalProbabilities(this,external, resultStore,tool);
 
218
        }
 
219
        public ConditionalProbabilityStore getRightExtendedConditionalProbabilities( FreeBranch callingConnection, UnconstrainedLikelihoodModel.External external, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) {
 
220
                final int callerIndex = getCallerIndex(callingConnection);
 
221
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
222
                return rightConnection.getExtendedConditionalProbabilities( this, external, resultStore,tool);
 
223
        }
 
224
        public PatternInfo getLeftPatternInfo(GeneralConstructionTool tool, FreeBranch caller) {
 
225
                final int callerIndex = getCallerIndex(caller);
 
226
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
227
                final FreeNode other = leftConnection.getOther(this);
 
228
                return other.getPatternInfo(tool, leftConnection);
 
229
        }
 
230
 
 
231
        public PatternInfo getRightPatternInfo(GeneralConstructionTool tool, FreeBranch caller) {
 
232
                final int callerIndex = getCallerIndex(caller);
 
233
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
234
                final FreeNode other = rightConnection.getOther(this);
 
235
                return other.getPatternInfo(tool, rightConnection);
 
236
        }
 
237
 
 
238
 
 
239
        public ConditionalProbabilityStore getFlatConditionalProbabilities(  final FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, GeneralConstructionTool tool) {
 
240
                final int callerIndex = getCallerIndex(callerConnection);
 
241
                final PatternInfo pi = getPatternInfo(tool, callerIndex);
 
242
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
243
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
244
 
 
245
                externalCalculator.calculateFlat(
 
246
                                 pi,
 
247
                                 leftConnection.getExtendedConditionalProbabilities(this,tool),
 
248
                                 rightConnection.getExtendedConditionalProbabilities(this,tool),
 
249
                                 resultStore
 
250
                                 );
 
251
                return resultStore;
 
252
 
 
253
        }
 
254
        public ConditionalProbabilityStore getFlatConditionalProbabilities(  final FreeBranch callerConnection, GeneralConstructionTool tool) {
 
255
                final int callerIndex = getCallerIndex(callerConnection);
 
256
                final PatternInfo pi = getPatternInfo(tool, callerIndex);
 
257
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
258
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
259
                final boolean childrenChanged = topologyChangedSinceLastFlat_;
 
260
                topologyChangedSinceLastFlat_ = false;
 
261
                return calculator_.calculateFlat( pi,
 
262
                                 leftConnection.getExtendedConditionalProbabilities(this,tool),
 
263
                                 rightConnection.getExtendedConditionalProbabilities(this,tool)
 
264
                                 );
 
265
        }
 
266
        public ConditionalProbabilityStore getExtendedConditionalProbabilities( final double distance,  final FreeBranch callerConnection, UnconstrainedLikelihoodModel.External externalCalculator, ConditionalProbabilityStore resultStore, final GeneralConstructionTool tool) {
 
267
                final int callerIndex = getCallerIndex(callerConnection);
 
268
                final PatternInfo pi = getPatternInfo(tool, callerIndex);
 
269
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
270
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
271
 
 
272
 
 
273
                externalCalculator.calculateExtended(
 
274
                        distance, pi,
 
275
                        leftConnection.getExtendedConditionalProbabilities(this,tool),
 
276
                        rightConnection.getExtendedConditionalProbabilities(this,tool),
 
277
                        resultStore
 
278
                        );
 
279
                return resultStore;
 
280
        }
 
281
        public ConditionalProbabilityStore getExtendedConditionalProbabilities( final double distance, final FreeBranch callerConnection, GeneralConstructionTool tool) {
 
282
                final int callerIndex = getCallerIndex(callerConnection);
 
283
                final PatternInfo pi = getPatternInfo(tool, callerIndex);
 
284
                final FreeBranch leftConnection = connections_[LEFT_LOOKUP[callerIndex]];
 
285
                final FreeBranch rightConnection = connections_[RIGHT_LOOKUP[callerIndex]];
 
286
                final boolean childrenChanged = topologyChangedSincleLastExtended_;
 
287
                topologyChangedSincleLastExtended_ = false;
 
288
                return calculator_.calculateExtended(
 
289
                        distance, pi,
 
290
                        leftConnection.getExtendedConditionalProbabilities(this,tool),
 
291
                        rightConnection.getExtendedConditionalProbabilities( this,tool)
 
292
                );
 
293
        }
 
294
}