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
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
|
package com.wcohen.ss.abbvGapsHmm;
import java.util.List;
import com.wcohen.ss.abbvGapsHmm.AbbvGapsHMM.Emissions;
/**
* @author Dana Movshovitz-Attias
*/
public class AbbreviationAlignmentContainer<T extends Enum<T>, S extends Enum<S>> {
private List<String> _lAlign;
private List<String> _sAlign;
private Double _bestProbability;
private List<T> _emissionsPath;
private List<S> _statesPath;
private int _numDeletionsInAcronym = -1;
private int _acronymScore = 0;
AbbreviationAlignmentContainer(List<String> sAlign, List<String> lAlign, List<T> emissionsPath, List<S> statesPath, Double probability){
_sAlign = sAlign;
_lAlign = lAlign;
_emissionsPath = emissionsPath;
_statesPath = statesPath;
_bestProbability = probability;
}
AbbreviationAlignmentContainer(List<String> sAlign, List<String> lAlign, List<T> emissionsPath, Double probability){
_sAlign = sAlign;
_lAlign = lAlign;
_emissionsPath = emissionsPath;
_statesPath = null;
_bestProbability = probability;
}
public Double getProbability(){
return _bestProbability;
}
public List<String> getLAlign(){
return _lAlign;
}
public List<String> getSAlign(){
return _sAlign;
}
public List<T> retrunBestStates(){
return _emissionsPath;
}
protected String getStrByEmission(String str, T emission){
String out = str;
if(Emissions.e_END_end.equals(emission) || Emissions.e_M_nonAlphaNumeric_to_none.equals(emission)){
out = "";
}
else if(Emissions.e_M_partialWord_to_letter.equals(emission) ||
Emissions.e_M_word_to_firstLetter.equals(emission)){
out = str.substring(0, 1);
}
if(Emissions.e_M_AND_to_symbol.equals(emission)){
out = "&";
}
return out;
}
public Acronym getAcronym(){
String sf = "";
String lf = "";
String preSF = "";
String preLF = "";
boolean started = false;
int latestWordStart = -1;
int numDeletions = 0;
int score = 0;
for (int i = 0; i < _sAlign.size(); i++) {
String sPart = _sAlign.get(i);
String lPart = _lAlign.get(i);
T emission = _emissionsPath.get(i);
if(!started && emission.name().contains("none") ){
// record latest word start
if(Character.isDigit(lPart.charAt(0))){
latestWordStart = i;
}
else if(Character.isWhitespace(lPart.charAt(0)) || Character.isLetter(lPart.charAt(0))){
latestWordStart = -1;
preSF = "";
preLF = "";
numDeletions = 0;
score = 0;
}
// Accumulate header
if(latestWordStart != -1){
preSF += sPart;
preLF += lPart;
if(emission.name().startsWith("e_D_") || emission.name().startsWith("e_DL_")){
numDeletions++;
score--;
}
else if(emission.name().startsWith("e_M_") || emission.name().contains("word")){
score++;
}
}
continue;
}
started = true;
if(emission.name().startsWith("e_D_") || emission.name().startsWith("e_DL_")){
numDeletions++;
score--;
}
else if(emission.name().startsWith("e_M_") && ( emission.name().contains("word") || emission.name().contains("Word") )){
score++;
}
sf += sPart;
lf += lPart;
}
if(sf.isEmpty() || lf.isEmpty())
return null;
if(sf.equalsIgnoreCase(lf))
return null;
String finalSF = preSF+sf;
String finalLF = preLF+lf;
// Single letter SF can only match one word
if(finalSF.length() == 1 && finalLF.indexOf(" ") != -1)
return null;
_numDeletionsInAcronym = numDeletions;
_acronymScore = score;
if(_acronymScore < 0)
return null;
return new Acronym(finalSF, finalLF);
}
public int getAcronymScore() {
return _acronymScore;
}
public int getNumDeletionsInAcronym() {
return _numDeletionsInAcronym;
}
public String toString(){
if(_statesPath == null)
return toStringNoStates();
return toStringWithStates();
}
public String toStringNoStates(){
String sFinal = "";
String lFinal = "";
int maxLen;
for (int i = 0; i < _sAlign.size(); i++) {
String sPart = _sAlign.get(i);
String lPart = _lAlign.get(i);
maxLen = Math.max(sPart.length(), lPart.length());
sFinal += String.format("%-"+maxLen+"s", sPart) + "|";
lFinal += String.format("%-"+maxLen+"s", lPart) + "|";
}
return sFinal+"\n"+lFinal;
}
public String toStringWithStates(){
String sFinal = "";
String lFinal = "";
String stateFinal = "";
int maxLen;
for (int i = 0; i < _sAlign.size(); i++) {
String sPart = _sAlign.get(i);
String lPart = _lAlign.get(i);
String statePart = _statesPath.get(i).name();
maxLen = Math.max(sPart.length(), lPart.length());
maxLen = Math.max(maxLen, statePart.length());
stateFinal += String.format("%-"+maxLen+"s", statePart) + "|";
sFinal += String.format("%-"+maxLen+"s", sPart) + "|";
lFinal += String.format("%-"+maxLen+"s", lPart) + "|";
}
return stateFinal+"\n"+sFinal+"\n"+lFinal;
}
public String toStringWithEmissions(){
String sFinal = "";
String lFinal = "";
String stateFinal = "";
String emissionsFinal = "Emissions: ";
int maxLen;
for (int i = 0; i < _sAlign.size(); i++) {
String sPart = _sAlign.get(i);
String lPart = _lAlign.get(i);
String statePart = _statesPath.get(i).name();
String emissionPart = _emissionsPath.get(i).name();
maxLen = Math.max(sPart.length(), lPart.length());
maxLen = Math.max(maxLen, statePart.length());
emissionsFinal += emissionPart + "|";
stateFinal += String.format("%-"+maxLen+"s", statePart) + "|";
sFinal += String.format("%-"+maxLen+"s", sPart) + "|";
lFinal += String.format("%-"+maxLen+"s", lPart) + "|";
}
return stateFinal+"\n"+sFinal+"\n"+lFinal+"\n\n"+emissionsFinal;
}
}
|
