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comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/tax/TaxNode.java @ 68:5028fdace37b

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planemo upload commit 2e9511a184a1ca667c7be0c6321a36dc4e3d116d
author jpayne
date Tue, 18 Mar 2025 16:23:26 -0400
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67:0e9998148a16 68:5028fdace37b
1 package tax;
2
3 import java.io.Serializable;
4 import java.util.Comparator;
5
6 import shared.Tools;
7
8 /**
9 * Represents a taxonomic identifier, such as a specific genus.
10 * Includes the name, NCBI numeric id, parent id, and taxonomic level.
11 * @author Brian Bushnell
12 * @date Mar 6, 2015
13 *
14 */
15 public class TaxNode implements Serializable{
16
17 /**
18 *
19 */
20 private static final long serialVersionUID = -4618526038942239246L;
21
22 /*--------------------------------------------------------------*/
23 /*---------------- Initialization ----------------*/
24 /*--------------------------------------------------------------*/
25
26 public TaxNode(int id_, String name_){
27 this(id_, -1, -1, -1, name_);
28 }
29
30 public TaxNode(int id_, int parent_, int level_, int levelExtended_, String name_){
31 id=id_;
32 pid=parent_;
33 level=level_;
34 levelExtended=levelExtended_;
35 setOriginalLevel(levelExtended);
36 name=name_;
37 }
38
39 /*--------------------------------------------------------------*/
40 /*---------------- Methods ----------------*/
41 /*--------------------------------------------------------------*/
42
43 /**
44 * @param split
45 * @param idx
46 * @return True if the node's name matches the
47 */
48 public boolean matchesName(String[] split, int idx, TaxTree tree) {
49 if(idx<0){return true;}
50 if(!split[idx].equalsIgnoreCase(name)){return false;}
51 return tree.getNode(pid).matchesName(split, idx-1, tree);
52 }
53
54 @Override
55 public String toString(){
56 return "("+id+","+pid+","+countRaw+","+countSum+",'"+levelStringExtended(false)+"',"+(canonical() ? "T" : "F")+",'"+name+"')";
57 }
58
59 public boolean equals(TaxNode b){
60 if(id!=b.id || pid!=b.pid || levelExtended!=b.levelExtended || flag!=b.flag){return false;}
61 if(name==b.name){return true;}
62 if((name==null) != (b.name==null)){return false;}
63 return name.equals(b.name);
64 }
65
66 public long incrementRaw(long amt){
67 if(amt==0){return countRaw;}
68 if(verbose){System.err.println("incrementRaw("+amt+") node: "+this);}
69 countRaw+=amt;
70 assert(countRaw>=0) : "Overflow! "+countRaw+", "+amt;
71 return countRaw;
72 }
73
74 public long incrementSum(long amt){
75 if(amt==0){return countSum;}
76 if(verbose){System.err.println("incrementSum("+amt+") node: "+this);}
77 countSum+=amt;
78 assert(countSum>=0 || amt<0) : "Overflow! "+countSum+", "+amt;
79 return countSum;
80 }
81
82 public boolean isSimple(){
83 return TaxTree.isSimple(levelExtended);
84 }
85
86 public boolean isSimple2(){
87 return TaxTree.isSimple2(levelExtended);
88 }
89
90 // public String levelString(){return level<0 ? "unknown" : TaxTree.levelToString(level);}
91
92 public String levelStringExtended(boolean original){
93 int x=(original ? originalLevel() : levelExtended);
94 return x<0 ? "unknown" : TaxTree.levelToStringExtended(x);
95 }
96
97 public String levelToStringShort() {return level<0 ? "x" : TaxTree.levelToStringShort(level);}
98
99
100
101 public boolean isUnclassified(){
102 return name.startsWith("unclassified");
103 }
104
105 public boolean isEnvironmentalSample(){
106 return name.startsWith("environmental");
107 }
108
109 /*--------------------------------------------------------------*/
110 /*---------------- Nested Classes ----------------*/
111 /*--------------------------------------------------------------*/
112
113 public static class CountComparator implements Comparator<TaxNode>{
114
115 @Override
116 public int compare(TaxNode a, TaxNode b) {
117 long x=b.countSum-a.countSum;
118 // System.err.println("x="+x+" -> "+Tools.longToInt(x));
119 if(x!=0){return Tools.longToInt(x);}
120 return a.levelExtended==b.levelExtended ? a.id-b.id : a.levelExtended-b.levelExtended;
121 }
122
123 }
124
125 /*--------------------------------------------------------------*/
126 /*---------------- Getters ----------------*/
127 /*--------------------------------------------------------------*/
128
129 @Override
130 public final int hashCode(){return id;}
131
132 /*--------------------------------------------------------------*/
133
134 public boolean canonical(){
135 return (flag&CANON_MASK)==CANON_MASK;
136 }
137
138 public boolean levelChanged(){
139 return originalLevel()!=levelExtended;
140 }
141
142 public int originalLevel(){
143 int x=(int)(flag&ORIGINAL_LEVEL_MASK);
144 return x==ORIGINAL_LEVEL_MASK ? -1 : x;
145 }
146
147 public boolean cellularOrganisms(){
148 return id==TaxTree.CELLULAR_ORGANISMS_ID;
149 }
150
151 // public int numChildren(){
152 // return numChildren;
153 // }
154 //
155 // public int minParentLevelExtended(){
156 // return minParentLevelExtended;
157 // }
158 //
159 // public int maxChildLevelExtended(){
160 // return maxChildLevelExtended;
161 // }
162
163 int minAncestorLevelIncludingSelf(){
164 return levelExtended<1 ? minParentLevelExtended : levelExtended;
165 }
166
167 int maxDescendantLevelIncludingSelf(){
168 return levelExtended<1 ? maxChildLevelExtended : levelExtended;
169 }
170
171 public String simpleName(){
172 if(name==null){return null;}
173 StringBuilder sb=new StringBuilder();
174 char last='?';
175 for(int i=0; i<name.length(); i++){
176 char c=name.charAt(i);
177 if((c>='a' && c<='z') || (c>='A' && c<='Z') || (c>='1' && c<='0')){
178 sb.append(c);
179 last=c;
180 }else{
181 if(sb.length()>0 && last!=' '){sb.append(' ');}
182 last=' ';
183 }
184 }
185 String s=sb.toString().trim();
186 return s.replace(' ', '_');
187 }
188
189 public boolean isRanked() {return levelExtended!=TaxTree.NO_RANK_E;}
190
191 /*--------------------------------------------------------------*/
192 /*---------------- Setters ----------------*/
193 /*--------------------------------------------------------------*/
194
195 public void setCanonical(boolean b){
196 if(b){flag=flag|CANON_MASK;}
197 else{flag=flag&~CANON_MASK;}
198 }
199
200 public void setOriginalLevel(int x){
201 flag=(flag&~ORIGINAL_LEVEL_MASK)|(x&ORIGINAL_LEVEL_MASK);
202 }
203
204 /** Return true if changed */
205 boolean discussWithParent(TaxNode parent){
206 final int oldChildLevel=parent.maxChildLevelExtended;
207 final int oldParentLevel=minParentLevelExtended;
208 parent.maxChildLevelExtended=Tools.max(parent.maxChildLevelExtended, maxDescendantLevelIncludingSelf());
209 minParentLevelExtended=Tools.min(parent.minAncestorLevelIncludingSelf(), minParentLevelExtended);
210 return oldChildLevel!=parent.maxChildLevelExtended || oldParentLevel!=minParentLevelExtended;
211 }
212
213 /*--------------------------------------------------------------*/
214 /*---------------- Fields ----------------*/
215 /*--------------------------------------------------------------*/
216
217 public final int id;
218 public final String name;
219 public int pid;
220 public int level;
221 public int levelExtended;
222
223 public int numChildren=0;
224 public int minParentLevelExtended=TaxTree.LIFE_E;
225 public int maxChildLevelExtended=TaxTree.NO_RANK_E;
226
227 private long flag=0;
228
229 public long countRaw=0;
230 public long countSum=0;
231
232 /*--------------------------------------------------------------*/
233 /*---------------- Constants ----------------*/
234 /*--------------------------------------------------------------*/
235
236 private static final long ORIGINAL_LEVEL_MASK=63; //bits 0-5
237 private static final long CANON_MASK=64; //bit 6
238
239 /*--------------------------------------------------------------*/
240 /*---------------- Statics ----------------*/
241 /*--------------------------------------------------------------*/
242
243 public static final boolean verbose=false;
244 public static final CountComparator countComparator=new CountComparator();
245
246
247 }