Mercurial > repos > rliterman > csp2

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