Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/fileIO/ChainLine.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 fileIO;
2
3 import dna.Data;
4 import dna.Gene;
5 import shared.Shared;
6
7 public class ChainLine implements Comparable<ChainLine> {
8
9
10 public static void main(String[] args){
11
12 int chrom=Gene.toChromosome(args[0]);
13
14 ChainLine[][] lines=ChainBlock.loadChainLines(Data.ROOT_CHAIN+"hg18ToHg19.over.chain");
15
16 for(int i=1; i<args.length; i++){
17 int loc=Integer.parseInt(args[i]);
18 int[] result=translate(loc, lines[chrom]);
19 System.out.print(chrom+"\t+\t"+loc+"\t->\t");
20 System.out.println(result==null ? "null" : result[0]+"\t"+Shared.strandCodes[result[1]]+"\t"+result[2]);
21 }
22
23 }
24
25
26 public ChainLine(int chromT, byte strandT, int startT, int stopT, int chromQ, byte strandQ, int startQ, int stopQ){
27 tChrom=chromT;
28 tStrand=strandT;
29 tStart=startT;
30 tStop=stopT;
31
32 qChrom=chromQ;
33 qStrand=strandQ;
34 qStart=startQ;
35 qStop=stopQ;
36 }
37
38
39 @Override
40 public String toString(){
41 return tChrom+"\t"+Shared.strandCodes[tStrand]+"\t"+tStart+"\t"+tStop+"\t"+
42 qChrom+"\t"+Shared.strandCodes[qStrand]+"\t"+qStart+"\t"+qStop;
43 }
44
45
46 public static int binarySearch(int loc, ChainLine[] array){
47 return binarySearch(loc, array, 0, array.length-1);
48 }
49
50
51 public static int binarySearch(int loc, ChainLine[] array, int first, int last){
52 // if(first>=last){
53 // if(first>last){return -1;}
54 // assert(first==last && first<array.length);
55 // return (array[first].tStart<=loc && array[first].tStop>=loc) ? first : -1;
56 // }
57 // System.out.println("BinarySearch "+loc+", "+first+", "+last);
58 if(first>last){return -1;}
59 int mid=(first+last)/2;
60 ChainLine midcl=array[mid];
61 // System.out.println("mid = "+midcl);
62 if(loc<midcl.tStart){return binarySearch(loc, array, first, mid-1);}
63 else if(loc>midcl.tStop){return binarySearch(loc, array, mid+1, last);}
64 return mid;
65 }
66
67 /** Returns {chrom, strand, loc} */
68 public static int[] translate(int loc, ChainLine[] array){
69 int index=binarySearch(loc, array);
70 if(index<0){return null;}
71 ChainLine cl=array[index];
72 return cl.translate(loc);
73 }
74
75 public int[] translate(int loc){
76 if(loc<tStart || loc>tStop){return null;}
77 // assert(loc>=tStart && loc<=tStop);
78 if(qChrom<1 || qChrom>25){return null;}
79 if(qStrand==Shared.PLUS){
80 return new int[] {qChrom, qStrand, qStart+loc-tStart};
81 }else{
82 assert(qStart>=qStop) : this;
83 return new int[] {qChrom, qStrand, qStart-(loc-tStart)};
84 }
85 }
86
87
88 public boolean contains(int a, int b){
89 assert(b>=a);
90 return a>=tStart && b<=tStop;
91 }
92
93
94 public boolean contains(int a){
95 return a>=tStart && a<=tStop;
96 }
97
98
99 @Override
100 public int compareTo(ChainLine other) {
101 int temp;
102
103 temp=tChrom-other.tChrom;
104 if(temp!=0){return temp;}
105
106 assert(tStrand==other.tStrand);
107
108 temp=tStart-other.tStart;
109 if(temp!=0){return temp;}
110
111 temp=tStop-other.tStop;
112 return temp;
113 }
114
115 public int tChrom;
116 public byte tStrand;
117 public int tStart;
118 public int tStop;
119
120 public int qChrom;
121 public byte qStrand;
122 public int qStart;
123 public int qStop;
124
125 }