Mercurial > repos > rliterman > csp2

comparison CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/prok/ScafData.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 prok;
2
3 import java.util.ArrayList;
4 import java.util.Arrays;
5
6 import dna.AminoAcid;
7 import gff.GffLine;
8 import stream.Read;
9 import structures.IntList;
10
11 /**
12 * Tracks information about a scaffold for AnalyzeGenes.
13 * @author Brian Bushnell
14 * @date Sep 24, 2018
15 *
16 */
17 class ScafData {
18
19 /*--------------------------------------------------------------*/
20 /*---------------- Initialization ----------------*/
21 /*--------------------------------------------------------------*/
22
23 ScafData(Read r){
24 this(r.id, r.bases, new byte[r.length()]);
25 }
26
27 ScafData(String name_, byte[] bases_, byte[] frames_){
28 name=name_;
29 bases=bases_;
30 frames=frames_;
31 cdsLines[0]=new ArrayList<GffLine>();
32 cdsLines[1]=new ArrayList<GffLine>();
33 rnaLines[0]=new ArrayList<GffLine>();
34 rnaLines[1]=new ArrayList<GffLine>();
35 }
36
37 /*--------------------------------------------------------------*/
38 /*---------------- Methods ----------------*/
39 /*--------------------------------------------------------------*/
40
41 void clear(){
42 Arrays.fill(frames, (byte)0);
43 starts.clear();
44 stops.clear();
45 }
46
47 void reverseComplement(){
48 AminoAcid.reverseComplementBasesInPlace(bases);
49 strand=1^strand;
50 }
51
52 void addCDS(GffLine gline){
53 assert(gline.strand>=0) : gline+"\n"+gline.strand;
54 cdsLines[gline.strand].add(gline);
55 }
56
57 void addRNA(GffLine gline){
58 assert(gline.strand>=0) : gline+"\n"+gline.strand;
59 rnaLines[gline.strand].add(gline);
60 }
61
62 byte[] fetch(int start, int stop){
63 assert(start>=0 && stop<bases.length);
64 assert(start<stop);
65 return Arrays.copyOfRange(bases, start, stop+1);
66 }
67
68 int strand(){return strand;}
69
70 public int length() {return bases==null ? 0 : bases.length;}
71
72 /*--------------------------------------------------------------*/
73 /*---------------- Fields ----------------*/
74 /*--------------------------------------------------------------*/
75
76 final String name;
77 final byte[] bases;
78 final byte[] frames;
79 final IntList starts=new IntList(8);
80 final IntList stops=new IntList(8);
81 private int strand=0;
82
83 /** gLines[strand] holds the GffLines for that strand */
84 @SuppressWarnings("unchecked")
85 ArrayList<GffLine>[] cdsLines=new ArrayList[2];
86 @SuppressWarnings("unchecked")
87 ArrayList<GffLine>[] rnaLines=new ArrayList[2];
88 }