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