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annotate CSP2/CSP2_env/env-d9b9114564458d9d-741b3de822f2aaca6c6caa4325c4afce/opt/bbmap-39.01-1/current/gff/GbffLocus.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 gff;
jpayne@68 2
jpayne@68 3 import java.util.ArrayList;
jpayne@68 4
jpayne@68 5 import fileIO.ByteStreamWriter;
jpayne@68 6 import shared.Tools;
jpayne@68 7
jpayne@68 8 public class GbffLocus {
jpayne@68 9
jpayne@68 10 public GbffLocus(ArrayList<byte[]> lines) {
jpayne@68 11 while(num<lines.size()){
jpayne@68 12 parseBlock(lines);
jpayne@68 13 }
jpayne@68 14 }
jpayne@68 15
jpayne@68 16 int parseBlock(ArrayList<byte[]> lines){
jpayne@68 17 byte[] line=lines.get(num);
jpayne@68 18 if(Tools.startsWith(line, " ")){
jpayne@68 19 assert(false) : line;
jpayne@68 20 num++;
jpayne@68 21 }else if(Tools.startsWith(line, "LOCUS ")){
jpayne@68 22 parseLocus(lines);
jpayne@68 23 }else if(Tools.startsWith(line, "DEFINITION ")){
jpayne@68 24 parseDefinition(lines);
jpayne@68 25 }else if(Tools.startsWith(line, "ACCESSION ")){
jpayne@68 26 parseAccession(lines);
jpayne@68 27 }else if(Tools.startsWith(line, "VERSION ")){
jpayne@68 28 parseVersion(lines);
jpayne@68 29 }else if(Tools.startsWith(line, "DBLINK ")){
jpayne@68 30 parseDBLink(lines);
jpayne@68 31 }else if(Tools.startsWith(line, "KEYWORDS ")){
jpayne@68 32 parseKeywords(lines);
jpayne@68 33 }else if(Tools.startsWith(line, "SOURCE ")){
jpayne@68 34 parseSource(lines);
jpayne@68 35 }else if(Tools.startsWith(line, "REFERENCE ")){
jpayne@68 36 parseReference(lines);
jpayne@68 37 }else if(Tools.startsWith(line, "COMMENT ")){
jpayne@68 38 parseComment(lines);
jpayne@68 39 }else if(Tools.startsWith(line, "FEATURES ")){
jpayne@68 40 parseFeatures(lines);
jpayne@68 41 }else if(Tools.startsWith(line, "CONTIG ")){
jpayne@68 42 parseContig(lines);
jpayne@68 43 }else if(Tools.startsWith(line, "ORIGIN ")){
jpayne@68 44 parseOrigin(lines);
jpayne@68 45 }else if(Tools.startsWith(line, "PRIMARY ")){
jpayne@68 46 parsePrimary(lines);
jpayne@68 47 }else{
jpayne@68 48 assert(false) : "Unhandled block type: "+new String(line);
jpayne@68 49 }
jpayne@68 50 return num;
jpayne@68 51 }
jpayne@68 52
jpayne@68 53 private byte[] nextLine(ArrayList<byte[]> lines){
jpayne@68 54 byte[] line=null;
jpayne@68 55 for(final int lim=lines.size()-1; num<lim && (line==null || line.length==0); ){
jpayne@68 56 // System.err.println(num+", "+lim);
jpayne@68 57 num++;
jpayne@68 58 line=lines.get(num);
jpayne@68 59 }
jpayne@68 60 // System.err.println(line);
jpayne@68 61 // assert(line!=null);
jpayne@68 62 return line;
jpayne@68 63 }
jpayne@68 64
jpayne@68 65 private byte[] getLine(ArrayList<byte[]> lines){
jpayne@68 66 return num>=lines.size() ? null : lines.get(num);
jpayne@68 67 }
jpayne@68 68
jpayne@68 69 /** Move pointer to next block start */
jpayne@68 70 private int advanceBlock(ArrayList<byte[]> lines){
jpayne@68 71 for(num++; num<lines.size(); num++){
jpayne@68 72 byte[] line=lines.get(num);
jpayne@68 73 if(line!=null && line.length>0 && line[0]!=' '){break;}
jpayne@68 74 }
jpayne@68 75 return num;
jpayne@68 76 }
jpayne@68 77
jpayne@68 78 /** Move pointer to next block start */
jpayne@68 79 private int advanceFeature(ArrayList<byte[]> lines){
jpayne@68 80 for(num++; num<lines.size(); num++){
jpayne@68 81 byte[] line=lines.get(num);
jpayne@68 82 if(line!=null && line.length>0 && (line[0]!=' ' || line[5]!=' ')){break;}
jpayne@68 83 }
jpayne@68 84 return num;
jpayne@68 85 }
jpayne@68 86
jpayne@68 87 private String trimBlockName(byte[] line){
jpayne@68 88 assert(line.length>=12 && line[11]==' ') : new String(line);
jpayne@68 89 return new String(line, 12, line.length-12);
jpayne@68 90 }
jpayne@68 91
jpayne@68 92 private String toFeatureType(byte[] line){
jpayne@68 93 assert(line[4]==' ');
jpayne@68 94 assert(line[5]!=' ');
jpayne@68 95 assert(line[20]==' ');
jpayne@68 96 int start=5, stop=6;
jpayne@68 97 for(; stop<21 && line[stop]!=' '; stop++){}
jpayne@68 98 return new String(line, start, stop-start);
jpayne@68 99 }
jpayne@68 100
jpayne@68 101 private int parseLocus(ArrayList<byte[]> lines){
jpayne@68 102 byte[] line=lines.get(num);
jpayne@68 103 // assert(Tools.startsWith(line, "LOCUS")) : new String(line);
jpayne@68 104 if(accession==null){
jpayne@68 105 String s=trimBlockName(line);
jpayne@68 106 String[] split=Tools.whitespacePlus.split(s);
jpayne@68 107 accession=split.length>0 ? split[0] : null;
jpayne@68 108 }
jpayne@68 109 return advanceBlock(lines);
jpayne@68 110 }
jpayne@68 111
jpayne@68 112 private int parseDefinition(ArrayList<byte[]> lines){
jpayne@68 113 byte[] line=lines.get(num);
jpayne@68 114 if(organism==null){
jpayne@68 115 String s=trimBlockName(line);
jpayne@68 116 String[] split=Tools.commaPattern.split(s);
jpayne@68 117 organism=split.length>0 ? split[0] : null;
jpayne@68 118 }
jpayne@68 119 return advanceBlock(lines);
jpayne@68 120 }
jpayne@68 121
jpayne@68 122 private int parseAccession(ArrayList<byte[]> lines){
jpayne@68 123 byte[] line=lines.get(num);
jpayne@68 124 if(accession==null){
jpayne@68 125 String s=trimBlockName(line);
jpayne@68 126 String[] split=Tools.whitespacePlus.split(s);
jpayne@68 127 accession=split.length>0 ? split[0] : null;
jpayne@68 128 }
jpayne@68 129 return advanceBlock(lines);
jpayne@68 130 }
jpayne@68 131
jpayne@68 132 private int parseVersion(ArrayList<byte[]> lines){
jpayne@68 133 byte[] line=lines.get(num);
jpayne@68 134 String s=trimBlockName(line);
jpayne@68 135 String[] split=Tools.whitespacePlus.split(s);
jpayne@68 136 s=split.length>0 ? split[0] : null;
jpayne@68 137 if(accession==null || (s!=null && s.length()>1)){
jpayne@68 138 accession=s;
jpayne@68 139 }
jpayne@68 140 return advanceBlock(lines);
jpayne@68 141 }
jpayne@68 142
jpayne@68 143 private int parseDBLink(ArrayList<byte[]> lines){
jpayne@68 144 return advanceBlock(lines);
jpayne@68 145 }
jpayne@68 146
jpayne@68 147 private int parseKeywords(ArrayList<byte[]> lines){
jpayne@68 148 return advanceBlock(lines);
jpayne@68 149 }
jpayne@68 150
jpayne@68 151 private int parseSource(ArrayList<byte[]> lines){
jpayne@68 152 byte[] line=lines.get(num);
jpayne@68 153 if(species==null){
jpayne@68 154 species=trimBlockName(line);
jpayne@68 155 }
jpayne@68 156 return advanceBlock(lines);
jpayne@68 157 }
jpayne@68 158
jpayne@68 159 private int parseReference(ArrayList<byte[]> lines){
jpayne@68 160 return advanceBlock(lines);
jpayne@68 161 }
jpayne@68 162
jpayne@68 163 private int parseComment(ArrayList<byte[]> lines){
jpayne@68 164 return advanceBlock(lines);
jpayne@68 165 }
jpayne@68 166
jpayne@68 167 private int parseFeatures(ArrayList<byte[]> lines){
jpayne@68 168 for(byte[] line=nextLine(lines); line!=null && line[0]==' '; line=getLine(lines)){
jpayne@68 169 // System.err.println(num+": "+new String(line));
jpayne@68 170 String type=toFeatureType(line);
jpayne@68 171 int idx=Tools.find(type, featureTypes);
jpayne@68 172 // System.err.println("idx="+idx+" for '"+type+"'");
jpayne@68 173 if(idx>=0){
jpayne@68 174 // System.err.println("parseFeature");
jpayne@68 175 parseFeature(lines, type);
jpayne@68 176 // System.err.println(features.get(features.size()-1));
jpayne@68 177 }else{
jpayne@68 178 // System.err.println("advanceFeature");
jpayne@68 179 advanceFeature(lines);
jpayne@68 180 }
jpayne@68 181 }
jpayne@68 182 return num;
jpayne@68 183 }
jpayne@68 184
jpayne@68 185 /** Move pointer to next block start */
jpayne@68 186 private int parseFeature(ArrayList<byte[]> lines, String type){
jpayne@68 187 ArrayList<byte[]> flist=new ArrayList<byte[]>();
jpayne@68 188 flist.add(lines.get(num));
jpayne@68 189 for(num++; num<lines.size(); num++){
jpayne@68 190 byte[] line=lines.get(num);
jpayne@68 191 if(line!=null && line.length>0 && (line[0]!=' ' || line[5]!=' ')){
jpayne@68 192 // assert(false) : Character.toString(line[0])+", "+Character.toString(line[5])+", "+Character.toString(line[6])+"\n"+new String(line);
jpayne@68 193 break;
jpayne@68 194 }
jpayne@68 195 flist.add(line);
jpayne@68 196 }
jpayne@68 197 GbffFeature f=new GbffFeature(flist, type, accession);
jpayne@68 198 if(!f.error){
jpayne@68 199 features.add(f);
jpayne@68 200 }else{
jpayne@68 201 // System.err.println("Failed to parse feature "+f);
jpayne@68 202 }
jpayne@68 203 return num;
jpayne@68 204 }
jpayne@68 205
jpayne@68 206 private int parseContig(ArrayList<byte[]> lines){
jpayne@68 207 return advanceBlock(lines);
jpayne@68 208 }
jpayne@68 209
jpayne@68 210 private int parseOrigin(ArrayList<byte[]> lines){
jpayne@68 211 return advanceBlock(lines);
jpayne@68 212 }
jpayne@68 213
jpayne@68 214 private int parsePrimary(ArrayList<byte[]> lines){
jpayne@68 215 return advanceBlock(lines);
jpayne@68 216 }
jpayne@68 217
jpayne@68 218 public void toGff(ByteStreamWriter bsw) {
jpayne@68 219 final byte[] accessionB=accession.getBytes();
jpayne@68 220 bsw.print(seqRegB);
jpayne@68 221 bsw.print(accessionB);
jpayne@68 222 if(start>0 && stop>0){
jpayne@68 223 bsw.print(' ').print(start).print(' ').print(stop);
jpayne@68 224 }
jpayne@68 225 bsw.println();
jpayne@68 226 for(GbffFeature f : features){
jpayne@68 227 if(f.type==GbffFeature.CDS || f.type==GbffFeature.tRNA || f.type==GbffFeature.rRNA){
jpayne@68 228 if(!f.pseudo && !f.error){
jpayne@68 229 f.toGff(bsw);
jpayne@68 230 }
jpayne@68 231 }
jpayne@68 232 }
jpayne@68 233 }
jpayne@68 234
jpayne@68 235
jpayne@68 236 /** Line number */
jpayne@68 237 int num=0;
jpayne@68 238
jpayne@68 239 boolean printGene=false;
jpayne@68 240 boolean printRepeat=false;
jpayne@68 241
jpayne@68 242 public static String[] featureTypes=GbffFeature.typeStrings;
jpayne@68 243 private static final byte[] seqRegB="##sequence-region ".getBytes();
jpayne@68 244
jpayne@68 245 String accession;
jpayne@68 246 String organism;
jpayne@68 247 String species;
jpayne@68 248 int start;
jpayne@68 249 int stop;
jpayne@68 250 ArrayList<GbffFeature> features=new ArrayList<GbffFeature>();
jpayne@68 251 }