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2f67 656e 6f6d  ojava/nbio/genom\n-000445f0: 652f 696f 2f66 6173 7471 2f53 616e 6765  e/io/fastq/Sange\n-00044600: 7246 6173 7471 5772 6974 6572 2e68 746d  rFastqWriter.htm\n+000445f0: 652f 696f 2f66 6173 7471 2f53 6f6c 6578  e/io/fastq/Solex\n+00044600: 6146 6173 7471 5772 6974 6572 2e68 746d  aFastqWriter.htm\n 00044610: 6c22 2074 6974 6c65 3d22 636c 6173 7320  l\" title=\"class \n 00044620: 696e 206f 7267 2e62 696f 6a61 7661 2e6e  in org.biojava.n\n 00044630: 6269 6f2e 6765 6e6f 6d65 2e69 6f2e 6661  bio.genome.io.fa\n-00044640: 7374 7122 3e53 616e 6765 7246 6173 7471  stq\">SangerFastq\n+00044640: 7374 7122 3e53 6f6c 6578 6146 6173 7471  stq\">SolexaFastq\n 00044650: 5772 6974 6572 3c2f 613e 3c2f 6474 3e0a  Writer</a></dt>.\n 00044660: 3c64 643e 266e 6273 703b 3c2f 6464 3e0a  <dd>&nbsp;</dd>.\n 00044670: 3c64 743e 3c61 2068 7265 663d 226f 7267  <dt><a href=\"org\n 00044680: 2f62 696f 6a61 7661 2f6e 6269 6f2f 6765  /biojava/nbio/ge\n 00044690: 6e6f 6d65 2f69 6f2f 6661 7374 712f 4661  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6269 6f2e  rg.biojava.nbio.\n 00476ee0: 6765 6e6f 6d65 2e69 6f2e 6661 7374 712e  genome.io.fastq.\n 00476ef0: 5061 7273 654c 6973 7465 6e65 7229 2220  ParseListener)\" \n 00476f00: 636c 6173 733d 226d 656d 6265 722d 6e61  class=\"member-na\n 00476f10: 6d65 2d6c 696e 6b22 3e70 6172 7365 2852  me-link\">parse(R\n 00476f20: 6561 6461 626c 652c 2050 6172 7365 4c69  eadable, ParseLi\n 00476f30: 7374 656e 6572 293c 2f61 3e20 2d20 4d65  stener)</a> - Me\n 00476f40: 7468 6f64 2069 6e20 636c 6173 7320 6f72  thod in class or\n 00476f50: 672e 6269 6f6a 6176 612e 6e62 696f 2e67  g.biojava.nbio.g\n 00476f60: 656e 6f6d 652e 696f 2e66 6173 7471 2e3c  enome.io.fastq.<\n 00476f70: 6120 6872 6566 3d22 6f72 672f 6269 6f6a  a href=\"org/bioj\n 00476f80: 6176 612f 6e62 696f 2f67 656e 6f6d 652f  ava/nbio/genome/\n-00476f90: 696f 2f66 6173 7471 2f53 6f6c 6578 6146  io/fastq/SolexaF\n+00476f90: 696f 2f66 6173 7471 2f53 616e 6765 7246  io/fastq/SangerF\n 00476fa0: 6173 7471 5265 6164 6572 2e68 746d 6c22  astqReader.html\"\n 00476fb0: 2074 6974 6c65 3d22 636c 6173 7320 696e   title=\"class in\n 00476fc0: 206f 7267 2e62 696f 6a61 7661 2e6e 6269   org.biojava.nbi\n 00476fd0: 6f2e 6765 6e6f 6d65 2e69 6f2e 6661 7374  o.genome.io.fast\n-00476fe0: 7122 3e53 6f6c 6578 6146 6173 7471 5265  q\">SolexaFastqRe\n+00476fe0: 7122 3e53 616e 6765 7246 6173 7471 5265  q\">SangerFastqRe\n 00476ff0: 6164 6572 3c2f 613e 3c2f 6474 3e0a 3c64  ader</a></dt>.<d\n 00477000: 643e 266e 6273 703b 3c2f 6464 3e0a 3c64  d>&nbsp;</dd>.<d\n 00477010: 743e 3c61 2068 7265 663d 226f 7267 2f62  t><a href=\"org/b\n 00477020: 696f 6a61 7661 2f6e 6269 6f2f 6765 6e6f  iojava/nbio/geno\n 00477030: 6d65 2f69 6f2f 6661 7374 712f 4661 7374  me/io/fastq/Fast\n 00477040: 7152 6561 6465 722e 6874 6d6c 2370 6172  qReader.html#par\n 00477050: 7365 286a 6176 612e 6c61 6e67 2e52 6561  se(java.lang.Rea\n@@ -313804,31 +313804,31 @@\n 004c9cb0: 7472 6978 3c2f 613e 3c2f 6474 3e0a 3c64  trix</a></dt>.<d\n 004c9cc0: 643e 0a3c 6469 7620 636c 6173 733d 2262  d>.<div class=\"b\n 004c9cd0: 6c6f 636b 223e 5265 6164 2061 206d 6174  lock\">Read a mat\n 004c9ce0: 7269 7820 6672 6f6d 2061 2073 7472 6561  rix from a strea\n 004c9cf0: 6d2e 3c2f 6469 763e 0a3c 2f64 643e 0a3c  m.</div>.</dd>.<\n 004c9d00: 6474 3e3c 6120 6872 6566 3d22 6f72 672f  dt><a href=\"org/\n 004c9d10: 6269 6f6a 6176 612f 6e62 696f 2f67 656e  biojava/nbio/gen\n-004c9d20: 6f6d 652f 696f 2f66 6173 7471 2f53 6f6c  ome/io/fastq/Sol\n-004c9d30: 6578 6146 6173 7471 5265 6164 6572 2e68  exaFastqReader.h\n+004c9d20: 6f6d 652f 696f 2f66 6173 7471 2f53 616e  ome/io/fastq/San\n+004c9d30: 6765 7246 6173 7471 5265 6164 6572 2e68  gerFastqReader.h\n 004c9d40: 746d 6c23 7265 6164 286a 6176 612e 696f  tml#read(java.io\n 004c9d50: 2e46 696c 6529 2220 636c 6173 733d 226d  .File)\" class=\"m\n 004c9d60: 656d 6265 722d 6e61 6d65 2d6c 696e 6b22  ember-name-link\"\n 004c9d70: 3e72 6561 6428 4669 6c65 293c 2f61 3e20  >read(File)</a> \n 004c9d80: 2d20 4d65 7468 6f64 2069 6e20 636c 6173 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tqReader</a></dt\n 004c9e40: 3e0a 3c64 643e 266e 6273 703b 3c2f 6464  >.<dd>&nbsp;</dd\n 004c9e50: 3e0a 3c64 743e 3c61 2068 7265 663d 226f  >.<dt><a href=\"o\n 004c9e60: 7267 2f62 696f 6a61 7661 2f6e 6269 6f2f  rg/biojava/nbio/\n 004c9e70: 6765 6e6f 6d65 2f69 6f2f 6661 7374 712f  genome/io/fastq/\n 004c9e80: 4661 7374 7152 6561 6465 722e 6874 6d6c  FastqReader.html\n 004c9e90: 2372 6561 6428 6a61 7661 2e69 6f2e 4669  #read(java.io.Fi\n@@ -313852,31 +313852,31 @@\n 004c9fb0: 6d6f 7265 2046 4153 5451 2066 6f72 6d61  more FASTQ forma\n 004c9fc0: 7474 6564 2073 6571 7565 6e63 6573 2066  tted sequences f\n 004c9fd0: 726f 6d20 7468 6520 7370 6563 6966 6965  rom the specifie\n 004c9fe0: 6420 6669 6c65 2e3c 2f64 6976 3e0a 3c2f  d file.</div>.</\n 004c9ff0: 6464 3e0a 3c64 743e 3c61 2068 7265 663d  dd>.<dt><a href=\n 004ca000: 226f 7267 2f62 696f 6a61 7661 2f6e 6269  \"org/biojava/nbi\n 004ca010: 6f2f 6765 6e6f 6d65 2f69 6f2f 6661 7374  o/genome/io/fast\n-004ca020: 712f 536f 6c65 7861 4661 7374 7152 6561  q/SolexaFastqRea\n+004ca020: 712f 5361 6e67 6572 4661 7374 7152 6561  q/SangerFastqRea\n 004ca030: 6465 722e 6874 6d6c 2372 6561 6428 6a61  der.html#read(ja\n 004ca040: 7661 2e69 6f2e 496e 7075 7453 7472 6561  va.io.InputStrea\n 004ca050: 6d29 2220 636c 6173 733d 226d 656d 6265  m)\" class=\"membe\n 004ca060: 722d 6e61 6d65 2d6c 696e 6b22 3e72 6561  r-name-link\">rea\n 004ca070: 6428 496e 7075 7453 7472 6561 6d29 3c2f  d(InputStream)</\n 004ca080: 613e 202d 204d 6574 686f 6420 696e 2063  a> - Method in c\n 004ca090: 6c61 7373 206f 7267 2e62 696f 6a61 7661  lass org.biojava\n 004ca0a0: 2e6e 6269 6f2e 6765 6e6f 6d65 2e69 6f2e  .nbio.genome.io.\n 004ca0b0: 6661 7374 712e 3c61 2068 7265 663d 226f  fastq.<a href=\"o\n 004ca0c0: 7267 2f62 696f 6a61 7661 2f6e 6269 6f2f  rg/biojava/nbio/\n 004ca0d0: 6765 6e6f 6d65 2f69 6f2f 6661 7374 712f  genome/io/fastq/\n-004ca0e0: 536f 6c65 7861 4661 7374 7152 6561 6465  SolexaFastqReade\n+004ca0e0: 5361 6e67 6572 4661 7374 7152 6561 6465  SangerFastqReade\n 004ca0f0: 722e 6874 6d6c 2220 7469 746c 653d 2263  r.html\" title=\"c\n 004ca100: 6c61 7373 2069 6e20 6f72 672e 6269 6f6a  lass in org.bioj\n 004ca110: 6176 612e 6e62 696f 2e67 656e 6f6d 652e  ava.nbio.genome.\n-004ca120: 696f 2e66 6173 7471 223e 536f 6c65 7861  io.fastq\">Solexa\n+004ca120: 696f 2e66 6173 7471 223e 5361 6e67 6572  io.fastq\">Sanger\n 004ca130: 4661 7374 7152 6561 6465 723c 2f61 3e3c  FastqReader</a><\n 004ca140: 2f64 743e 0a3c 6464 3e26 6e62 7370 3b3c  /dt>.<dd>&nbsp;<\n 004ca150: 2f64 643e 0a3c 6474 3e3c 6120 6872 6566  /dd>.<dt><a href\n 004ca160: 3d22 6f72 672f 6269 6f6a 6176 612f 6e62  =\"org/biojava/nb\n 004ca170: 696f 2f67 656e 6f6d 652f 696f 2f66 6173  io/genome/io/fas\n 004ca180: 7471 2f46 6173 7471 5265 6164 6572 2e68  tq/FastqReader.h\n 004ca190: 746d 6c23 7265 6164 286a 6176 612e 696f  tml#read(java.io\n@@ -314001,31 +314001,31 @@\n 004ca900: 723c 2f61 3e3c 2f64 743e 0a3c 6464 3e0a  r</a></dt>.<dd>.\n 004ca910: 3c64 6976 2063 6c61 7373 3d22 626c 6f63  <div class=\"bloc\n 004ca920: 6b22 3e52 6561 6420 6120 6669 6c65 2069  k\">Read a file i\n 004ca930: 6e74 6f20 6120 4665 6174 7572 654c 6973  nto a FeatureLis\n 004ca940: 742e 3c2f 6469 763e 0a3c 2f64 643e 0a3c  t.</div>.</dd>.<\n 004ca950: 6474 3e3c 6120 6872 6566 3d22 6f72 672f  dt><a href=\"org/\n 004ca960: 6269 6f6a 6176 612f 6e62 696f 2f67 656e  biojava/nbio/gen\n-004ca970: 6f6d 652f 696f 2f66 6173 7471 2f53 6f6c  ome/io/fastq/Sol\n-004ca980: 6578 6146 6173 7471 5265 6164 6572 2e68  exaFastqReader.h\n+004ca970: 6f6d 652f 696f 2f66 6173 7471 2f53 616e  ome/io/fastq/San\n+004ca980: 6765 7246 6173 7471 5265 6164 6572 2e68  gerFastqReader.h\n 004ca990: 746d 6c23 7265 6164 286a 6176 612e 6e65  tml#read(java.ne\n 004ca9a0: 742e 5552 4c29 2220 636c 6173 733d 226d  t.URL)\" class=\"m\n 004ca9b0: 656d 6265 722d 6e61 6d65 2d6c 696e 6b22  ember-name-link\"\n 004ca9c0: 3e72 6561 6428 5552 4c29 3c2f 613e 202d  >read(URL)</a> -\n 004ca9d0: 204d 6574 686f 6420 696e 2063 6c61 7373   Method in class\n 004ca9e0: 206f 7267 2e62 696f 6a61 7661 2e6e 6269   org.biojava.nbi\n 004ca9f0: 6f2e 6765 6e6f 6d65 2e69 6f2e 6661 7374  o.genome.io.fast\n 004caa00: 712e 3c61 2068 7265 663d 226f 7267 2f62  q.<a href=\"org/b\n 004caa10: 696f 6a61 7661 2f6e 6269 6f2f 6765 6e6f  iojava/nbio/geno\n-004caa20: 6d65 2f69 6f2f 6661 7374 712f 536f 6c65  me/io/fastq/Sole\n-004caa30: 7861 4661 7374 7152 6561 6465 722e 6874  xaFastqReader.ht\n+004caa20: 6d65 2f69 6f2f 6661 7374 712f 5361 6e67  me/io/fastq/Sang\n+004caa30: 6572 4661 7374 7152 6561 6465 722e 6874  erFastqReader.ht\n 004caa40: 6d6c 2220 7469 746c 653d 2263 6c61 7373  ml\" title=\"class\n 004caa50: 2069 6e20 6f72 672e 6269 6f6a 6176 612e   in org.biojava.\n 004caa60: 6e62 696f 2e67 656e 6f6d 652e 696f 2e66  nbio.genome.io.f\n-004caa70: 6173 7471 223e 536f 6c65 7861 4661 7374  astq\">SolexaFast\n+004caa70: 6173 7471 223e 5361 6e67 6572 4661 7374  astq\">SangerFast\n 004caa80: 7152 6561 6465 723c 2f61 3e3c 2f64 743e  qReader</a></dt>\n 004caa90: 0a3c 6464 3e26 6e62 7370 3b3c 2f64 643e  .<dd>&nbsp;</dd>\n 004caaa0: 0a3c 6474 3e3c 6120 6872 6566 3d22 6f72  .<dt><a href=\"or\n 004caab0: 672f 6269 6f6a 6176 612f 6e62 696f 2f67  g/biojava/nbio/g\n 004caac0: 656e 6f6d 652f 696f 2f66 6173 7471 2f46  enome/io/fastq/F\n 004caad0: 6173 7471 5265 6164 6572 2e68 746d 6c23  astqReader.html#\n 004caae0: 7265 6164 286a 6176 612e 6e65 742e 5552  read(java.net.UR\n@@ -407797,15 +407797,15 @@\n 00638f40: 612e 6e62 696f 2e73 7472 7563 7475 7265  a.nbio.structure\n 00638f50: 2e61 6c69 676e 2e70 6169 7277 6973 6522  .align.pairwise\"\n 00638f60: 3e53 7472 436f 6d70 416c 6967 6e6d 656e  >StrCompAlignmen\n 00638f70: 743c 2f61 3e3c 2f64 743e 0a3c 6464 3e26  t</a></dt>.<dd>&\n 00638f80: 6e62 7370 3b3c 2f64 643e 0a3c 6474 3e3c  nbsp;</dd>.<dt><\n 00638f90: 6120 6872 6566 3d22 6f72 672f 6269 6f6a  a href=\"org/bioj\n 00638fa0: 6176 612f 6e62 696f 2f67 656e 6f6d 652f  ava/nbio/genome/\n-00638fb0: 696f 2f66 6173 7471 2f53 6f6c 6578 6146  io/fastq/SolexaF\n+00638fb0: 696f 2f66 6173 7471 2f53 616e 6765 7246  io/fastq/SangerF\n 00638fc0: 6173 7471 5265 6164 6572 2e68 746d 6c23  astqReader.html#\n 00638fd0: 7374 7265 616d 286a 6176 612e 6c61 6e67  stream(java.lang\n 00638fe0: 2e52 6561 6461 626c 652c 6f72 672e 6269  .Readable,org.bi\n 00638ff0: 6f6a 6176 612e 6e62 696f 2e67 656e 6f6d  ojava.nbio.genom\n 00639000: 652e 696f 2e66 6173 7471 2e53 7472 6561  e.io.fastq.Strea\n 00639010: 6d4c 6973 7465 6e65 7229 2220 636c 6173  mListener)\" clas\n 00639020: 733d 226d 656d 6265 722d 6e61 6d65 2d6c  s=\"member-name-l\n@@ -407813,20 +407813,20 @@\n 00639040: 6162 6c65 2c20 5374 7265 616d 4c69 7374  able, StreamList\n 00639050: 656e 6572 293c 2f61 3e20 2d20 4d65 7468  ener)</a> - Meth\n 00639060: 6f64 2069 6e20 636c 6173 7320 6f72 672e  od in class org.\n 00639070: 6269 6f6a 6176 612e 6e62 696f 2e67 656e  biojava.nbio.gen\n 00639080: 6f6d 652e 696f 2e66 6173 7471 2e3c 6120  ome.io.fastq.<a \n 00639090: 6872 6566 3d22 6f72 672f 6269 6f6a 6176  href=\"org/biojav\n 006390a0: 612f 6e62 696f 2f67 656e 6f6d 652f 696f  a/nbio/genome/io\n-006390b0: 2f66 6173 7471 2f53 6f6c 6578 6146 6173  /fastq/SolexaFas\n+006390b0: 2f66 6173 7471 2f53 616e 6765 7246 6173  /fastq/SangerFas\n 006390c0: 7471 5265 6164 6572 2e68 746d 6c22 2074  tqReader.html\" t\n 006390d0: 6974 6c65 3d22 636c 6173 7320 696e 206f  itle=\"class in o\n 006390e0: 7267 2e62 696f 6a61 7661 2e6e 6269 6f2e  rg.biojava.nbio.\n 006390f0: 6765 6e6f 6d65 2e69 6f2e 6661 7374 7122  genome.io.fastq\"\n-00639100: 3e53 6f6c 6578 6146 6173 7471 5265 6164  >SolexaFastqRead\n+00639100: 3e53 616e 6765 7246 6173 7471 5265 6164  >SangerFastqRead\n 00639110: 6572 3c2f 613e 3c2f 6474 3e0a 3c64 643e  er</a></dt>.<dd>\n 00639120: 266e 6273 703b 3c2f 6464 3e0a 3c64 743e  &nbsp;</dd>.<dt>\n 00639130: 3c61 2068 7265 663d 226f 7267 2f62 696f  <a href=\"org/bio\n 00639140: 6a61 7661 2f6e 6269 6f2f 6765 6e6f 6d65  java/nbio/genome\n 00639150: 2f69 6f2f 6661 7374 712f 4661 7374 7152  /io/fastq/FastqR\n 00639160: 6561 6465 722e 6874 6d6c 2373 7472 6561  eader.html#strea\n 00639170: 6d28 6a61 7661 2e6c 616e 672e 5265 6164  m(java.lang.Read\n@@ -450770,34 +450770,34 @@\n 006e0d10: 2263 6c61 7373 2069 6e20 6f72 672e 6269  \"class in org.bi\n 006e0d20: 6f6a 6176 612e 6e62 696f 2e72 6f6e 6e22  ojava.nbio.ronn\"\n 006e0d30: 3e4e 756c 6c4f 7574 7075 7453 7472 6561  >NullOutputStrea\n 006e0d40: 6d3c 2f61 3e3c 2f64 743e 0a3c 6464 3e26  m</a></dt>.<dd>&\n 006e0d50: 6e62 7370 3b3c 2f64 643e 0a3c 6474 3e3c  nbsp;</dd>.<dt><\n 006e0d60: 6120 6872 6566 3d22 6f72 672f 6269 6f6a  a href=\"org/bioj\n 006e0d70: 6176 612f 6e62 696f 2f67 656e 6f6d 652f  ava/nbio/genome/\n-006e0d80: 696f 2f66 6173 7471 2f53 616e 6765 7246  io/fastq/SangerF\n+006e0d80: 696f 2f66 6173 7471 2f53 6f6c 6578 6146  io/fastq/SolexaF\n 006e0d90: 6173 7471 5772 6974 6572 2e68 746d 6c23  astqWriter.html#\n 006e0da0: 7772 6974 6528 6a61 7661 2e69 6f2e 4669  write(java.io.Fi\n 006e0db0: 6c65 2c6a 6176 612e 6c61 6e67 2e49 7465  le,java.lang.Ite\n 006e0dc0: 7261 626c 6529 2220 636c 6173 733d 226d  rable)\" class=\"m\n 006e0dd0: 656d 6265 722d 6e61 6d65 2d6c 696e 6b22  ember-name-link\"\n 006e0de0: 3e77 7269 7465 2846 696c 652c 2049 7465  >write(File, Ite\n 006e0df0: 7261 626c 6526 6c74 3b46 6173 7471 2667  rable&lt;Fastq&g\n 006e0e00: 743b 293c 2f61 3e20 2d20 4d65 7468 6f64  t;)</a> - Method\n 006e0e10: 2069 6e20 636c 6173 7320 6f72 672e 6269   in class org.bi\n 006e0e20: 6f6a 6176 612e 6e62 696f 2e67 656e 6f6d  ojava.nbio.genom\n 006e0e30: 652e 696f 2e66 6173 7471 2e3c 6120 6872  e.io.fastq.<a hr\n 006e0e40: 6566 3d22 6f72 672f 6269 6f6a 6176 612f  ef=\"org/biojava/\n 006e0e50: 6e62 696f 2f67 656e 6f6d 652f 696f 2f66  nbio/genome/io/f\n-006e0e60: 6173 7471 2f53 616e 6765 7246 6173 7471  astq/SangerFastq\n+006e0e60: 6173 7471 2f53 6f6c 6578 6146 6173 7471  astq/SolexaFastq\n 006e0e70: 5772 6974 6572 2e68 746d 6c22 2074 6974  Writer.html\" tit\n 006e0e80: 6c65 3d22 636c 6173 7320 696e 206f 7267  le=\"class in org\n 006e0e90: 2e62 696f 6a61 7661 2e6e 6269 6f2e 6765  .biojava.nbio.ge\n 006e0ea0: 6e6f 6d65 2e69 6f2e 6661 7374 7122 3e53  nome.io.fastq\">S\n-006e0eb0: 616e 6765 7246 6173 7471 5772 6974 6572  angerFastqWriter\n+006e0eb0: 6f6c 6578 6146 6173 7471 5772 6974 6572  olexaFastqWriter\n 006e0ec0: 3c2f 613e 3c2f 6474 3e0a 3c64 643e 266e  </a></dt>.<dd>&n\n 006e0ed0: 6273 703b 3c2f 6464 3e0a 3c64 743e 3c61  bsp;</dd>.<dt><a\n 006e0ee0: 2068 7265 663d 226f 7267 2f62 696f 6a61   href=\"org/bioja\n 006e0ef0: 7661 2f6e 6269 6f2f 6765 6e6f 6d65 2f69  va/nbio/genome/i\n 006e0f00: 6f2f 6661 7374 712f 4661 7374 7157 7269  o/fastq/FastqWri\n 006e0f10: 7465 722e 6874 6d6c 2377 7269 7465 286a  ter.html#write(j\n 006e0f20: 6176 612e 696f 2e46 696c 652c 6a61 7661  ava.io.File,java\n@@ -450823,34 +450823,34 @@\n 006e1060: 2073 7065 6369 6669 6564 2046 4153 5451   specified FASTQ\n 006e1070: 2066 6f72 6d61 7474 6564 2073 6571 7565   formatted seque\n 006e1080: 6e63 6573 2074 6f20 7468 6520 7370 6563  nces to the spec\n 006e1090: 6966 6965 6420 6669 6c65 2e3c 2f64 6976  ified file.</div\n 006e10a0: 3e0a 3c2f 6464 3e0a 3c64 743e 3c61 2068  >.</dd>.<dt><a h\n 006e10b0: 7265 663d 226f 7267 2f62 696f 6a61 7661  ref=\"org/biojava\n 006e10c0: 2f6e 6269 6f2f 6765 6e6f 6d65 2f69 6f2f  /nbio/genome/io/\n-006e10d0: 6661 7374 712f 5361 6e67 6572 4661 7374  fastq/SangerFast\n+006e10d0: 6661 7374 712f 536f 6c65 7861 4661 7374  fastq/SolexaFast\n 006e10e0: 7157 7269 7465 722e 6874 6d6c 2377 7269  qWriter.html#wri\n 006e10f0: 7465 286a 6176 612e 696f 2e46 696c 652c  te(java.io.File,\n 006e1100: 6f72 672e 6269 6f6a 6176 612e 6e62 696f  org.biojava.nbio\n 006e1110: 2e67 656e 6f6d 652e 696f 2e66 6173 7471  .genome.io.fastq\n 006e1120: 2e46 6173 7471 2e2e 2e29 2220 636c 6173  .Fastq...)\" clas\n 006e1130: 733d 226d 656d 6265 722d 6e61 6d65 2d6c  s=\"member-name-l\n 006e1140: 696e 6b22 3e77 7269 7465 2846 696c 652c  ink\">write(File,\n 006e1150: 2046 6173 7471 2e2e 2e29 3c2f 613e 202d   Fastq...)</a> -\n 006e1160: 204d 6574 686f 6420 696e 2063 6c61 7373   Method in class\n 006e1170: 206f 7267 2e62 696f 6a61 7661 2e6e 6269   org.biojava.nbi\n 006e1180: 6f2e 6765 6e6f 6d65 2e69 6f2e 6661 7374  o.genome.io.fast\n 006e1190: 712e 3c61 2068 7265 663d 226f 7267 2f62  q.<a href=\"org/b\n 006e11a0: 696f 6a61 7661 2f6e 6269 6f2f 6765 6e6f  iojava/nbio/geno\n-006e11b0: 6d65 2f69 6f2f 6661 7374 712f 5361 6e67  me/io/fastq/Sang\n-006e11c0: 6572 4661 7374 7157 7269 7465 722e 6874  erFastqWriter.ht\n+006e11b0: 6d65 2f69 6f2f 6661 7374 712f 536f 6c65  me/io/fastq/Sole\n+006e11c0: 7861 4661 7374 7157 7269 7465 722e 6874  xaFastqWriter.ht\n 006e11d0: 6d6c 2220 7469 746c 653d 2263 6c61 7373  ml\" title=\"class\n 006e11e0: 2069 6e20 6f72 672e 6269 6f6a 6176 612e   in org.biojava.\n 006e11f0: 6e62 696f 2e67 656e 6f6d 652e 696f 2e66  nbio.genome.io.f\n-006e1200: 6173 7471 223e 5361 6e67 6572 4661 7374  astq\">SangerFast\n+006e1200: 6173 7471 223e 536f 6c65 7861 4661 7374  astq\">SolexaFast\n 006e1210: 7157 7269 7465 723c 2f61 3e3c 2f64 743e  qWriter</a></dt>\n 006e1220: 0a3c 6464 3e26 6e62 7370 3b3c 2f64 643e  .<dd>&nbsp;</dd>\n 006e1230: 0a3c 6474 3e3c 6120 6872 6566 3d22 6f72  .<dt><a href=\"or\n 006e1240: 672f 6269 6f6a 6176 612f 6e62 696f 2f67  g/biojava/nbio/g\n 006e1250: 656e 6f6d 652f 696f 2f66 6173 7471 2f46  enome/io/fastq/F\n 006e1260: 6173 7471 5772 6974 6572 2e68 746d 6c23  astqWriter.html#\n 006e1270: 7772 6974 6528 6a61 7661 2e69 6f2e 4669  write(java.io.Fi\n@@ -450877,35 +450877,35 @@\n 006e13c0: 6520 7370 6563 6966 6965 6420 4641 5354  e specified FAST\n 006e13d0: 5120 666f 726d 6174 7465 6420 7365 7175  Q formatted sequ\n 006e13e0: 656e 6365 7320 746f 2074 6865 2073 7065  ences to the spe\n 006e13f0: 6369 6669 6564 2066 696c 652e 3c2f 6469  cified file.</di\n 006e1400: 763e 0a3c 2f64 643e 0a3c 6474 3e3c 6120  v>.</dd>.<dt><a \n 006e1410: 6872 6566 3d22 6f72 672f 6269 6f6a 6176  href=\"org/biojav\n 006e1420: 612f 6e62 696f 2f67 656e 6f6d 652f 696f  a/nbio/genome/io\n-006e1430: 2f66 6173 7471 2f53 616e 6765 7246 6173  /fastq/SangerFas\n+006e1430: 2f66 6173 7471 2f53 6f6c 6578 6146 6173  /fastq/SolexaFas\n 006e1440: 7471 5772 6974 6572 2e68 746d 6c23 7772  tqWriter.html#wr\n 006e1450: 6974 6528 6a61 7661 2e69 6f2e 4f75 7470  ite(java.io.Outp\n 006e1460: 7574 5374 7265 616d 2c6a 6176 612e 6c61  utStream,java.la\n 006e1470: 6e67 2e49 7465 7261 626c 6529 2220 636c  ng.Iterable)\" cl\n 006e1480: 6173 733d 226d 656d 6265 722d 6e61 6d65  ass=\"member-name\n 006e1490: 2d6c 696e 6b22 3e77 7269 7465 284f 7574  -link\">write(Out\n 006e14a0: 7075 7453 7472 6561 6d2c 2049 7465 7261  putStream, Itera\n 006e14b0: 626c 6526 6c74 3b46 6173 7471 2667 743b  ble&lt;Fastq&gt;\n 006e14c0: 293c 2f61 3e20 2d20 4d65 7468 6f64 2069  )</a> - Method i\n 006e14d0: 6e20 636c 6173 7320 6f72 672e 6269 6f6a  n class org.bioj\n 006e14e0: 6176 612e 6e62 696f 2e67 656e 6f6d 652e  ava.nbio.genome.\n 006e14f0: 696f 2e66 6173 7471 2e3c 6120 6872 6566  io.fastq.<a href\n 006e1500: 3d22 6f72 672f 6269 6f6a 6176 612f 6e62  =\"org/biojava/nb\n 006e1510: 696f 2f67 656e 6f6d 652f 696f 2f66 6173  io/genome/io/fas\n-006e1520: 7471 2f53 616e 6765 7246 6173 7471 5772  tq/SangerFastqWr\n+006e1520: 7471 2f53 6f6c 6578 6146 6173 7471 5772  tq/SolexaFastqWr\n 006e1530: 6974 6572 2e68 746d 6c22 2074 6974 6c65  iter.html\" title\n 006e1540: 3d22 636c 6173 7320 696e 206f 7267 2e62  =\"class in org.b\n 006e1550: 696f 6a61 7661 2e6e 6269 6f2e 6765 6e6f  iojava.nbio.geno\n-006e1560: 6d65 2e69 6f2e 6661 7374 7122 3e53 616e  me.io.fastq\">San\n-006e1570: 6765 7246 6173 7471 5772 6974 6572 3c2f  gerFastqWriter</\n+006e1560: 6d65 2e69 6f2e 6661 7374 7122 3e53 6f6c  me.io.fastq\">Sol\n+006e1570: 6578 6146 6173 7471 5772 6974 6572 3c2f  exaFastqWriter</\n 006e1580: 613e 3c2f 6474 3e0a 3c64 643e 266e 6273  a></dt>.<dd>&nbs\n 006e1590: 703b 3c2f 6464 3e0a 3c64 743e 3c61 2068  p;</dd>.<dt><a h\n 006e15a0: 7265 663d 226f 7267 2f62 696f 6a61 7661  ref=\"org/biojava\n 006e15b0: 2f6e 6269 6f2f 6765 6e6f 6d65 2f69 6f2f  /nbio/genome/io/\n 006e15c0: 6661 7374 712f 4661 7374 7157 7269 7465  fastq/FastqWrite\n 006e15d0: 722e 6874 6d6c 2377 7269 7465 286a 6176  r.html#write(jav\n 006e15e0: 612e 696f 2e4f 7574 7075 7453 7472 6561  a.io.OutputStrea\n@@ -450962,36 +450962,36 @@\n 006e1910: 6474 3e0a 3c64 643e 0a3c 6469 7620 636c  dt>.<dd>.<div cl\n 006e1920: 6173 733d 2262 6c6f 636b 223e 4f75 7470  ass=\"block\">Outp\n 006e1930: 7574 2067 6666 3320 666f 726d 6174 2066  ut gff3 format f\n 006e1940: 6f72 2061 2044 4e41 2053 6571 7565 6e63  or a DNA Sequenc\n 006e1950: 653c 2f64 6976 3e0a 3c2f 6464 3e0a 3c64  e</div>.</dd>.<d\n 006e1960: 743e 3c61 2068 7265 663d 226f 7267 2f62  t><a href=\"org/b\n 006e1970: 696f 6a61 7661 2f6e 6269 6f2f 6765 6e6f  iojava/nbio/geno\n-006e1980: 6d65 2f69 6f2f 6661 7374 712f 5361 6e67  me/io/fastq/Sang\n-006e1990: 6572 4661 7374 7157 7269 7465 722e 6874  erFastqWriter.ht\n+006e1980: 6d65 2f69 6f2f 6661 7374 712f 536f 6c65  me/io/fastq/Sole\n+006e1990: 7861 4661 7374 7157 7269 7465 722e 6874  xaFastqWriter.ht\n 006e19a0: 6d6c 2377 7269 7465 286a 6176 612e 696f  ml#write(java.io\n 006e19b0: 2e4f 7574 7075 7453 7472 6561 6d2c 6f72  .OutputStream,or\n 006e19c0: 672e 6269 6f6a 6176 612e 6e62 696f 2e67  g.biojava.nbio.g\n 006e19d0: 656e 6f6d 652e 696f 2e66 6173 7471 2e46  enome.io.fastq.F\n 006e19e0: 6173 7471 2e2e 2e29 2220 636c 6173 733d  astq...)\" class=\n 006e19f0: 226d 656d 6265 722d 6e61 6d65 2d6c 696e  \"member-name-lin\n 006e1a00: 6b22 3e77 7269 7465 284f 7574 7075 7453  k\">write(OutputS\n 006e1a10: 7472 6561 6d2c 2046 6173 7471 2e2e 2e29  tream, Fastq...)\n 006e1a20: 3c2f 613e 202d 204d 6574 686f 6420 696e  </a> - Method in\n 006e1a30: 2063 6c61 7373 206f 7267 2e62 696f 6a61   class org.bioja\n 006e1a40: 7661 2e6e 6269 6f2e 6765 6e6f 6d65 2e69  va.nbio.genome.i\n 006e1a50: 6f2e 6661 7374 712e 3c61 2068 7265 663d  o.fastq.<a href=\n 006e1a60: 226f 7267 2f62 696f 6a61 7661 2f6e 6269  \"org/biojava/nbi\n 006e1a70: 6f2f 6765 6e6f 6d65 2f69 6f2f 6661 7374  o/genome/io/fast\n-006e1a80: 712f 5361 6e67 6572 4661 7374 7157 7269  q/SangerFastqWri\n+006e1a80: 712f 536f 6c65 7861 4661 7374 7157 7269  q/SolexaFastqWri\n 006e1a90: 7465 722e 6874 6d6c 2220 7469 746c 653d  ter.html\" title=\n 006e1aa0: 2263 6c61 7373 2069 6e20 6f72 672e 6269  \"class in org.bi\n 006e1ab0: 6f6a 6176 612e 6e62 696f 2e67 656e 6f6d  ojava.nbio.genom\n-006e1ac0: 652e 696f 2e66 6173 7471 223e 5361 6e67  e.io.fastq\">Sang\n-006e1ad0: 6572 4661 7374 7157 7269 7465 723c 2f61  erFastqWriter</a\n+006e1ac0: 652e 696f 2e66 6173 7471 223e 536f 6c65  e.io.fastq\">Sole\n+006e1ad0: 7861 4661 7374 7157 7269 7465 723c 2f61  xaFastqWriter</a\n 006e1ae0: 3e3c 2f64 743e 0a3c 6464 3e26 6e62 7370  ></dt>.<dd>&nbsp\n 006e1af0: 3b3c 2f64 643e 0a3c 6474 3e3c 6120 6872  ;</dd>.<dt><a hr\n 006e1b00: 6566 3d22 6f72 672f 6269 6f6a 6176 612f  ef=\"org/biojava/\n 006e1b10: 6e62 696f 2f67 656e 6f6d 652f 696f 2f66  nbio/genome/io/f\n 006e1b20: 6173 7471 2f46 6173 7471 5772 6974 6572  astq/FastqWriter\n 006e1b30: 2e68 746d 6c23 7772 6974 6528 6a61 7661  .html#write(java\n 006e1b40: 2e69 6f2e 4f75 7470 7574 5374 7265 616d  .io.OutputStream\n", "details": [{"source1": "html2text {}", "source2": "html2text {}", "unified_diff": "@@ -1945,22 +1945,22 @@\n   App - Class in org.biojava.nbio.ontology\n       Hello world!\n   App() - Constructor for class org.biojava.nbio.genome.App\n       \u00a0\n   App() - Constructor for class org.biojava.nbio.ontology.App\n       \u00a0\n   append(T,_Iterable<Fastq>) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SangerFastqWriter\n+  org.biojava.nbio.genome.io.fastq.SolexaFastqWriter\n       \u00a0\n   append(T,_Iterable<Fastq>) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqWriter\n       Append the specified FASTQ formatted sequences to the specified\n       appendable.\n   append(T,_Fastq...) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SangerFastqWriter\n+  org.biojava.nbio.genome.io.fastq.SolexaFastqWriter\n       \u00a0\n   append(T,_Fastq...) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqWriter\n       Append the specified FASTQ formatted sequences to the specified\n       appendable.\n   appendClose(Writer,_String) - Static method in class\n   org.forester.phylogeny.data.PhylogenyDataUtil\n@@ -34708,15 +34708,15 @@\n   parse(Object,_char,_boolean,_boolean) - Static method in class\n   org.forester.util.BasicTableParser\n       \u00a0\n   parse(Object,_char,_boolean,_boolean,_String,_boolean) - Static method in\n   class org.forester.util.BasicTableParser\n       \u00a0\n   parse(Readable,_ParseListener) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SolexaFastqReader\n+  org.biojava.nbio.genome.io.fastq.SangerFastqReader\n       \u00a0\n   parse(Readable,_ParseListener) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqReader\n       Parse the specified readable.\n   parse(String) - Method in class\n   org.biojava.nbio.alignment.io.StockholmFileParser\n       Parses a Stockholm file and returns a StockholmStructure object with its\n@@ -37163,20 +37163,20 @@\n   read(char[],_int,_int) - Method in class\n   org.biojava.nbio.core.sequence.io.BufferedReaderBytesRead\n       Reads characters into a portion of an array.\n   read(BufferedReader) - Static method in class\n   org.biojava.nbio.structure.jama.Matrix\n       Read a matrix from a stream.\n   read(File) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SolexaFastqReader\n+  org.biojava.nbio.genome.io.fastq.SangerFastqReader\n       \u00a0\n   read(File) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader\n       Read zero or more FASTQ formatted sequences from the specified file.\n   read(InputStream) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SolexaFastqReader\n+  org.biojava.nbio.genome.io.fastq.SangerFastqReader\n       \u00a0\n   read(InputStream) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqReader\n       Read zero or more FASTQ formatted sequences from the specified input\n       stream.\n   read(String) - Static method in class\n   org.biojava.nbio.genome.parsers.gff.GeneIDGFF2Reader\n@@ -37187,15 +37187,15 @@\n   read(String) - Static method in class\n   org.biojava.nbio.genome.parsers.gff.GFF3Reader\n       \u00a0\n   read(String,_List<String>) - Static method in class\n   org.biojava.nbio.genome.parsers.gff.GFF3Reader\n       Read a file into a FeatureList.\n   read(URL) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SolexaFastqReader\n+  org.biojava.nbio.genome.io.fastq.SangerFastqReader\n       \u00a0\n   read(URL) - Method in interface org.biojava.nbio.genome.io.fastq.FastqReader\n       Read zero or more FASTQ formatted sequences from the specified url.\n   readableFiles - Static variable in class\n   org.biojava.nbio.core.sequence.io.GenbankSequenceParser\n       \u00a0\n   readCSV(File,_char) - Static method in class\n@@ -48232,15 +48232,15 @@\n       \u00a0\n   StrCompAlignment - Class in org.biojava.nbio.structure.align.pairwise\n       \u00a0\n   StrCompAlignment(int,_int) - Constructor for class\n   org.biojava.nbio.structure.align.pairwise.StrCompAlignment\n       \u00a0\n   stream(Readable,_StreamListener) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SolexaFastqReader\n+  org.biojava.nbio.genome.io.fastq.SangerFastqReader\n       \u00a0\n   stream(Readable,_StreamListener) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqReader\n       Stream the specified readable.\n   StreamListener - Interface in org.biojava.nbio.genome.io.fastq\n       Event based parser callback.\n   STRING_LIMIT - Static variable in class\n@@ -53282,37 +53282,37 @@\n   wrapToRna(Sequence<NucleotideCompound>) - Method in class\n   org.biojava.nbio.core.sequence.transcription.DNAToRNATranslator\n       Takes in the given DNA Sequence and returns an instance of RNASequence\n       which is using RnaSequenceView as a ProxySequenceReader.\n   write(int) - Method in class org.biojava.nbio.ronn.NullOutputStream\n       \u00a0\n   write(File,_Iterable<Fastq>) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SangerFastqWriter\n+  org.biojava.nbio.genome.io.fastq.SolexaFastqWriter\n       \u00a0\n   write(File,_Iterable<Fastq>) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqWriter\n       Write the specified FASTQ formatted sequences to the specified file.\n   write(File,_Fastq...) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SangerFastqWriter\n+  org.biojava.nbio.genome.io.fastq.SolexaFastqWriter\n       \u00a0\n   write(File,_Fastq...) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqWriter\n       Write the specified FASTQ formatted sequences to the specified file.\n   write(OutputStream,_Iterable<Fastq>) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SangerFastqWriter\n+  org.biojava.nbio.genome.io.fastq.SolexaFastqWriter\n       \u00a0\n   write(OutputStream,_Iterable<Fastq>) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqWriter\n       Write the specified FASTQ formatted sequences to the specified output\n       stream.\n   write(OutputStream,_LinkedHashMap<String,_ChromosomeSequence>) - Method in\n   class org.biojava.nbio.genome.parsers.gff.GFF3Writer\n       Output gff3 format for a DNA Sequence\n   write(OutputStream,_Fastq...) - Method in class\n-  org.biojava.nbio.genome.io.fastq.SangerFastqWriter\n+  org.biojava.nbio.genome.io.fastq.SolexaFastqWriter\n       \u00a0\n   write(OutputStream,_Fastq...) - Method in interface\n   org.biojava.nbio.genome.io.fastq.FastqWriter\n       Write the specified FASTQ formatted sequences to the specified output\n       stream.\n   write(Writer) - Method in class\n   org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix\n"}]}, {"source1": "./usr/share/doc/libbiojava5-java/apidocs/member-search-index.js", "source2": "./usr/share/doc/libbiojava5-java/apidocs/member-search-index.js", "unified_diff": null, "details": [{"source1": "js-beautify {}", "source2": "js-beautify {}", "unified_diff": "@@ -2590,25 +2590,25 @@\n }, {\n     \"p\": \"org.biojava.nbio.ontology\",\n     \"c\": \"App\",\n     \"l\": \"App()\",\n     \"u\": \"%3Cinit%3E()\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SangerFastqWriter\",\n+    \"c\": \"SolexaFastqWriter\",\n     \"l\": \"append(T, Fastq...)\",\n     \"u\": \"append(T,org.biojava.nbio.genome.io.fastq.Fastq...)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqWriter\",\n     \"l\": \"append(T, Fastq...)\",\n     \"u\": \"append(T,org.biojava.nbio.genome.io.fastq.Fastq...)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SangerFastqWriter\",\n+    \"c\": \"SolexaFastqWriter\",\n     \"l\": \"append(T, Iterable<Fastq>)\",\n     \"u\": \"append(T,java.lang.Iterable)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqWriter\",\n     \"l\": \"append(T, Iterable<Fastq>)\",\n     \"u\": \"append(T,java.lang.Iterable)\"\n@@ -47944,15 +47944,15 @@\n }, {\n     \"p\": \"org.forester.util\",\n     \"c\": \"BasicTableParser\",\n     \"l\": \"parse(Object, char, boolean, boolean, String, boolean)\",\n     \"u\": \"parse(java.lang.Object,char,boolean,boolean,java.lang.String,boolean)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SolexaFastqReader\",\n+    \"c\": \"SangerFastqReader\",\n     \"l\": \"parse(Readable, ParseListener)\",\n     \"u\": \"parse(java.lang.Readable,org.biojava.nbio.genome.io.fastq.ParseListener)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqReader\",\n     \"l\": \"parse(Readable, ParseListener)\",\n     \"u\": \"parse(java.lang.Readable,org.biojava.nbio.genome.io.fastq.ParseListener)\"\n@@ -51131,25 +51131,25 @@\n }, {\n     \"p\": \"org.biojava.nbio.core.sequence.io\",\n     \"c\": \"BufferedReaderBytesRead\",\n     \"l\": \"read(char[], int, int)\",\n     \"u\": \"read(char[],int,int)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SolexaFastqReader\",\n+    \"c\": \"SangerFastqReader\",\n     \"l\": \"read(File)\",\n     \"u\": \"read(java.io.File)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqReader\",\n     \"l\": \"read(File)\",\n     \"u\": \"read(java.io.File)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SolexaFastqReader\",\n+    \"c\": \"SangerFastqReader\",\n     \"l\": \"read(InputStream)\",\n     \"u\": \"read(java.io.InputStream)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqReader\",\n     \"l\": \"read(InputStream)\",\n     \"u\": \"read(java.io.InputStream)\"\n@@ -51171,15 +51171,15 @@\n }, {\n     \"p\": \"org.biojava.nbio.genome.parsers.gff\",\n     \"c\": \"GFF3Reader\",\n     \"l\": \"read(String, List<String>)\",\n     \"u\": \"read(java.lang.String,java.util.List)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SolexaFastqReader\",\n+    \"c\": \"SangerFastqReader\",\n     \"l\": \"read(URL)\",\n     \"u\": \"read(java.net.URL)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqReader\",\n     \"l\": \"read(URL)\",\n     \"u\": \"read(java.net.URL)\"\n@@ -67923,15 +67923,15 @@\n }, {\n     \"p\": \"org.biojava.nbio.structure.align.pairwise\",\n     \"c\": \"StrCompAlignment\",\n     \"l\": \"StrCompAlignment(int, int)\",\n     \"u\": \"%3Cinit%3E(int,int)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SolexaFastqReader\",\n+    \"c\": \"SangerFastqReader\",\n     \"l\": \"stream(Readable, StreamListener)\",\n     \"u\": \"stream(java.lang.Readable,org.biojava.nbio.genome.io.fastq.StreamListener)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqReader\",\n     \"l\": \"stream(Readable, StreamListener)\",\n     \"u\": \"stream(java.lang.Readable,org.biojava.nbio.genome.io.fastq.StreamListener)\"\n@@ -74863,49 +74863,49 @@\n }, {\n     \"p\": \"org.biojava.nbio.genome.parsers.gff\",\n     \"c\": \"GeneIDGFF2Reader\",\n     \"l\": \"write(FeatureList, String)\",\n     \"u\": \"write(org.biojava.nbio.genome.parsers.gff.FeatureList,java.lang.String)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SangerFastqWriter\",\n+    \"c\": \"SolexaFastqWriter\",\n     \"l\": \"write(File, Fastq...)\",\n     \"u\": \"write(java.io.File,org.biojava.nbio.genome.io.fastq.Fastq...)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqWriter\",\n     \"l\": \"write(File, Fastq...)\",\n     \"u\": 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Fastq...)\",\n     \"u\": \"write(java.io.OutputStream,org.biojava.nbio.genome.io.fastq.Fastq...)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n-    \"c\": \"SangerFastqWriter\",\n+    \"c\": \"SolexaFastqWriter\",\n     \"l\": \"write(OutputStream, Iterable<Fastq>)\",\n     \"u\": \"write(java.io.OutputStream,java.lang.Iterable)\"\n }, {\n     \"p\": \"org.biojava.nbio.genome.io.fastq\",\n     \"c\": \"FastqWriter\",\n     \"l\": \"write(OutputStream, Iterable<Fastq>)\",\n     \"u\": \"write(java.io.OutputStream,java.lang.Iterable)\"\n"}]}]}]}]}]}