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/* Working with locations */
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Lines changed: 35 additions & 26 deletions

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‎wiki/BioJava:BioJavaXDocs.md‎

Lines changed: 17 additions & 17 deletions
Original file line numberDiff line numberDiff line change
@@ -1420,36 +1420,36 @@ implemented by the SimpleRichLocation class.
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This example describes the GenBank-style location string "56":
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<java> Position pos = new SimplePosition(56); RichLocation loc = new
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SimpleRichLocation(pos,0); // the 0 is an arbitrary value for the rank
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of this location </java>
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<java> Position pos = new SimplePosition(56); // the 0 is an arbitrary
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value for the rank of this location RichLocation loc = new
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SimpleRichLocation(pos,0); </java>
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This example describes the GenBank-style location string
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"(23^34)..57\>":
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<java> Position min = new SimplePosition(false,false,23,34,"^"); // two
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falses = not fuzzy at all Position max = new
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SimplePosition(false,true,57); // false = non-fuzzy start, true = fuzzy
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end RichLocation loc = new SimpleRichLocation(min,max,0); // the 0 is an
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arbitrary value for the rank of this location </java>
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<java> // two falses = not fuzzy at all Position min = new
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SimplePosition(false,false,23,34,"^"); // false = non-fuzzy start, true
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= fuzzy end Position max = new SimplePosition(false,true,57); // the 0
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is an arbitrary value for the rank of this location RichLocation loc =
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new SimpleRichLocation(min,max,0); </java>
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This example describes the GenBank-style location string
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"complement((23^34)..57\>)":
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<java> Position min = new SimplePosition(false,false,23,34,"^"); // two
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falses = not fuzzy at all Position max = new
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SimplePosition(false,true,57); // false = non-fuzzy start, true = fuzzy
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end RichLocation loc = new
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<java> // two falses = not fuzzy at all Position min = new
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SimplePosition(false,false,23,34,"^"); // false = non-fuzzy start, true
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= fuzzy end Position max = new SimplePosition(false,true,57);
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RichLocation loc = new
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SimpleRichLocation(min,max,0,Strand.NEGATIVE\_STRAND); </java>
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This example describes the GenBank-style location string
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"A12345.3:complement((23^34)..57\>)":
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<java> CrossRef cr = new SimpleCrossRef("GenBank","A12345",3); //
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version 3 of accession A12345 in the GenBank database Position min = new
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SimplePosition(false,false,23,34,"^"); // two falses = not fuzzy at all
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Position max = new SimplePosition(false,true,57); // false = non-fuzzy
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start, true = fuzzy end RichLocation loc = new
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<java> // version 3 of accession A12345 in the GenBank database CrossRef
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cr = new SimpleCrossRef("GenBank","A12345",3); // two falses = not fuzzy
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at all Position min = new SimplePosition(false,false,23,34,"^"); //
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false = non-fuzzy start, true = fuzzy end Position max = new
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SimplePosition(false,true,57); RichLocation loc = new
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SimpleRichLocation(min,max,Strand.NEGATIVE\_STRAND,cr); </java>
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If you require locations that cover more than one range, you must use

‎wiki/BioJava:BioJavaXDocs.mediawiki‎

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Original file line numberDiff line numberDiff line change
@@ -1490,31 +1490,40 @@ This example describes the GenBank-style location string "56":
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<java>
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Position pos = new SimplePosition(56);
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RichLocation loc = new SimpleRichLocation(pos,0); // the 0 is an arbitrary value for the rank of this location
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// the 0 is an arbitrary value for the rank of this location
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RichLocation loc = new SimpleRichLocation(pos,0);
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</java>
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This example describes the GenBank-style location string "(23^34)..57>":
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<java>
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Position min = new SimplePosition(false,false,23,34,"^"); // two falses = not fuzzy at all
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Position max = new SimplePosition(false,true,57); // false = non-fuzzy start, true = fuzzy end
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RichLocation loc = new SimpleRichLocation(min,max,0); // the 0 is an arbitrary value for the rank of this location
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// two falses = not fuzzy at all
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Position min = new SimplePosition(false,false,23,34,"^");
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// false = non-fuzzy start, true = fuzzy end
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Position max = new SimplePosition(false,true,57);
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// the 0 is an arbitrary value for the rank of this location
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RichLocation loc = new SimpleRichLocation(min,max,0);
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</java>
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This example describes the GenBank-style location string "complement((23^34)..57>)":
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<java>
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Position min = new SimplePosition(false,false,23,34,"^"); // two falses = not fuzzy at all
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Position max = new SimplePosition(false,true,57); // false = non-fuzzy start, true = fuzzy end
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// two falses = not fuzzy at all
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Position min = new SimplePosition(false,false,23,34,"^");
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// false = non-fuzzy start, true = fuzzy end
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Position max = new SimplePosition(false,true,57);
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RichLocation loc = new SimpleRichLocation(min,max,0,Strand.NEGATIVE_STRAND);
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</java>
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This example describes the GenBank-style location string "A12345.3:complement((23^34)..57>)":
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<java>
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CrossRef cr = new SimpleCrossRef("GenBank","A12345",3); // version 3 of accession A12345 in the GenBank database
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Position min = new SimplePosition(false,false,23,34,"^"); // two falses = not fuzzy at all
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Position max = new SimplePosition(false,true,57); // false = non-fuzzy start, true = fuzzy end
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// version 3 of accession A12345 in the GenBank database
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CrossRef cr = new SimpleCrossRef("GenBank","A12345",3);
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// two falses = not fuzzy at all
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Position min = new SimplePosition(false,false,23,34,"^");
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// false = non-fuzzy start, true = fuzzy end
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Position max = new SimplePosition(false,true,57);
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RichLocation loc = new SimpleRichLocation(min,max,Strand.NEGATIVE_STRAND,cr);
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</java>
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