diff --git a/README.md b/README.md index 3875d1a..a76fbd4 100644 --- a/README.md +++ b/README.md @@ -2,7 +2,7 @@ ##Installation - $ go get github.com/kortschak/BioGo/... + $ go get github.com/kortschak/biogo/... ##Overview diff --git a/align/align.go b/align/align.go index 238d51a..574a6b1 100644 --- a/align/align.go +++ b/align/align.go @@ -17,7 +17,7 @@ package align // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/seq" ) type Aligner interface { diff --git a/align/nw/example_test.go b/align/nw/example_test.go index 9274630..a498884 100644 --- a/align/nw/example_test.go +++ b/align/nw/example_test.go @@ -17,7 +17,7 @@ package nw import ( "fmt" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/seq" ) func ExampleAligner_Align() { diff --git a/align/nw/nw.go b/align/nw/nw.go index a926639..d9f4487 100644 --- a/align/nw/nw.go +++ b/align/nw/nw.go @@ -17,9 +17,9 @@ package nw // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" ) // Default character table lookups. diff --git a/align/nw/nw_test.go b/align/nw/nw_test.go index 706acee..848ecd6 100644 --- a/align/nw/nw_test.go +++ b/align/nw/nw_test.go @@ -16,7 +16,7 @@ package nw // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/io/seqio/fasta" + "github.com/kortschak/biogo/io/seqio/fasta" check "launchpad.net/gocheck" "testing" ) diff --git a/align/pals/dp/align.go b/align/pals/dp/align.go index e54bc46..b4bb595 100644 --- a/align/pals/dp/align.go +++ b/align/pals/dp/align.go @@ -17,9 +17,9 @@ package dp // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/align/pals/filter" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/align/pals/filter" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/seq" "sort" ) diff --git a/align/pals/dp/dp_test.go b/align/pals/dp/dp_test.go index 40ad72e..ec626eb 100644 --- a/align/pals/dp/dp_test.go +++ b/align/pals/dp/dp_test.go @@ -16,10 +16,10 @@ package dp // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/align/pals/filter" - "github.com/kortschak/BioGo/align/sw" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/align/pals/filter" + "github.com/kortschak/biogo/align/sw" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" check "launchpad.net/gocheck" "testing" ) diff --git a/align/pals/dp/kernel.go b/align/pals/dp/kernel.go index 5df8f81..33a94e2 100644 --- a/align/pals/dp/kernel.go +++ b/align/pals/dp/kernel.go @@ -16,8 +16,8 @@ package dp // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/align/pals/filter" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/align/pals/filter" + "github.com/kortschak/biogo/seq" ) const ( diff --git a/align/pals/dp/lookup.go b/align/pals/dp/lookup.go index 8afb2f8..cc161b2 100644 --- a/align/pals/dp/lookup.go +++ b/align/pals/dp/lookup.go @@ -16,8 +16,8 @@ package dp // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/util" ) var lookUp util.CTL diff --git a/align/pals/filter/filter.go b/align/pals/filter/filter.go index bb2ba6b..539fed1 100644 --- a/align/pals/filter/filter.go +++ b/align/pals/filter/filter.go @@ -19,10 +19,10 @@ package filter // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/morass" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/morass" + "github.com/kortschak/biogo/seq" ) // Ukonnen's Lemma: U(n, q, š›œ) := (n + 1) - q(āŒŠš›œnāŒ‹ + 1) diff --git a/align/pals/filter/filter_test.go b/align/pals/filter/filter_test.go index a501620..2250877 100644 --- a/align/pals/filter/filter_test.go +++ b/align/pals/filter/filter_test.go @@ -16,10 +16,10 @@ package filter // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/morass" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/morass" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" check "launchpad.net/gocheck" "testing" ) diff --git a/align/pals/filter/lookup.go b/align/pals/filter/lookup.go index a0e88e6..bf82a25 100644 --- a/align/pals/filter/lookup.go +++ b/align/pals/filter/lookup.go @@ -16,8 +16,8 @@ package filter // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/util" ) var lookUp util.CTL diff --git a/align/pals/filter/merge.go b/align/pals/filter/merge.go index d046b6e..43aa56a 100644 --- a/align/pals/filter/merge.go +++ b/align/pals/filter/merge.go @@ -16,8 +16,8 @@ package filter // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/seq" "sort" ) diff --git a/align/pals/packseqs.go b/align/pals/packseqs.go index db28d1b..03f2589 100644 --- a/align/pals/packseqs.go +++ b/align/pals/packseqs.go @@ -18,8 +18,8 @@ package pals import ( "bytes" "fmt" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" ) var ( diff --git a/align/pals/pair.go b/align/pals/pair.go index 54aab8c..69d139c 100644 --- a/align/pals/pair.go +++ b/align/pals/pair.go @@ -17,10 +17,10 @@ package pals import ( "fmt" - "github.com/kortschak/BioGo/align/pals/dp" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/align/pals/dp" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/seq" ) // A FeaturePair holds a pair of features with additional information relating the two. diff --git a/align/pals/pals.go b/align/pals/pals.go index 8a9293a..ca5260c 100644 --- a/align/pals/pals.go +++ b/align/pals/pals.go @@ -17,13 +17,13 @@ package pals // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/align/pals/dp" - "github.com/kortschak/BioGo/align/pals/filter" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/morass" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/align/pals/dp" + "github.com/kortschak/biogo/align/pals/filter" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/morass" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" "io" "os" "unsafe" diff --git a/align/pals/pals_test.go b/align/pals/pals_test.go index 503d1ae..b9c7f9a 100644 --- a/align/pals/pals_test.go +++ b/align/pals/pals_test.go @@ -18,10 +18,10 @@ package pals import ( "bytes" "fmt" - "github.com/kortschak/BioGo/align/pals/dp" - "github.com/kortschak/BioGo/align/pals/filter" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/align/pals/dp" + "github.com/kortschak/biogo/align/pals/filter" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" check "launchpad.net/gocheck" "math" "testing" diff --git a/align/pals/write.go b/align/pals/write.go index 5fd593a..b2b75e0 100644 --- a/align/pals/write.go +++ b/align/pals/write.go @@ -17,8 +17,8 @@ package pals import ( "fmt" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/io/featio/gff" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/io/featio/gff" "io" "os" ) diff --git a/align/sw/example_test.go b/align/sw/example_test.go index 3675d6b..c646f44 100644 --- a/align/sw/example_test.go +++ b/align/sw/example_test.go @@ -17,7 +17,7 @@ package sw import ( "fmt" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/seq" ) func ExampleAligner_Align() { diff --git a/align/sw/sw.go b/align/sw/sw.go index 45cebcd..5cc5a1e 100644 --- a/align/sw/sw.go +++ b/align/sw/sw.go @@ -17,9 +17,9 @@ package sw // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" ) // Default character table lookups. diff --git a/align/sw/sw_test.go b/align/sw/sw_test.go index c48a66c..e410815 100644 --- a/align/sw/sw_test.go +++ b/align/sw/sw_test.go @@ -16,7 +16,7 @@ package sw // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/io/seqio/fasta" + "github.com/kortschak/biogo/io/seqio/fasta" check "launchpad.net/gocheck" "testing" ) diff --git a/alphabet/alphabet.go b/alphabet/alphabet.go index 1a7a624..5855442 100644 --- a/alphabet/alphabet.go +++ b/alphabet/alphabet.go @@ -18,7 +18,7 @@ package alphabet import ( "errors" "fmt" - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "sort" "strings" "unicode" diff --git a/bio/defs.go b/bio/defs.go index c5c45bd..9d38ffe 100644 --- a/bio/defs.go +++ b/bio/defs.go @@ -17,6 +17,6 @@ package bio // Output defaults. var ( - Precision = 4 // BioGo global precision value. - FloatFormat byte = 'f' // BioGo global float format. + Precision = 4 // biogo global precision value. + FloatFormat byte = 'f' // biogo global float format. ) diff --git a/bio/errors_test.go b/bio/errors_test.go index 8641658..9d26056 100644 --- a/bio/errors_test.go +++ b/bio/errors_test.go @@ -35,9 +35,9 @@ func (s *S) TestCaller(c *check.C) { err := NewError("message", 0, "item") c.Check(err.Error(), check.Equals, "message") fn, ln := err.FileLine() - c.Check(fn, check.Matches, "/.*/BioGo/bio/errors_test.go") + c.Check(fn, check.Matches, "/.*/biogo/bio/errors_test.go") c.Check(ln, check.Equals, 35) - c.Check(err.Package(), check.Equals, "github.com/kortschak/BioGo/bio.(*S)") + c.Check(err.Package(), check.Equals, "github.com/kortschak/biogo/bio.(*S)") c.Check(err.Function(), check.Equals, "TestCaller") err = f(5).(Error) fmt.Println(err.Tracef(10)) diff --git a/concurrent/map.go b/concurrent/map.go index fb8c619..7c6e2e2 100644 --- a/concurrent/map.go +++ b/concurrent/map.go @@ -16,8 +16,8 @@ package concurrent // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/util" "math" ) diff --git a/concurrent/processor.go b/concurrent/processor.go index b978a4a..992e449 100644 --- a/concurrent/processor.go +++ b/concurrent/processor.go @@ -16,7 +16,7 @@ package concurrent // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "runtime" "sync" ) diff --git a/concurrent/promise.go b/concurrent/promise.go index 3fde768..0cc98ef 100644 --- a/concurrent/promise.go +++ b/concurrent/promise.go @@ -16,7 +16,7 @@ package concurrent // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "sync" ) diff --git a/doc.go b/doc.go index 19d0ac2..4bc6765 100644 --- a/doc.go +++ b/doc.go @@ -201,4 +201,4 @@ PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program. If not, see . */ -package BioGo +package biogo diff --git a/examples/brahma/main.go b/examples/brahma/main.go index 7bb5c4b..eb8b217 100644 --- a/examples/brahma/main.go +++ b/examples/brahma/main.go @@ -5,10 +5,10 @@ import ( "encoding/gob" "flag" "fmt" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/io/featio/gff" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/io/featio/gff" + "github.com/kortschak/biogo/util" "os" "runtime" "sort" diff --git a/examples/cgr/main.go b/examples/cgr/main.go index 7d7a835..518ccdf 100644 --- a/examples/cgr/main.go +++ b/examples/cgr/main.go @@ -3,10 +3,10 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/graphics/color" - "github.com/kortschak/BioGo/graphics/kmercolor" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/io/seqio/fasta" + "github.com/kortschak/biogo/graphics/color" + "github.com/kortschak/biogo/graphics/kmercolor" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/io/seqio/fasta" "image/png" "os" ) diff --git a/examples/distance/main.go b/examples/distance/main.go index 9681638..fb23e6f 100644 --- a/examples/distance/main.go +++ b/examples/distance/main.go @@ -3,8 +3,8 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/io/seqio/fasta" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/io/seqio/fasta" "os" ) diff --git a/examples/ganesh/main.go b/examples/ganesh/main.go index b9928e3..15e77e0 100644 --- a/examples/ganesh/main.go +++ b/examples/ganesh/main.go @@ -4,9 +4,9 @@ import ( "bufio" "flag" "fmt" - "github.com/kortschak/BioGo/matrix" - "github.com/kortschak/BioGo/matrix/sparse" - "github.com/kortschak/BioGo/nmf" + "github.com/kortschak/biogo/matrix" + "github.com/kortschak/biogo/matrix/sparse" + "github.com/kortschak/biogo/nmf" "io" "math/rand" "os" diff --git a/examples/gayatri/main.go b/examples/gayatri/main.go index d710aca..3d0246f 100644 --- a/examples/gayatri/main.go +++ b/examples/gayatri/main.go @@ -3,11 +3,11 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/matrix" - "github.com/kortschak/BioGo/matrix/sparse" - "github.com/kortschak/BioGo/nmf" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/matrix" + "github.com/kortschak/biogo/matrix/sparse" + "github.com/kortschak/biogo/nmf" "math/rand" "os" "runtime" diff --git a/examples/krishna/main.go b/examples/krishna/main.go index 5efd0e7..391a19d 100644 --- a/examples/krishna/main.go +++ b/examples/krishna/main.go @@ -3,10 +3,10 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/align/pals" - "github.com/kortschak/BioGo/align/pals/filter" - "github.com/kortschak/BioGo/morass" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/align/pals" + "github.com/kortschak/biogo/align/pals/filter" + "github.com/kortschak/biogo/morass" + "github.com/kortschak/biogo/seq" "io" "log" "os" diff --git a/examples/krishna/packseqs.go b/examples/krishna/packseqs.go index 22062ed..a5d641b 100644 --- a/examples/krishna/packseqs.go +++ b/examples/krishna/packseqs.go @@ -3,10 +3,10 @@ package main import ( "crypto/md5" "fmt" - "github.com/kortschak/BioGo/align/pals" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/align/pals" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" "os" "path/filepath" ) diff --git a/examples/krishna/write.go b/examples/krishna/write.go index 3b65487..a86cdc8 100644 --- a/examples/krishna/write.go +++ b/examples/krishna/write.go @@ -1,9 +1,9 @@ package main import ( - "github.com/kortschak/BioGo/align/pals" - "github.com/kortschak/BioGo/align/pals/dp" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/align/pals" + "github.com/kortschak/biogo/align/pals/dp" + "github.com/kortschak/biogo/seq" ) func WriteDPHits(w *pals.Writer, target, query *seq.Seq, hits []dp.DPHit, comp bool) (n int, err error) { diff --git a/examples/motifmap/main.go b/examples/motifmap/main.go index e8bbff2..ea8eeab 100644 --- a/examples/motifmap/main.go +++ b/examples/motifmap/main.go @@ -18,8 +18,8 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/io/featio/bed" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/io/featio/bed" "math" "os" ) diff --git a/examples/paint/main.go b/examples/paint/main.go index 16c7a44..248ee86 100644 --- a/examples/paint/main.go +++ b/examples/paint/main.go @@ -3,10 +3,10 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/graphics/color" - "github.com/kortschak/BioGo/graphics/kmercolor" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/io/seqio/fasta" + "github.com/kortschak/biogo/graphics/color" + "github.com/kortschak/biogo/graphics/kmercolor" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/io/seqio/fasta" "image" "image/png" "os" diff --git a/examples/pairwise/main.go b/examples/pairwise/main.go index 2d1e01a..0047192 100644 --- a/examples/pairwise/main.go +++ b/examples/pairwise/main.go @@ -3,9 +3,9 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/seq" "os" ) diff --git a/examples/pwmscan/main.go b/examples/pwmscan/main.go index c877328..586571d 100644 --- a/examples/pwmscan/main.go +++ b/examples/pwmscan/main.go @@ -4,12 +4,12 @@ import ( "bufio" "flag" "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/io/alignio" - "github.com/kortschak/BioGo/io/featio/gff" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/pwm" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/io/alignio" + "github.com/kortschak/biogo/io/featio/gff" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/pwm" + "github.com/kortschak/biogo/seq" "os" "strconv" "strings" diff --git a/examples/shiva/main.go b/examples/shiva/main.go index fe624bc..15a6625 100644 --- a/examples/shiva/main.go +++ b/examples/shiva/main.go @@ -3,8 +3,8 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/seq" "os" "runtime/pprof" ) diff --git a/examples/tihar/main.go b/examples/tihar/main.go index 01ca1ae..50e9125 100644 --- a/examples/tihar/main.go +++ b/examples/tihar/main.go @@ -3,11 +3,11 @@ package main import ( "flag" "fmt" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/matrix" - "github.com/kortschak/BioGo/matrix/sparse" - "github.com/kortschak/BioGo/nmf" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/matrix" + "github.com/kortschak/biogo/matrix/sparse" + "github.com/kortschak/biogo/nmf" "math/rand" "os" "runtime" diff --git a/exp/alphabet/alphabet.go b/exp/alphabet/alphabet.go index 1222856..ba294a7 100644 --- a/exp/alphabet/alphabet.go +++ b/exp/alphabet/alphabet.go @@ -19,7 +19,7 @@ package alphabet import ( "errors" "fmt" - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "sort" "strings" "unicode" diff --git a/exp/alphabet/letters.go b/exp/alphabet/letters.go index 9263e5a..7e4e320 100644 --- a/exp/alphabet/letters.go +++ b/exp/alphabet/letters.go @@ -16,7 +16,7 @@ package alphabet // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "math" "unsafe" ) diff --git a/exp/seq/nucleic/alignment/alignment.go b/exp/seq/nucleic/alignment/alignment.go index 66eed04..93cdd1c 100644 --- a/exp/seq/nucleic/alignment/alignment.go +++ b/exp/seq/nucleic/alignment/alignment.go @@ -18,13 +18,13 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/util" ) // Alignment nucleic acid. diff --git a/exp/seq/nucleic/alignment/alignment_example_test.go b/exp/seq/nucleic/alignment/alignment_example_test.go index 64fc4b7..69bb5c6 100644 --- a/exp/seq/nucleic/alignment/alignment_example_test.go +++ b/exp/seq/nucleic/alignment/alignment_example_test.go @@ -17,10 +17,10 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/feat" ) var ( diff --git a/exp/seq/nucleic/alignment/qalignment.go b/exp/seq/nucleic/alignment/qalignment.go index f882107..2459d9f 100644 --- a/exp/seq/nucleic/alignment/qalignment.go +++ b/exp/seq/nucleic/alignment/qalignment.go @@ -17,13 +17,13 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/util" ) // Aligned nucleic acid with quality scores. diff --git a/exp/seq/nucleic/alignment/qalignment_example_test.go b/exp/seq/nucleic/alignment/qalignment_example_test.go index c996ec2..5e8b1fa 100644 --- a/exp/seq/nucleic/alignment/qalignment_example_test.go +++ b/exp/seq/nucleic/alignment/qalignment_example_test.go @@ -17,10 +17,10 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/feat" ) var ( diff --git a/exp/seq/nucleic/multi/multi.go b/exp/seq/nucleic/multi/multi.go index 8a5ab09..1eba7cf 100644 --- a/exp/seq/nucleic/multi/multi.go +++ b/exp/seq/nucleic/multi/multi.go @@ -18,14 +18,14 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/exp/seq/nucleic/packed" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/exp/seq/nucleic/packed" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" "reflect" "sync" ) diff --git a/exp/seq/nucleic/multi/multi_example_test.go b/exp/seq/nucleic/multi/multi_example_test.go index f982ce0..2ac8431 100644 --- a/exp/seq/nucleic/multi/multi_example_test.go +++ b/exp/seq/nucleic/multi/multi_example_test.go @@ -17,10 +17,10 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/feat" "strings" ) diff --git a/exp/seq/nucleic/multi/set.go b/exp/seq/nucleic/multi/set.go index b4287fd..57cec49 100644 --- a/exp/seq/nucleic/multi/set.go +++ b/exp/seq/nucleic/multi/set.go @@ -17,11 +17,11 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/util" ) type Set []nucleic.Sequence diff --git a/exp/seq/nucleic/multi/set_example_test.go b/exp/seq/nucleic/multi/set_example_test.go index 826100e..50afd66 100644 --- a/exp/seq/nucleic/multi/set_example_test.go +++ b/exp/seq/nucleic/multi/set_example_test.go @@ -17,8 +17,8 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq/nucleic" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq/nucleic" ) var set Set diff --git a/exp/seq/nucleic/nucleic.go b/exp/seq/nucleic/nucleic.go index d101e6f..70d5bcf 100644 --- a/exp/seq/nucleic/nucleic.go +++ b/exp/seq/nucleic/nucleic.go @@ -21,8 +21,8 @@ package nucleic // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" "math" ) diff --git a/exp/seq/nucleic/nucleic_test.go b/exp/seq/nucleic/nucleic_test.go index d01b2d4..c86ec0e 100644 --- a/exp/seq/nucleic/nucleic_test.go +++ b/exp/seq/nucleic/nucleic_test.go @@ -16,7 +16,7 @@ package nucleic // along with this program. If not, see . import ( - //"github.com/kortschak/BioGo/feat" + //"github.com/kortschak/biogo/feat" check "launchpad.net/gocheck" //"reflect" "testing" diff --git a/exp/seq/nucleic/packed/packed.go b/exp/seq/nucleic/packed/packed.go index c4aab4f..56584b7 100644 --- a/exp/seq/nucleic/packed/packed.go +++ b/exp/seq/nucleic/packed/packed.go @@ -21,14 +21,14 @@ package packed import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" ) var emptyString = "" diff --git a/exp/seq/nucleic/packed/packed_example_test.go b/exp/seq/nucleic/packed/packed_example_test.go index 27b1a1d..806d53e 100644 --- a/exp/seq/nucleic/packed/packed_example_test.go +++ b/exp/seq/nucleic/packed/packed_example_test.go @@ -17,10 +17,10 @@ package packed import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/feat" ) func ExampleNewSeq_1() { diff --git a/exp/seq/nucleic/packed/qpacked.go b/exp/seq/nucleic/packed/qpacked.go index 36c804e..889921c 100644 --- a/exp/seq/nucleic/packed/qpacked.go +++ b/exp/seq/nucleic/packed/qpacked.go @@ -17,13 +17,13 @@ package packed import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/nucleic" - "github.com/kortschak/BioGo/exp/seq/quality" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/nucleic" + "github.com/kortschak/biogo/exp/seq/quality" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) // QSeq is a packed nucleic acid with Phred quality scores allowing one byte per quality base. diff --git a/exp/seq/nucleic/packed/qpacked_example_test.go b/exp/seq/nucleic/packed/qpacked_example_test.go index 3e7622e..c002b7d 100644 --- a/exp/seq/nucleic/packed/qpacked_example_test.go +++ b/exp/seq/nucleic/packed/qpacked_example_test.go @@ -17,8 +17,8 @@ package packed import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" _ "strings" ) diff --git a/exp/seq/nucleic/qseq.go b/exp/seq/nucleic/qseq.go index 3d2c76d..1df8af5 100644 --- a/exp/seq/nucleic/qseq.go +++ b/exp/seq/nucleic/qseq.go @@ -16,11 +16,11 @@ package nucleic // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) // QSeq is a basic nucleic acid sequence with Phred quality scores. diff --git a/exp/seq/nucleic/qseq_example_test.go b/exp/seq/nucleic/qseq_example_test.go index f4992fb..f851976 100644 --- a/exp/seq/nucleic/qseq_example_test.go +++ b/exp/seq/nucleic/qseq_example_test.go @@ -17,8 +17,8 @@ package nucleic import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" "strings" ) diff --git a/exp/seq/nucleic/seq.go b/exp/seq/nucleic/seq.go index d091181..0c653b0 100644 --- a/exp/seq/nucleic/seq.go +++ b/exp/seq/nucleic/seq.go @@ -16,11 +16,11 @@ package nucleic // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) // Seq is a basic nucleic acid sequence. diff --git a/exp/seq/nucleic/seq_example_test.go b/exp/seq/nucleic/seq_example_test.go index 83dc7e8..985e892 100644 --- a/exp/seq/nucleic/seq_example_test.go +++ b/exp/seq/nucleic/seq_example_test.go @@ -17,9 +17,9 @@ package nucleic import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/feat" "strings" ) diff --git a/exp/seq/protein/alignment/alignment.go b/exp/seq/protein/alignment/alignment.go index 628ec91..0498ec9 100644 --- a/exp/seq/protein/alignment/alignment.go +++ b/exp/seq/protein/alignment/alignment.go @@ -18,13 +18,13 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/util" ) // Alignment protein sequence. diff --git a/exp/seq/protein/alignment/alignment_example_test.go b/exp/seq/protein/alignment/alignment_example_test.go index 6592d33..c770473 100644 --- a/exp/seq/protein/alignment/alignment_example_test.go +++ b/exp/seq/protein/alignment/alignment_example_test.go @@ -17,10 +17,10 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/feat" ) var ( diff --git a/exp/seq/protein/alignment/qalignment.go b/exp/seq/protein/alignment/qalignment.go index 28a8d41..cbe6973 100644 --- a/exp/seq/protein/alignment/qalignment.go +++ b/exp/seq/protein/alignment/qalignment.go @@ -17,13 +17,13 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/util" ) // Aligned protein with quality scores. diff --git a/exp/seq/protein/alignment/qalignment_example_test.go b/exp/seq/protein/alignment/qalignment_example_test.go index adaae7e..1affa77 100644 --- a/exp/seq/protein/alignment/qalignment_example_test.go +++ b/exp/seq/protein/alignment/qalignment_example_test.go @@ -17,10 +17,10 @@ package alignment import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/feat" ) var ( diff --git a/exp/seq/protein/multi/multi.go b/exp/seq/protein/multi/multi.go index ce58c26..8c5fa8c 100644 --- a/exp/seq/protein/multi/multi.go +++ b/exp/seq/protein/multi/multi.go @@ -18,13 +18,13 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" "reflect" "sync" ) diff --git a/exp/seq/protein/multi/multi_example_test.go b/exp/seq/protein/multi/multi_example_test.go index deb407b..cab9050 100644 --- a/exp/seq/protein/multi/multi_example_test.go +++ b/exp/seq/protein/multi/multi_example_test.go @@ -17,10 +17,10 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/feat" "strings" ) diff --git a/exp/seq/protein/multi/set.go b/exp/seq/protein/multi/set.go index 8699d12..ff898f7 100644 --- a/exp/seq/protein/multi/set.go +++ b/exp/seq/protein/multi/set.go @@ -17,11 +17,11 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/protein" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/protein" + "github.com/kortschak/biogo/util" ) type Set []protein.Sequence diff --git a/exp/seq/protein/multi/set_example_test.go b/exp/seq/protein/multi/set_example_test.go index 7b6139a..59b902c 100644 --- a/exp/seq/protein/multi/set_example_test.go +++ b/exp/seq/protein/multi/set_example_test.go @@ -17,8 +17,8 @@ package multi import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq/protein" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq/protein" ) var set Set diff --git a/exp/seq/protein/protein.go b/exp/seq/protein/protein.go index 3b61021..fe91200 100644 --- a/exp/seq/protein/protein.go +++ b/exp/seq/protein/protein.go @@ -21,8 +21,8 @@ package protein // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" "math" ) diff --git a/exp/seq/protein/protein_test.go b/exp/seq/protein/protein_test.go index 59ca5ab..11a3817 100644 --- a/exp/seq/protein/protein_test.go +++ b/exp/seq/protein/protein_test.go @@ -16,7 +16,7 @@ package protein // along with this program. If not, see . import ( - //"github.com/kortschak/BioGo/feat" + //"github.com/kortschak/biogo/feat" check "launchpad.net/gocheck" //"reflect" "testing" diff --git a/exp/seq/protein/qseq.go b/exp/seq/protein/qseq.go index 6d7ce87..6c6011d 100644 --- a/exp/seq/protein/qseq.go +++ b/exp/seq/protein/qseq.go @@ -16,11 +16,11 @@ package protein // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) // QSeq is a basic protein sequence with Phred quality scores. diff --git a/exp/seq/protein/qseq_example_test.go b/exp/seq/protein/qseq_example_test.go index 093de7e..1f410bc 100644 --- a/exp/seq/protein/qseq_example_test.go +++ b/exp/seq/protein/qseq_example_test.go @@ -17,8 +17,8 @@ package protein import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" "strings" ) diff --git a/exp/seq/protein/seq.go b/exp/seq/protein/seq.go index 55790b4..320eeae 100644 --- a/exp/seq/protein/seq.go +++ b/exp/seq/protein/seq.go @@ -16,11 +16,11 @@ package protein // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) // Seq is a basic protein sequence. diff --git a/exp/seq/protein/seq_example_test.go b/exp/seq/protein/seq_example_test.go index 9721351..e58be2c 100644 --- a/exp/seq/protein/seq_example_test.go +++ b/exp/seq/protein/seq_example_test.go @@ -17,9 +17,9 @@ package protein import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/feat" "strings" ) diff --git a/exp/seq/quality/illumina/illumina.go b/exp/seq/quality/illumina/illumina.go index d285241..5fd2f3a 100644 --- a/exp/seq/quality/illumina/illumina.go +++ b/exp/seq/quality/illumina/illumina.go @@ -17,9 +17,9 @@ package illumina // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/quality" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/quality" ) type Illumina1_3 struct { diff --git a/exp/seq/quality/phred.go b/exp/seq/quality/phred.go index feb074f..a986256 100644 --- a/exp/seq/quality/phred.go +++ b/exp/seq/quality/phred.go @@ -17,11 +17,11 @@ package quality // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) type Appender interface { diff --git a/exp/seq/quality/sanger/sanger.go b/exp/seq/quality/sanger/sanger.go index cc94f50..33ebe71 100644 --- a/exp/seq/quality/sanger/sanger.go +++ b/exp/seq/quality/sanger/sanger.go @@ -17,9 +17,9 @@ package sanger // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/quality" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/quality" ) type Sanger struct { diff --git a/exp/seq/quality/solexa/solexa.go b/exp/seq/quality/solexa/solexa.go index 0df827f..d61ee64 100644 --- a/exp/seq/quality/solexa/solexa.go +++ b/exp/seq/quality/solexa/solexa.go @@ -19,11 +19,11 @@ package quality // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/exp/seq/sequtils" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/exp/seq/sequtils" + "github.com/kortschak/biogo/feat" ) type Appender interface { diff --git a/exp/seq/seq.go b/exp/seq/seq.go index c3f4f58..a7756a2 100644 --- a/exp/seq/seq.go +++ b/exp/seq/seq.go @@ -25,8 +25,8 @@ package seq // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/feat" ) const ( diff --git a/exp/seq/sequtils/example_test.go b/exp/seq/sequtils/example_test.go index d732765..0c70a32 100644 --- a/exp/seq/sequtils/example_test.go +++ b/exp/seq/sequtils/example_test.go @@ -17,9 +17,9 @@ package sequtils import ( "fmt" - "github.com/kortschak/BioGo/exp/alphabet" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/alphabet" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/feat" ) func ExampleTruncate_1() { diff --git a/exp/seq/sequtils/utils.go b/exp/seq/sequtils/utils.go index a5c9e42..2bee88f 100644 --- a/exp/seq/sequtils/utils.go +++ b/exp/seq/sequtils/utils.go @@ -17,11 +17,11 @@ package sequtils // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" "reflect" ) diff --git a/exp/seq/sequtils/utils_test.go b/exp/seq/sequtils/utils_test.go index 04a6a2d..3b7348e 100644 --- a/exp/seq/sequtils/utils_test.go +++ b/exp/seq/sequtils/utils_test.go @@ -16,8 +16,8 @@ package sequtils // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/exp/seq" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/exp/seq" + "github.com/kortschak/biogo/feat" check "launchpad.net/gocheck" "reflect" "testing" diff --git a/feat/feat.go b/feat/feat.go index ca520d6..504f631 100644 --- a/feat/feat.go +++ b/feat/feat.go @@ -17,7 +17,7 @@ package feat // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "strconv" ) diff --git a/graphics/kmercolor/kmercolor.go b/graphics/kmercolor/kmercolor.go index 54e63e0..3ecc8b8 100644 --- a/graphics/kmercolor/kmercolor.go +++ b/graphics/kmercolor/kmercolor.go @@ -17,9 +17,9 @@ package kmercolor // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/graphics/color" - "github.com/kortschak/BioGo/index/kmerindex" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/graphics/color" + "github.com/kortschak/biogo/index/kmerindex" + "github.com/kortschak/biogo/util" "image" imagecolor "image/color" ) diff --git a/index/kmerindex/kmerindex.go b/index/kmerindex/kmerindex.go index 6540e41..8b55b34 100644 --- a/index/kmerindex/kmerindex.go +++ b/index/kmerindex/kmerindex.go @@ -20,9 +20,9 @@ package kmerindex import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" "math" ) diff --git a/index/kmerindex/kmerindex_test.go b/index/kmerindex/kmerindex_test.go index 0b6a8bf..9522b05 100644 --- a/index/kmerindex/kmerindex_test.go +++ b/index/kmerindex/kmerindex_test.go @@ -16,8 +16,8 @@ package kmerindex // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" check "launchpad.net/gocheck" "math/rand" "testing" diff --git a/interval/interval.go b/interval/interval.go index b1331ed..43da7e8 100644 --- a/interval/interval.go +++ b/interval/interval.go @@ -19,8 +19,8 @@ package interval import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/util" "math" "math/rand" ) diff --git a/interval/serialise.go b/interval/serialise.go index 83b4f6a..65b0485 100644 --- a/interval/serialise.go +++ b/interval/serialise.go @@ -19,7 +19,7 @@ package interval import ( "bytes" "encoding/gob" - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" ) const Version int = 1 diff --git a/io/alignio/alignio.go b/io/alignio/alignio.go index 605db1f..9a0d8f7 100644 --- a/io/alignio/alignio.go +++ b/io/alignio/alignio.go @@ -17,8 +17,8 @@ package alignio // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/io/seqio" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/io/seqio" + "github.com/kortschak/biogo/seq" "io" ) diff --git a/io/alignio/alignio_test.go b/io/alignio/alignio_test.go index ff2c0e4..7758244 100644 --- a/io/alignio/alignio_test.go +++ b/io/alignio/alignio_test.go @@ -16,8 +16,8 @@ package alignio // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/io/seqio/fastq" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/io/seqio/fastq" check "launchpad.net/gocheck" "testing" ) diff --git a/io/featio/bed/bed.go b/io/featio/bed/bed.go index d3577e4..83a56e4 100644 --- a/io/featio/bed/bed.go +++ b/io/featio/bed/bed.go @@ -19,8 +19,8 @@ package bed import ( "bufio" "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" "io" "os" "strconv" diff --git a/io/featio/bed/bed_test.go b/io/featio/bed/bed_test.go index e6dc884..c06cdf7 100644 --- a/io/featio/bed/bed_test.go +++ b/io/featio/bed/bed_test.go @@ -16,8 +16,8 @@ package bed // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" "io" "io/ioutil" check "launchpad.net/gocheck" diff --git a/io/featio/featio.go b/io/featio/featio.go index 88eb05c..e6e2374 100644 --- a/io/featio/featio.go +++ b/io/featio/featio.go @@ -16,7 +16,7 @@ package featio // You should have received a copy of the GNU General Public License // along with this program. If not, see . -import "github.com/kortschak/BioGo/feat" +import "github.com/kortschak/biogo/feat" type Reader interface { Read() (*feat.Feature, error) diff --git a/io/featio/gff/gff.go b/io/featio/gff/gff.go index db237f7..e47d37c 100644 --- a/io/featio/gff/gff.go +++ b/io/featio/gff/gff.go @@ -20,10 +20,10 @@ import ( "bufio" "bytes" "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/io/seqio/fasta" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/io/seqio/fasta" + "github.com/kortschak/biogo/seq" "io" "math" "os" diff --git a/io/featio/gff/gff_test.go b/io/featio/gff/gff_test.go index 6200c0f..351eea1 100644 --- a/io/featio/gff/gff_test.go +++ b/io/featio/gff/gff_test.go @@ -17,9 +17,9 @@ package gff import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/seq" "io" "io/ioutil" check "launchpad.net/gocheck" diff --git a/io/lexbytes/fastareader/fastareader.go b/io/lexbytes/fastareader/fastareader.go index 37a9032..aed2d6e 100644 --- a/io/lexbytes/fastareader/fastareader.go +++ b/io/lexbytes/fastareader/fastareader.go @@ -19,9 +19,9 @@ package fastareader import ( "bufio" "fmt" - "github.com/kortschak/BioGo/bio" - lex "github.com/kortschak/BioGo/io/lexbytes" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/bio" + lex "github.com/kortschak/biogo/io/lexbytes" + "github.com/kortschak/biogo/seq" "io" "os" ) diff --git a/io/seqio/fasta/fasta.go b/io/seqio/fasta/fasta.go index 94dc6a9..0dff6ee 100644 --- a/io/seqio/fasta/fasta.go +++ b/io/seqio/fasta/fasta.go @@ -19,9 +19,9 @@ package fasta import ( "bufio" "bytes" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" "io" "os" ) diff --git a/io/seqio/fasta/fasta_test.go b/io/seqio/fasta/fasta_test.go index 13cc454..b5910dd 100644 --- a/io/seqio/fasta/fasta_test.go +++ b/io/seqio/fasta/fasta_test.go @@ -16,7 +16,7 @@ package fasta // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/seq" "io" "io/ioutil" check "launchpad.net/gocheck" diff --git a/io/seqio/fastq/fastq.go b/io/seqio/fastq/fastq.go index 19ebe3c..273b2d6 100644 --- a/io/seqio/fastq/fastq.go +++ b/io/seqio/fastq/fastq.go @@ -19,8 +19,8 @@ package fastq import ( "bufio" "bytes" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/seq" "io" "os" ) diff --git a/io/seqio/fastq/fastq_test.go b/io/seqio/fastq/fastq_test.go index f1358d3..acd95a7 100644 --- a/io/seqio/fastq/fastq_test.go +++ b/io/seqio/fastq/fastq_test.go @@ -16,7 +16,7 @@ package fastq // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/seq" + "github.com/kortschak/biogo/seq" "io" "io/ioutil" check "launchpad.net/gocheck" diff --git a/io/seqio/seqio.go b/io/seqio/seqio.go index 407444f..8de0479 100644 --- a/io/seqio/seqio.go +++ b/io/seqio/seqio.go @@ -16,7 +16,7 @@ package seqio // You should have received a copy of the GNU General Public License // along with this program. If not, see . -import "github.com/kortschak/BioGo/seq" +import "github.com/kortschak/biogo/seq" type Reader interface { Read() (*seq.Seq, error) diff --git a/matrix/sparse/sparse.go b/matrix/sparse/sparse.go index 0b70a32..ccddd2b 100644 --- a/matrix/sparse/sparse.go +++ b/matrix/sparse/sparse.go @@ -21,7 +21,7 @@ package sparse import ( "errors" "fmt" - "github.com/kortschak/BioGo/matrix" + "github.com/kortschak/biogo/matrix" "math" "math/rand" "runtime" diff --git a/nmf/nmf.go b/nmf/nmf.go index 5badc4a..71732a6 100644 --- a/nmf/nmf.go +++ b/nmf/nmf.go @@ -19,8 +19,8 @@ package nmf // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/matrix" - "github.com/kortschak/BioGo/matrix/sparse" + "github.com/kortschak/biogo/matrix" + "github.com/kortschak/biogo/matrix/sparse" "math" "time" ) diff --git a/pwm/pwm.go b/pwm/pwm.go index 5041c9c..5a99381 100644 --- a/pwm/pwm.go +++ b/pwm/pwm.go @@ -19,10 +19,10 @@ package pwm // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/seq" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/seq" + "github.com/kortschak/biogo/util" "math" "sort" "strconv" diff --git a/seq/alignment.go b/seq/alignment.go index 7f1d511..97b0b87 100644 --- a/seq/alignment.go +++ b/seq/alignment.go @@ -17,10 +17,10 @@ package seq import ( "bytes" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" "strings" ) diff --git a/seq/example_test.go b/seq/example_test.go index b8c9aa5..0653164 100644 --- a/seq/example_test.go +++ b/seq/example_test.go @@ -17,8 +17,8 @@ package seq import ( "fmt" - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" "strings" ) diff --git a/seq/qual.go b/seq/qual.go index af6b497..f8067cf 100644 --- a/seq/qual.go +++ b/seq/qual.go @@ -16,10 +16,10 @@ package seq // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" ) type Quality struct { diff --git a/seq/seq.go b/seq/seq.go index 22cc7b2..0db2c4a 100644 --- a/seq/seq.go +++ b/seq/seq.go @@ -17,10 +17,10 @@ package seq // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" - "github.com/kortschak/BioGo/feat" - "github.com/kortschak/BioGo/interval" - "github.com/kortschak/BioGo/util" + "github.com/kortschak/biogo/bio" + "github.com/kortschak/biogo/feat" + "github.com/kortschak/biogo/interval" + "github.com/kortschak/biogo/util" ) const ( diff --git a/util/calls_test.go b/util/calls_test.go index cde68d6..44b9764 100644 --- a/util/calls_test.go +++ b/util/calls_test.go @@ -21,25 +21,25 @@ import ( // Helpers func f1(c *check.C) { - c.Check(GetCaller(0).Package, check.Equals, "github.com/kortschak/BioGo/util") + c.Check(GetCaller(0).Package, check.Equals, "github.com/kortschak/biogo/util") c.Check(GetCaller(0).Function, check.Equals, "f1") - c.Check(GetCaller(1).Package, check.Equals, "github.com/kortschak/BioGo/util.(*S)") + c.Check(GetCaller(1).Package, check.Equals, "github.com/kortschak/biogo/util.(*S)") c.Check(GetCaller(1).Function, check.Equals, "TestCaller") f2(c) } func f2(c *check.C) { - c.Check(GetCaller(0).Package, check.Equals, "github.com/kortschak/BioGo/util") + c.Check(GetCaller(0).Package, check.Equals, "github.com/kortschak/biogo/util") c.Check(GetCaller(0).Function, check.Equals, "f2") - c.Check(GetCaller(1).Package, check.Equals, "github.com/kortschak/BioGo/util") + c.Check(GetCaller(1).Package, check.Equals, "github.com/kortschak/biogo/util") c.Check(GetCaller(1).Function, check.Equals, "f1") - c.Check(GetCaller(2).Package, check.Equals, "github.com/kortschak/BioGo/util.(*S)") + c.Check(GetCaller(2).Package, check.Equals, "github.com/kortschak/biogo/util.(*S)") c.Check(GetCaller(2).Function, check.Equals, "TestCaller") } // Tests func (s *S) TestCaller(c *check.C) { - c.Check(GetCaller(0).Package, check.Equals, "github.com/kortschak/BioGo/util.(*S)") + c.Check(GetCaller(0).Package, check.Equals, "github.com/kortschak/biogo/util.(*S)") c.Check(GetCaller(0).Function, check.Equals, "TestCaller") f1(c) } diff --git a/util/files.go b/util/files.go index 4afc731..20c2afd 100644 --- a/util/files.go +++ b/util/files.go @@ -16,7 +16,7 @@ package util // along with this program. If not, see . import ( - "github.com/kortschak/BioGo/bio" + "github.com/kortschak/biogo/bio" "hash" "io" "os" diff --git a/version.go b/version.go index f58a50f..9ed6c37 100644 --- a/version.go +++ b/version.go @@ -1,4 +1,4 @@ -package BioGo +package biogo // Copyright Ā©2011 Dan Kortschak //