<classpathentry kind="lib" path="lib/VARNAv3-93.jar"/>
<classpathentry kind="lib" path="lib/jfreesvg-2.1.jar"/>
<classpathentry kind="lib" path="lib/quaqua-filechooser-only-8.0.jar"/>
+ <classpathentry kind="lib" path="lib/htsjdk-1.133.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.USER_LIBRARY/plugin"/>
<classpathentry kind="lib" path="lib/xml-apis.jar"/>
<classpathentry kind="con" path="org.eclipse.jdt.junit.JUNIT_CONTAINER/4"/>
quaqua: v.8.0 (latest stable) by Randel S Hofer. LGPL and BSD Modified license: downloaded from http://www.randelshofer.ch/quaqua/
+lib/htsjdk-1.120-SNAPSHOT.jar: built from maven master at https://github.com/samtools/htsjdk MIT License to Broad Institute
+
+
Additional dependencies
examples/javascript/deployJava.js : http://java.com/js/deployJava.js
--- /dev/null
+package jalview.ext.htsjdk;
+
+import htsjdk.samtools.SAMSequenceDictionary;
+import htsjdk.samtools.SAMSequenceRecord;
+import htsjdk.samtools.reference.ReferenceSequence;
+import htsjdk.samtools.reference.ReferenceSequenceFile;
+import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
+import htsjdk.samtools.util.StringUtil;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+import java.math.BigInteger;
+import java.security.MessageDigest;
+import java.security.NoSuchAlgorithmException;
+import java.util.ArrayList;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Set;
+
+/**
+ * a source of sequence data accessed via the HTSJDK
+ *
+ * @author jprocter
+ *
+ */
+public class HtsContigDb
+{
+
+ private String name;
+
+ private File dbLocation;
+
+ private htsjdk.samtools.reference.ReferenceSequenceFile refFile = null;
+
+ public HtsContigDb(String name, File descriptor) throws Exception
+ {
+ if (descriptor.isFile())
+ {
+ this.name = name;
+ dbLocation = descriptor;
+ }
+ initSource();
+ }
+
+ private void initSource() throws Exception
+ {
+ if (refFile != null)
+ {
+ return;
+ }
+
+ refFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(
+ dbLocation, true);
+ if (refFile == null || refFile.getSequenceDictionary() == null)
+ {
+ // refFile = initSequenceDictionaryFor(dbLocation);
+ }
+
+ }
+
+
+ SAMSequenceDictionary rrefDict = null;
+ private ReferenceSequenceFile initSequenceDictionaryFor(File dbLocation2) throws Exception
+ {
+ rrefDict = getDictionary(dbLocation2, true);
+ if (rrefDict != null)
+ {
+ ReferenceSequenceFile rrefFile = ReferenceSequenceFileFactory.getReferenceSequenceFile(dbLocation2, true);
+ return rrefFile;
+ }
+ return null;
+ }
+ /**
+ * code below hacked out from picard ----
+ *
+ * picard/src/java/picard/sam/CreateSequenceDictionary.java
+ * https://github.com/
+ * broadinstitute/picard/commit/270580d3e28123496576f0b91b3433179bb5d876
+ */
+
+
+ /*
+ * The MIT License
+ *
+ * Copyright (c) 2009 The Broad Institute
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a
+ * copy of this software and associated documentation files (the "Software"),
+ * to deal in the Software without restriction, including without limitation
+ * the rights to use, copy, modify, merge, publish, distribute, sublicense,
+ * and/or sell copies of the Software, and to permit persons to whom the
+ * Software is furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
+ * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER
+ * DEALINGS IN THE SOFTWARE.
+ */
+ /**
+ *
+ * @param f
+ * @param truncate
+ * @return
+ * @throws Exception
+ */
+ SAMSequenceDictionary getDictionary(File f, boolean truncate)
+ throws Exception
+ {
+ if (md5 == null)
+ {
+ initCreateSequenceDictionary();
+ }
+ final ReferenceSequenceFile refSeqFile = ReferenceSequenceFileFactory
+ .getReferenceSequenceFile(f, truncate);
+ ReferenceSequence refSeq;
+ List<SAMSequenceRecord> ret = new ArrayList<SAMSequenceRecord>();
+ Set<String> sequenceNames = new HashSet<String>();
+ for (int numSequences = 0; (refSeq = refSeqFile.nextSequence()) != null; ++numSequences)
+ {
+ if (sequenceNames.contains(refSeq.getName()))
+ {
+ throw new Exception(
+ "Sequence name appears more than once in reference: "
+ + refSeq.getName());
+ }
+ sequenceNames.add(refSeq.getName());
+ ret.add(makeSequenceRecord(refSeq));
+ }
+ return new SAMSequenceDictionary(ret);
+ }
+
+ public boolean isValid()
+ {
+ return dbLocation != null && refFile != null;
+ }
+
+ /**
+ * Create one SAMSequenceRecord from a single fasta sequence
+ */
+ private SAMSequenceRecord makeSequenceRecord(
+ final ReferenceSequence refSeq)
+ {
+
+ final SAMSequenceRecord ret = new SAMSequenceRecord(refSeq.getName(),
+ refSeq.length());
+
+ // Compute MD5 of upcased bases
+ final byte[] bases = refSeq.getBases();
+ for (int i = 0; i < bases.length; ++i)
+ {
+ bases[i] = StringUtil.toUpperCase(bases[i]);
+ }
+
+ ret.setAttribute(SAMSequenceRecord.MD5_TAG, md5Hash(bases));
+ // if (GENOME_ASSEMBLY != null) {
+ // ret.setAttribute(SAMSequenceRecord.ASSEMBLY_TAG, GENOME_ASSEMBLY);
+ // }
+ // ret.setAttribute(SAMSequenceRecord.URI_TAG, URI);
+ // if (SPECIES != null) {
+ // ret.setAttribute(SAMSequenceRecord.SPECIES_TAG, SPECIES);
+ // }
+ return ret;
+ }
+
+ private MessageDigest md5;
+
+ public void initCreateSequenceDictionary() throws Exception
+ {
+ try
+ {
+ md5 = MessageDigest.getInstance("MD5");
+ } catch (NoSuchAlgorithmException e)
+ {
+ throw new Exception("MD5 algorithm not found", e);
+ }
+ }
+
+ private String md5Hash(final byte[] bytes)
+ {
+ md5.reset();
+ md5.update(bytes);
+ String s = new BigInteger(1, md5.digest()).toString(16);
+ if (s.length() != 32)
+ {
+ final String zeros = "00000000000000000000000000000000";
+ s = zeros.substring(0, 32 - s.length()) + s;
+ }
+ return s;
+ }
+
+ // ///// end of hts bits.
+
+ SequenceI getSequenceProxy(String id)
+ {
+ if (!isValid())
+ {
+ return null;
+ }
+
+ ReferenceSequence sseq = refFile.getSequence(id);
+ return new Sequence(sseq.getName(), new String(sseq.getBases()));
+ }
+}
@Override
public void addAnnotations(AlignmentI al)
{
- // TODO Auto-generated method stub
super.addAnnotations(al);
}
@Override
public void addProperties(AlignmentI al)
{
- // TODO Auto-generated method stub
super.addProperties(al);
}
@Override
public void addSeqGroups(AlignmentI al)
{
- // TODO Auto-generated method stub
super.addSeqGroups(al);
}
import org.testng.annotations.Test;
+@Test
public class SequenceDummyTest
{
/**
--- /dev/null
+/**
+ *
+ */
+package jalview.ext.htsjdk;
+
+import jalview.datamodel.SequenceI;
+
+import java.io.File;
+
+import org.testng.Assert;
+import org.testng.annotations.Test;
+
+/**
+ * @author jprocter
+ *
+ */
+public class TestHtsContigDb
+{
+ @Test
+ public final void testHTSReferenceSequence() throws Exception
+ {
+ HtsContigDb remmadb = new HtsContigDb("REEMADB", new File(
+ "test/jalview/ext/htsjdk/pgmb.fasta"));
+
+ Assert.assertTrue(remmadb.isValid());
+
+ SequenceI sq = remmadb.getSequenceProxy("Deminut");
+ Assert.assertNotNull(sq);
+ Assert.assertNotEquals(0, sq.getLength());
+ }
+
+}
--- /dev/null
+>DDB_G0280897
+MTDKINNLINQWLKWDKNEITRKEIEQLKENNNEKELLVRLEERIQFGTAGLRGAMRAGF
+SCMNDLTVTQASQGLCEYVIETIEQSKSKGIVIGYDGRHNSYIFAKITAATFKSKGFKVY
+LFSHIVPTPYVSFAVPNLKAAIGVMITASHNPKNDNGYKVYWETGCQINTPHDKGISKKI
+DENLEPWSNVDATSDIKYGNGDDGESMIDPLSVITELYNKNIKEYSVGSKIELANEPIVY
+TAMHGVGGVYAKKAFETFQLKPFIPVAQQIEPDAEFPTVTYPNPEEGKGALKLSIETAEA
+NNSRLILANDPDADRLAVAEKLADGSWKVFNGNEIGVLLADWAWTNRSTLTKGGSTLENN
+KYFMINTAVSSAMLKTMSEKEGFIHQECLTGFKWIGNAAYNAINNNDGTTFLFGYEEAIG
+FQYGDVSFDKDGVRAAAIFAEFALSLYKKGSSVQDHLESMYKRYGYHISKNRYFFCYEPS
+KMVSIFNKIRNDGKYLTKLGDDDDEQFTITRIRDLTTGYDNGYPDCKARLPVSSSTQMIT
+FYFKNGGIATLRGSGTEPKLKYYVEMIGEVKSNVESTLTKAVELVINQLLKPIENQLEPP
+KDD
+>PPL_06716
+MSNIKELAESWLKWDKNAETRKEIQSLLESDNQSELKSRLEQRIAFGTAGLRGPMKAGFS
+CMNDLTVIQASQGLCIYVEQTLSNSKNSGIVVGYDGRHHSKEFARLTAATFASRGFKVYL
+FSKIVPTPYVVILYLISNYMDCYVHQAFAVPELKASVGVMITASHNPKDDNGYKVYWDNG
+CQINTPHDIRIAMQIDLNLEPWNIDVNELLNGSLVSDPLDTITKSYFGKIAKYSVKNEVK
+LATSEKIVYTAMHGVGGEYAKMAFETFGLPAFIPVDQQIQPDPEFPTVAFPNPEEGKGAL
+KLSIETAERNNSRLILANDPDADRLAVAERQPDGQWKVFNGNEIGVLFADWAWQNARRAD
+STTPAERFCMINTAVSSSMLKTMANKDGYRHEECLTGFKWVGNKARELMDKGYNFLFAYE
+EAIGFMYGDVSLDKDGVRCAPIFAELALTCYQAGKSCQDHLEELYKRYGYHISKNRYFFC
+YDPKKMVAIFDKIRNYGQFPTNCGDFYITRVRDLTVGYDSGYPDHKARLPVSSSTQMITF
+YFENGGIATLRGSGTEPKLKYYVEMIGSDRQLVESTLSQLVEQVINQFLRPVENELTPPK
+DD
+>DFA_03821
+MTDINQLAQNWLKWDRNPKTHKEIEQLVEAKDENELRARLENRIAFGTAGIVSTTIVQSH
+MNIGPMKAGFANMNDLTVIQASQGLSIYVQETISQAQSKGVVVGYDGRYNSEVFAKLTAA
+TFASKGFKVYLFSKIVPTPFVAFAVPELGASVGVMVTASHNPKDDNGYKVYWDNGCQINT
+PHDKGIAKQIDLNLEPWTINIDKLLSSELVNDPLETISNAYFSKIYSYSVKNRSTPLELA
+NEKVVYTAMHGVGGDYVKKAFETFKLPPYVEVAQQIKPDPAFPTVAFPNPEEGKGALKLS
+IETAESVNSRLILANDPDADRLAVAEKLKDGSWKVFNGNEIGILLADWAWTNAKINHPDV
+PAEKFFMINTAVSSAMLKTMAKKEGYICEETLTGFKWVGNKAKEMIDQGYKFLFAYEEAI
+GFMYGDVSLDKDGVRCAPIFAEYALNLYANGSSCQDHLDHLMQRYGYHISKNRYFFCYEP
+SKMVRIFNDIRKSNNGQFPDKCGPYEIIRIRDLTVDYDTAYPDNKARLPVSTSTQMITFY
+FKNGAIATLRGSGTEPKLKYYVEMIGDNKQEVESTLQQVVQQVIDNFLQPVVNQLTPPKD
+D
+>DLA_10096
+MDIYTLANKWLEWDKNEKNRKEIQHFVDEKNEQELRERLENRIQFGTAGLRGPMKAGFAN
+MNDLTVIQASQGLALYVKETIDSALTKGVVVGYDGRHNSQTFARLTAATFLSKGFKVYLF
+SKLVPTPFVAFAVPELGASCGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGISKLIDE
+NLVPWTMNLDDLNKSDLVSDPLERVSKSYFTKISKYSVVKSGATIKQEKVVYTPMHGVGG
+DYAAEAFKVFDLHPFIPVELQIKPDAEFPTVAFPNPEEGKGALKLAIETAESNQSRLILA
+NDPDADRLAVAEKQSSDGSWKVFNGNEIGVLFADWAWRKERALFSEGYNCKPSEYTMIST
+AVSSAMLSTMAKKEGFQHEEVLTGFKWVGNAAKQAMDRGQKFLFAYEEAIGFMYGDVSLD
+KDGVRGASIFAELAFDLYQQGSSCQEHLESLYKKYGYHISNNRYFFCYDPKKMVRIFNEI
+RGNNREYVKELGEFKVERIRDLTTGYDTAFPPEFKAQLPTSSSTQMITFYFTNGSIATLR
+GSGTEPKLKYYVESIGSDKLQVQQTLTKLVSLVIEKLLRPKENELTPPKESVGSERLLAL
+LSEVMSTSMKIQVKYNESITEYNIIKGVKLLTQIDVLCQIFKVDANPDRFVLNYRESNLI
+LSEDNLSKLFSNEISSCSSQSQNGSNGELSSLYSSFGENSSNNNNNSTLKFELILAPIYQ
+VDSVLEHLNNSNLIKKRII
+>DPU1265769
+MSMIRSISGVRGVIGQSWTPTLVSNHIIGFTQLLESEKYYNQKQKKIVVGRDSRVSGPWI
+EMIVNGSLISMGYQVIHIDIAATPTVQYMVEKTKSSGGIVITSSHNPVEWNGLKFVGPDG
+LFIAPVECEVLFSLADNPSSFKFPNYDKLGSVVCNTTANKEHIEAIFKLPFISVDKIKEK
+KFKVCLDSVNGAGGPIMSYLLTELGCEVIGINLEPTGLFAHTPEPVPANLGQLCELVKTH
+KADFGIAVDPDVDRCVFIDDKGVPLGEEYTLAMAVELLLGDCGRRGNVCKNLSSSRAIDD
+ICKKYDSQVICAPVGEIQVAKKMQQVNAVIGGEGNGGVMLPDIHIGRDAPVAATLALQLL
+ANRNAASISEFKRTTLPTYEIVKLKAGIEGLDPDAILAEYTKQYENKEGVVINQEDGLKI
+DSADWWVHLRKSNTEHIIRVISEAKNTKEATDIATKFINEIESKRK
+>440792448
+MASRVSGRMRKISDETQQMVNAWLSVDWDPESREHVKGLVAAGKEEELVAHLGRRISFGT
+AGLRGKMKWGFAFMNAVTVTQASQGLCAYLRTVHPCLTDLRERGVIVGHDGRYNSRMFAR
+LTAAVFLSRKIKVHLFRDDVPTPLVAFGVRHLKCAAGVMVTASHNPKEDNGYKVYWANSA
+QITAPHDAQIARAIEANFSIWDRMPDDKAIDEHPLCLDPTTDVCAAYLAAARHWSFRTPQ
+QNAAAQLRVVYTAMHGVGGQSVERIFDAFGLPPVIAVREQHDPDPDFTTVEFPNPEEANG
+CSLRLAMSTADREGAPLILANDPDADRLAVAERQRDSGEWRILDGNEIALLLADWLWRNY
+TERHPEVDRAKIVMLNSTVSSKALAAMAAKEGFHYRETLTGFKWLGNLADELVRAGYTFL
+FAYEVEIGFMIGDMSLDTDGVRAAPVFVEMANHLYERGLTLSDHLDNLYHKYGYYKMAVG
+YYFCHDPRLMDQIFNEIRNDGLYISTCGDHKVQYVRDLTTGFDNSQPHNRAVLPVSSAAH
+MITFTFENECVATFRGSGTEPKLKYYIEVANASNEQLATDLLDSMKQEIIDRFLQPSQNG
+LRPPAAAEDAHNSPHNSGNSPEQMAPARIARDVIHKEIQALQNLEATLGRDFEKVVEIIE
+SRGSGRVIFTGVGKSGIIAQKISASFSSLGISSFFVHATEAAHGDLGVITAEDVIIAISN
+SGNTPELIFIIPSLRVLAGKIIGITSNKDSLLARYSDASIITGKIMEADQHKIAPTASTI
+VCLAIGDALAVTLSARMKFTLPEFGLRHPGGVLGEKVLGKVFQEFAMKGQGRFLRFWKRM
+TNEERDKLRRDFERIDLAELSRIYLQCRSKAEKGAIDPHSLEPLPSHTWVKLHESDPAAV
+AAWRDAGLRALREGKIGVVLMAGGQATRLGMTMPKGFLDLNLPSHKSLYQLHAEKLLRLQ
+DEVRQTFGGGGGDEEVQQQQQQIQIPFYVMTSPEALQQTHQFFIKHQFFGLCPKQVFFFK
+QRSLPCVAPSGEIIMDTKCSVVFSPDGHGGLFVALKDAKAYEDMKRRGVEYVFAFGVDNP
+LCEVADPAYMGYCIQRNVKMGYKVVDRRDPQETAGVVCVRDGVINCVEYSELPESVAELR
+DEQSGELVYNAANMLNLFFTLRFMRKIADNPSLMEYHLAKKRIPFVNDNGVRTEPLVPNG
+WKFEKYLVDCTPYANNSVAVMFVKREEEFAPIKNGWNSEVDSPRSARRLLAAHYRRRIER
+AGGKLAADDPDKMVEVSPLVTDRKLAQLLQDKHLVTGPAVLQ
+>ENY64621.1
+MALNNYIKKTEMDYLYEQAALWLKWDKTPETRKEIEDLVASKNEEELKKRFCKRIEFGTA
+GLRGKMCAGFNCMNNLIVQQASQGLALAVEELVQNAHEKGVVIGYDGRYHSKEFAAITAK
+VFISKGFKTYLFSTLCPTPWTAFAVGYLKTACGVMVTASHNPKADNGYKVYWENGCQIIE
+PIDANIASKIHSNLEPWDLSNVDISKVIDPLADVSAEYYKQMMLTIPHFECPEQPKVKYV
+YTAMHGVGSKYVQDAFKTAKLPQPILVPLQNEPDPEFPTVPFPNPEEGKGALKCSIEVAE
+ANGATVIIANDPDADRLSVAVKSGNGWRQFTGNEMANLIADWTYNKYIVSGDKTPAFMVR
+STVSSSFISKMGEVEGFDTYETLTGFKWIGNKAKEIVDTQHKKLLMAYEEAIGFVIGNMS
+YDKDGVRAAVCFAAMALEYAEQGFNLEDRLNMLYEKYGYFASNNKYYFCYDPKLMEKIFN
+KMRNNGQYYWKFGKYAVKSIRDLTVGIDTAQPDKKPLLPVSASTQMITYTFENGCKATLR
+GSGTEPKLKYYIELPGKKGVKAEDVIAELMDLSHELLQASLEPEKNGLIPPKAE
+>Ppo014092.000
+MSISPSVQELVGKWLQWDKNPQNIKEIKDLVAANNEAELKNRLATRIAFGTAGLRGPMRA
+GFSCMNDLTVIQASQGLCKYLQQMVSDIKTRGIVVGYDGRHHSKEFAEWTAATFLSQGIT
+VYLFTRLVPTPFVSYATPLLRCAAGIMITASHNPKDDNGYKVYWDNGCQINVPHDKGISD
+CIEQNLTPWDINKAELLKSELVKDPTETVASAYLKEIKAKCCFHHDENSQKIPVTYTAMH
+GVGSEWVARAFEVFGLAPYVPVAPQISADPEFPTVAFPNPEEGKGALKLSMEAADKAGST
+LILATDPDADRLAVAEKLPSGSWKIFTGNEIGALLAYWAWLKYKERNPKVDPSKCVVINS
+TVSSKLLKALADKEGLKYDETLTGFKWIGGQAAIRIKEGYTFIFGFEEAIGFLFGDVNLD
+KDGVRAAAVFAEMNIQLHKQGITVVQQLEKIYKLYGYFITRNRYFFCYDPAKMERIFNAI
+RNYNNSGTYPTSCGPFKIKNTRDLTTGYDDSQTDKKAILPVSKSTQMITFFFENGGVVTL
+RGSGTEPKLKYYTELSGSDPEKVKSTLDEMVQAIIDTCLKPVENQLQPPSDE
+>ADB0001102_3
+MSTTTSINKLAQDWLKWDKNPKTRAEIQELVEQNDVKELTARLENRIAFGTAGLRGPMKA
+GFSCMNDLTVIQASQGLCLYVIDTIPNAIKSGVVIGYDGRYNSKEFAKYTAATFLSKGYK
+VYLFSKVVPTPYVAFAVTDLKASIGVMITASHNPKDDNGYKVYWENGCQINTPHDKGIAK
+LIDLNLEPWEINVDQLLSGPLVEDPLDRIVSSYNTKIAQYSVASHVKFANEKIIYTAMHG
+VGGEYTKMAFEAFKLPPFIPVAQQYQPDPAFPTVTFPNPEEGKGALKLSIETAEANGSRL
+ILANDPDADRLAVAERLKDGTWKVFNGNEIGVLLADWAWQNARRSHPDTPAEKFFMINTA
+VSSAMLKTMAKKDGYRCEETLTGFKWVGNRAREVMDAEGLHFLFAYEEAIGFLYGDVSLD
+KDGVRCAAIFAELALSYYANGSSCEDHLESLYKRYGYHISRNRYFFCYEPPKMVAIFNKI
+RNNRNFPTKCGRFEIERVRDLTIDYDDGFPDKKARLPVSTSTQMITFYFKNGAIATLRGS
+GTEPKLKYYVEMIGQDKAHVQQELAELVQCIINEFLRPVENELTPPKDD
+>Carpum
+MTQSTCITSMVINNYLSIYIFIYTINDYLKRSLFVLCLVAKMSHHKVAITHPISSYNSII
+NELAQNWLRWDKNKETRKEIEQLVEQKNEKELYDCLAKRIAFGTADNEIMMLLTHTLHTG
+LRGQMKAGFSNMNDLTVIQASQGLCKYVKETIPEAQKKGVVVGYDCRHHSETFARLTAAT
+FASQGFTVYLYSKMVPTPFVAFGVTDLKACVGVMVTASHNPKEDNGYKVYWENGCQINSP
+HDKGISQQIELNLEPWTIDVNSLLEKVDDPLERVTKSYMDQISKYSVRGSVDMATENVVY
+TAMHGVGGVFVKDAFAAFGLAPYIPVPAQVGPDAEFPTVTLPNPEEGKGALKLSIETAEA
+NNSRLIVANDPDADRLAAAEKLKDGSWKVFNGNEIGVLFADWAWQNARRQHGGDSINPSE
+YFMVTTAVSSSMLRTMATKEGYGYDETLTGFKWVGNKARDLIDQGKKFLFAYEESIGYMY
+GEVSLDKDGVRGAAVFTEMALSCYARGTSCQEHLESLYVKYGYHLSKNRYYFCYDPSKMV
+SIFNRIRNNGEFPKTCGPFEITRIRDLTVDYDNGYEDKKARLPVSSSTQMITFYFKNGAI
+ATLRGSGTEPKLKYYVEMIGDDKEQVKATLDQVHDQVIQQFLRPTENQLSPPSDE
+>Cephalum
+MTTDIYQIAQNWLRWDRNPKTHKEISQLVQDKNESELKARLESRIAFGTAGLRGPMKAGF
+SCMNDLTVIQASQGLCMYVKQTLAPDAERKGIVVGYDGRYNSEVFAKLTAATFVSQGFKV
+HLFSRLVPTPFVAFAVPFLKACVGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGIAKQ
+IELNLEPWNVFYKEYFDRIERYTVRHNKQMAREKIVYSAMHGVGGEYTKRAFEVFALDPF
+IAVKEQFHPDPAFPTVTFPNPEEGKGALKLSIETAEANNNWAWKNGKPYYEKGLGSFPND
+QYFMINTAVSSAMLKTMAMKEGFTYEEVLTGFKWVGNAAQNLIEKGKHLLFAYEEAIGFM
+YGDVSLDKDGVRCAPIFAELAQHLYSKGSSCQDHLEELYKRYGYHISKNRYFFCYDPLKM
+EKIFNRIRNGGQYPTKCGDFEITRIRDLTTGYDTGYPPENKAQLPTSTSTQMITFYFKNG
+GIATLRGSGTEPKLKYYVEMIGDDKENVELILQSMVDQVINQFLRPIENELIPPKD
+>Violaceum
+MVINPFYPYYLYFCYSPGISYQGVKINKTKLEQSTLTTINQWLNGNYDEQTKKNIQNLLD
+QESYTELTDAFYRNLEFGTGGLRGIMGAGSNRINKYTIGTATQGLSNYLLKKYPGEKIKV
+AIAHDSRNNSDQFAKITADVFSANGIYVYFFKELRPTPELSFAIRELGCRSGVMLTASHN
+PKEYNGYKAYGADGGQFTAPDDRLVMDEVAKITSIDEVKFTRIDANIELIGEEIDQLYLD
+KITALSVSPEAISRQKDLKIVYSPIHGTGITLVPKALAQFGFDNVTIVEEQSKPDGNFPT
+VVYPNPEEKEAMTLALKKAQEIDADLVLATDPDADRVGIAVKNNNNEWILLNGNQTGSLL
+VHYVLTAWEEKGKIDGNQYIVKTVVTSNLIEAIAKAKKVDCYNTLTGFKWIGQLITSLQG
+KKTFVVGGEESYGYSVGELVRDKDAVISCAFIAEMTAYYKDKGSSLYNALIDMYVTHGLY
+KEELVSLTKKGKTGAEEIKAMMEKFRNNPPASLGGSKVSTLKDYELGTETDLNTGKISKL
+SLPKSDVLQFVTEDGSIVSARPSGTEPKIKFYCSVNATLSQASEFDKTDEKLGLKINALM
+EDLQK
+>Deminut
+MTDIYQIAQNWLKWDRNPKTHKEISTLVEKKDEAELRARLETRIAFGTAGLRGPMKAGFS
+CMNDLTVIQASQGLSLYVKKTLAGSESKGAVVGYDGRYNSEVFAKLTAATFASQGFKVYL
+FSKVVPTPYVAFAVPELGASVGVMVTASHNPKDDNGYKVYWDNGCQINTPHDKHISELIE
+SNLEPWNVCIYITLQINIDKLLSGVIDPLQVVTSSYMSKIEKYSVKHLPQPLKLATEQKI
+VYTAMHGVGAEYAKLAFEAFSLPPFIPVTQQVTPDPAFPTVAFPNPEEGKGALKLAIETA
+EANKSRIILANDPDADRLAVAEKQPEYVFLFYLISNNGTWKVFNGNEIGILFADWAWQNC
+RRVYPDVPADQFFMINTAVSSAMLKSMAKKDGYIHEETLTGFKWVGNKARELLDQNKRFL
+FAYEEAIGFMYGDVSLDKDGVRCAAIFAELALYQYANGSSCQRHLDSLYERYGYHISKNR
+YFFCYEPPKMVAIFNAIRNNKNYPTKCGEFEIERIRDLTDDYDNGYPDNKARLPISKSTQ
+MITFFFKNGAIATLRGSGTEPKLKYYVEMIGDNKSEVEAILAKVVTAVIDNFLRPVENQL
+TPPKDD
+>Ellipt
+MADLDKLVEDWMRWDKNTKTRDEVQKMVAQGDKKALAAALQNRIAFGTAGLRGPMKAGFA
+NMNDLTVIQASQGLCIYVSATIADAAKKGVVVGYDGRHNSLQFARLTAATFRSKGFKVYL
+FSTVVPTPYVAFSVPELGACVGVMVTASHNPKDDNGYKIDVEKLLKEDGVEDPLEKITAS
+YMSKVADYSIKSHPATKDIVMSDDKIVYTAMHGVGGEYTRRSFKAFSLPEFIPVVQQFHP
+DPEFPTVTFPNPEEGKGALKLAIETAEKNNSRLILANDPDADRLAVAERQPDGTWKVFNG
+NEIGVLFADWAWKNARARDPTTPASEFFMVNTAVSSAMLKTMAKTEGYTYEETLTGFKWV
+GNKAKEAIDKGGRFLFAYEEAIGFMYGDVSLDKDGVRTAPIFAQMALSLYAKGLSCVDHL
+EQLMKTYGYHISRNRYFFCYEPPKMVAIFDKIRNNGNFPKHCGPFEIVRVRDLTVDYDDA
+YEDKKARLPVSTSTQMITFYFKNGAIATLRGSGTEPKLKYYVEMIGDKSAKKEDVEKTLA
+EVVKQVIDNFLRPVENELTPPKDD
+>Lepto
+MASSERLQQLIQDWLKWDKNPTTLSEIQELVKKNDEKELRARLENRIAFGTAGMFLLGPM
+KAGFSCMNDLTVIQASQGLCIYVSDTIPNALNSGVVVGYDGRYNSKEFAKYTAATFLSKG
+YKVYLFSKVVPTPYVAFAVTELKAAIGVMITASHNPKDDNGYKVYWDNGCQINTPHDKGI
+AKQIQLNLEPWNVCAFFLDINANELLSGSSVVDPLDTIVNSYNSKITSYSVGNSGVKLAN
+EKIVYTAMHGVGGEYTKLAFEAFKLPPFVPVPQQYTPDPAFPTVAFPNPEEGKGALKLSI
+ETAEANGSRLILANDPDADRLAVAERNTNGTWKVFNGNEIGVLLADWAWQNARRAHPDTP
+ANRYFMINTAVSSAMLKTMAKHEGYRCDETLTGFKWVGNQARKVIDEEKLNFLFAYEEAI
+GFMYGDVSLDKDGVRCAPIFAEMALSYYAQGHSCEDHLETLYKRYGYHISRNRYFFCYEP
+PKMVAIFDRIRNGRNFPTKCGRFEIERVRDLTVDYDDAYPDKKARLPVSTSTQMITFWFK
+NGGIATLRGSGTEPKLKYYVEMIGQDKQVVEKELAELVDAVIQQFLRPVENELTPPKDD
--- /dev/null
+DDB_G0280897 603 15 60 61
+PPL_06716 602 641 60 61
+DFA_03821 601 1266 60 61
+DLA_10096 739 1890 60 61
+DPU1265769 466 2654 60 61
+440792448 1302 3139 60 61
+ENY64621.1 594 4476 60 61
+Ppo014092.000 592 5095 60 61
+ADB0001102_3 589 5711 60 61
+Carpum 655 6318 60 61
+Cephalum 536 6994 60 61
+Violaceum 605 7550 60 61
+Deminut 606 8175 60 61
+Ellipt 564 8800 60 61
+Lepto 599 9381 60 61
import java.io.File;
-import org.junit.Assert;
+import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
af.loadJalviewDataFile(exonerateOutput, FormatAdapter.FILE, null, null);
- assertTrue("Expected at least one DNA protein association", af
- .getViewport().getAlignment().getDataset().getCodonFrames()
- .size() > 0);
+ assertNotEquals("Expected at least one DNA protein association",
+ 0, af.getViewport().getAlignment().getDataset()
+ .getCodonFrames().size(),
+ );
}
assertFalse(
"Failed to replace dummy seq2 with real sequence",
seq2 instanceof SequenceDummy
- && ((SequenceDummy) seq2).isDummy());
+ && ((SequenceDummy) seq2).isDummy(),
+ "Failed to replace dummy seq2 with real sequence");
String placeholderseq = new SequenceDummy("foo").getSequenceAsString();
assertFalse("dummy replacement buggy for seq1",
placeholderseq.equals(seq1.getSequenceAsString()));
assertFalse("dummy replacement buggy for seq2",
placeholderseq.equals(seq2.getSequenceAsString()));
- assertNotNull("No features added to seq1", seq1.getSequenceFeatures());// !=
- // null);
+ assertNotNull("No features added to seq1", seq1.getSequenceFeatures());
assertEquals("Wrong number of features", 3,
seq1.getSequenceFeatures().length);
assertNull(seq2.getSequenceFeatures());
assertTrue(
"Expected at least one CDNA/Protein mapping for seq1",
dataset.getCodonFrame(seq1) != null
- && dataset.getCodonFrame(seq1).size() > 0);
+ && dataset.getCodonFrame(seq1).size() > 0,
+ "Expected at least one CDNA/Protein mapping for seq1");
}
// @Test(groups ={ "Functional" })
*/
package jalview.io;
-import static org.junit.Assert.fail;
-
import org.testng.annotations.Test;
public class HtmlFileTest
@Test(groups = { "Functional" }, enabled = false)
public void test()
{
- fail("Not yet implemented");
+ org.testng.AssertJUnit.fail("Not yet implemented");
}
}
*/
package jalview.ws.jabaws;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
-
import jalview.ws.jws2.Jws2Discoverer;
import java.util.Vector;
+import org.testng.Assert;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
@Test(groups = { "Functional" }, enabled = false)
public void testAnnotExport()
{
- fail("Not yet implemented");
+ Assert.fail("Not yet implemented");
}
public static jalview.ws.jws2.Jws2Discoverer getJabawsDiscoverer()
} catch (Exception e)
{
e.printStackTrace();
- fail("Aborting. Problem discovering services. Tried " + svcurls);
+ Assert.fail("Aborting. Problem discovering services. Tried "
+ + svcurls);
}
- assertTrue("Failed to discover any services at ", disc.getServices()
- .size() > 0);
+ Assert.assertTrue(disc.getServices().size() > 0,
+ "Failed to discover any services at ");
return disc;
}
</property>
</object>
</method>
+ <method name="addElement">
+ <object class="com.zerog.ia.installer.actions.InstallZipfile" objectID="1000ddddfab93">
+ <property name="belongsToUninstallPhase">
+ <boolean>false</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ <property name="unixPermissions">
+ <string><![CDATA[664]]></string>
+ </property>
+ <property name="sourceName">
+ <string><![CDATA[htsjdk-1.133.jar]]></string>
+ </property>
+ <property name="overrideUnixPermissions">
+ <boolean>false</boolean>
+ </property>
+ <property name="sourcePath">
+ <string><![CDATA[/home/cruisecontrol/jalview/lib/]]></string>
+ </property>
+ <property name="shouldUninstall">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledCancel">
+ <boolean>true</boolean>
+ </property>
+ <property name="rollbackEnabledError">
+ <boolean>true</boolean>
+ </property>
+ <property name="destinationName">
+ <string><![CDATA[htsjdk-1.133.jar]]></string>
+ </property>
+ <property name="fileSize">
+ <long>16046</long>
+ </property>
+ <property name="macBinary">
+ <boolean>false</boolean>
+ </property>
+ <property name="targetCheckKind">
+ <int>0</int>
+ </property>
+ <property name="ruleExpression">
+ <string><![CDATA[]]></string>
+ </property>
+ </object>
+ </method>
</object>
</property>
<property name="rulesFailedMessage">
<object refID="1f46cffffab93"/>
<object refID="1f46efeefab93"/>
<object refID="1936efeefab93"/>
+ <object refID="1000ddddfab93"/>
<object refID="10936efeefab93"/>
<object refID="11936efeefab93"/>
<object refID="12936efeefab93"/>
<object refID="1f46cffffab93"/>
<object refID="1f46efeefab93"/>
<object refID="1936efeefab93"/>
+ <object refID="1000ddddfab93"/>
<object refID="10936efeefab93"/>
<object refID="11936efeefab93"/>
<object refID="12936efeefab93"/>
git://source.jalview.org / jalview.git / commitdiff