import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+import java.util.NoSuchElementException;
import java.util.Set;
import java.util.TreeMap;
} catch (IncompleteCodonException e)
{
// possible incomplete trailing codon - ignore
+ } catch (NoSuchElementException e)
+ {
+ // possibly peptide lacking STOP
}
}
}
import com.stevesoft.pat.Regex;
+/**
+ * A client to fetch CDNA sequence from Ensembl (i.e. that part of the genomic
+ * sequence that is transcribed to RNA, but not necessarily translated to
+ * protein)
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblCdna extends EnsemblSeqProxy
{
/*
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblCdna()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblCdna(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyI;
+import java.util.ArrayList;
import java.util.List;
+/**
+ * A client for direct fetching of CDS sequences from Ensembl (i.e. that part of
+ * the genomic sequence that is translated to protein)
+ *
+ * TODO: not currently used as CDS sequences are computed from CDS features on
+ * transcripts - delete this class?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblCds extends EnsemblSeqProxy
{
/*
EnsemblFeatureType.variation };
/**
- * Constructor
+ * Default constructor (to use rest.ensembl.org)
*/
public EnsemblCds()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblCds(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
* they are redundant information).
*/
@Override
- protected int getCdsRanges(SequenceI dnaSeq, List<int[]> ranges)
+ protected List<int[]> getCdsRanges(SequenceI dnaSeq)
{
int len = dnaSeq.getLength();
+ List<int[]> ranges = new ArrayList<int[]>();
ranges.add(new int[] { 1, len });
- return len;
+ return ranges;
}
}
private EnsemblFeatureType[] featuresWanted = { EnsemblFeatureType.cds,
EnsemblFeatureType.exon, EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblFeatures()
+ {
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblFeatures(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
protected URL getUrl(List<String> ids) throws MalformedURLException
{
StringBuffer urlstring = new StringBuffer(128);
- urlstring.append(ENSEMBL_REST).append("/overlap/id/")
+ urlstring.append(getDomain()).append("/overlap/id/")
.append(ids.get(0));
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
EnsemblFeatureType.exon, EnsemblFeatureType.cds,
EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblGene()
+ {
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblGene(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
- return "ENSEMBL (GENE)";
+ return "ENSEMBL";
}
@Override
if (isTranscriptIdentifier(query))
{
// we are assuming all transcripts have the same gene parent here
- query = new EnsemblLookup().getParent(queries[0]);
+ query = new EnsemblLookup(getDomain()).getParent(queries[0]);
if (query == null)
{
return null;
*/
if (!isGeneIdentifier(query))
{
- List<String> geneIds = new EnsemblSymbol().getIds(query);
+ List<String> geneIds = new EnsemblSymbol(getDomain()).getIds(query);
if (geneIds.isEmpty())
{
return null;
*/
protected String getGeneIdentifiersForName(String query)
{
- List<String> ids = new EnsemblSymbol().getIds(query);
+ List<String> ids = new EnsemblSymbol(getDomain()).getIds(query);
if (ids != null)
{
for (String id : ids)
List<int[]> mapTo = new ArrayList<int[]>();
mapTo.add(new int[] { 1, transcriptLength });
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
- new EnsemblCdna().transferFeatures(gene.getSequenceFeatures(),
- transcript.getDatasetSequence(), mapping, parentId);
+ new EnsemblCdna(getDomain()).transferFeatures(
+ gene.getSequenceFeatures(), transcript.getDatasetSequence(),
+ mapping, parentId);
/*
* fetch and save cross-references
/*
* and finally fetch the protein product and save as a cross-reference
*/
- new EnsemblCdna().addProteinProduct(transcript);
+ new EnsemblCdna(getDomain()).addProteinProduct(transcript);
return transcript;
}
import jalview.datamodel.SequenceFeature;
+/**
+ * A client to fetch genomic sequence from Ensembl
+ *
+ * TODO: not currently used - delete?
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblGenome extends EnsemblSeqProxy
{
/*
EnsemblFeatureType.transcript, EnsemblFeatureType.exon,
EnsemblFeatureType.cds, EnsemblFeatureType.variation };
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblGenome()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblGenome(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
--- /dev/null
+package jalview.ext.ensembl;
+
+
+/**
+ * A class to behave much like EnsemblGene but referencing the ensemblgenomes
+ * domain and data
+ *
+ * @author gmcarstairs
+ *
+ */
+public class EnsemblGenomes extends EnsemblGene
+{
+ /**
+ * Constructor sets domain to rest.ensemblgenomes.org instead of the 'usual'
+ * rest.ensembl.org
+ */
+ public EnsemblGenomes()
+ {
+ super(ENSEMBL_GENOMES_REST);
+ }
+
+ @Override
+ public boolean isGeneIdentifier(String query)
+ {
+ return true;
+ }
+
+ @Override
+ public String getDbName()
+ {
+ return "EnsemblGenomes";
+ }
+
+ @Override
+ public String getTestQuery()
+ {
+ return "DDB_G0283883";
+ }
+
+}
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+/**
+ * A client for the Ensembl lookup REST endpoint; used to find the Parent gene
+ * identifier given a transcript identifier.
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblLookup extends EnsemblRestClient
{
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblLookup()
+ {
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param
+ */
+ public EnsemblLookup(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
*/
protected URL getUrl(String identifier)
{
- String url = ENSEMBL_REST + "/lookup/id/" + identifier
+ String url = getDomain() + "/lookup/id/" + identifier
+ "?content-type=application/json";
try
{
import com.stevesoft.pat.Regex;
+/**
+ * A client to fetch protein translated sequence for an Ensembl identifier
+ *
+ * @author gmcarstairs
+ *
+ */
public class EnsemblProtein extends EnsemblSeqProxy
{
/*
private static final List<String> CROSSREFS = Arrays.asList(new String[] {
"PDB", "Uniprot/SPTREMBL", "Uniprot/SWISSPROT" });
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
public EnsemblProtein()
{
super();
}
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblProtein(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
*/
abstract class EnsemblRestClient extends EnsemblSequenceFetcher
{
- protected final static String ENSEMBL_REST = "http://rest.ensembl.org";
+ private final static String ENSEMBL_REST = "http://rest.ensembl.org";
- protected static final String SEQUENCE_ID_URL = ENSEMBL_REST
- + "/sequence/id";
+ protected final static String ENSEMBL_GENOMES_REST = "http://rest.ensemblgenomes.org";
// @see https://github.com/Ensembl/ensembl-rest/wiki/Output-formats
private static final String PING_URL = "http://rest.ensembl.org/info/ping.json";
private static final Regex GENE_REGEX = new Regex(
"(ENS)([A-Z]{3}|)G[0-9]{11}$");
+ private String domain = ENSEMBL_REST;
+
private static boolean ensemblRestAvailable = false;
private static long lastCheck = -1;
protected volatile boolean inProgress = false;
- public static boolean isTranscriptIdentifier(String query)
+ /**
+ * Default constructor to use rest.ensembl.org
+ */
+ public EnsemblRestClient()
+ {
+ this(ENSEMBL_REST);
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblRestClient(String d)
+ {
+ domain = d;
+ }
+
+ String getDomain()
+ {
+ return domain;
+ }
+
+ void setDomain(String d)
+ {
+ domain = d;
+ }
+
+ public boolean isTranscriptIdentifier(String query)
{
return query == null ? false : TRANSCRIPT_REGEX.search(query);
}
- public static boolean isGeneIdentifier(String query)
+ public boolean isGeneIdentifier(String query)
{
return query == null ? false : GENE_REGEX.search(query);
}
{
try
{
- URL ping = new URL(PING_URL);
+ // note this format works for both ensembl and ensemblgenomes
+ // info/ping.json works for ensembl only (March 2016)
+ URL ping = new URL(getDomain()
+ + "/info/ping?content-type=application/json");
HttpURLConnection conn = (HttpURLConnection) ping.openConnection();
int rc = conn.getResponseCode();
conn.disconnect();
/**
* Base class for Ensembl sequence fetchers
*
+ * @see http://rest.ensembl.org/documentation/info/sequence_id
* @author gmcarstairs
*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
}
/**
- * Constructor
+ * Default constructor (to use rest.ensembl.org)
*/
public EnsemblSeqProxy()
{
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ */
+ public EnsemblSeqProxy(String d)
+ {
+ super(d);
}
/**
* get 'dummy' genomic sequence with exon, cds and variation features
*/
SequenceI genomicSequence = null;
- EnsemblFeatures gffFetcher = new EnsemblFeatures();
+ EnsemblFeatures gffFetcher = new EnsemblFeatures(getDomain());
EnsemblFeatureType[] features = getFeaturesToFetch();
AlignmentI geneFeatures = gffFetcher.getSequenceRecords(accId,
features);
String accId = querySeq.getName();
try
{
- AlignmentI protein = new EnsemblProtein().getSequenceRecords(accId);
+ AlignmentI protein = new EnsemblProtein(getDomain())
+ .getSequenceRecords(accId);
if (protein == null || protein.getHeight() == 0)
{
System.out.println("Failed to retrieve protein for " + accId);
seq = seq.getDatasetSequence();
}
- EnsemblXref xrefFetcher = new EnsemblXref();
+ EnsemblXref xrefFetcher = new EnsemblXref(getDomain());
List<DBRefEntry> xrefs = xrefFetcher.getCrossReferences(seq.getName(),
getCrossReferenceDatabases());
for (DBRefEntry xref : xrefs)
*/
protected MapList mapCdsToProtein(SequenceI dnaSeq, SequenceI proteinSeq)
{
- List<int[]> ranges = new ArrayList<int[]>(50);
-
- int mappedDnaLength = getCdsRanges(dnaSeq, ranges);
+ List<int[]> ranges = getCdsRanges(dnaSeq);
+ int mappedDnaLength = MappingUtils.getLength(ranges);
int proteinLength = proteinSeq.getLength();
int proteinEnd = proteinLength;
int codesForResidues = mappedDnaLength / 3;
if (codesForResidues == (proteinLength + 1))
{
- MappingUtils.unmapStopCodon(ranges, mappedDnaLength);
+ // assuming extra codon is for STOP and not in peptide
codesForResidues--;
}
if (codesForResidues == proteinLength)
}
/**
- * Adds CDS ranges to the ranges list, and returns the total length mapped
- * from.
+ * Returns a list of CDS ranges found.
*
* No need to worry about reverse strand dna, here since the retrieved
* sequence is as transcribed (reverse complement for reverse strand), i.e in
* the same sense as the peptide.
*
* @param dnaSeq
- * @param ranges
* @return
*/
- protected int getCdsRanges(SequenceI dnaSeq, List<int[]> ranges)
+ protected List<int[]> getCdsRanges(SequenceI dnaSeq)
{
+ List<int[]> result = new ArrayList<int[]>();
SequenceFeature[] sfs = dnaSeq.getSequenceFeatures();
if (sfs == null)
{
- return 0;
+ return result;
}
SequenceOntologyI so = SequenceOntologyFactory.getInstance();
- int mappedDnaLength = 0;
for (SequenceFeature sf : sfs)
{
/*
*/
int begin = sf.getBegin();
int end = sf.getEnd();
- if (ranges.isEmpty())
+ if (result.isEmpty())
{
begin += phase;
if (begin > end)
continue; // shouldn't happen?
}
}
- ranges.add(new int[] { begin, end });
- mappedDnaLength += Math.abs(end - begin) + 1;
+ result.add(new int[] { begin, end });
}
}
- return mappedDnaLength;
+ return result;
}
/**
* multiple ids go in the POST body instead
*/
StringBuffer urlstring = new StringBuffer(128);
- urlstring.append(SEQUENCE_ID_URL);
+ urlstring.append(getDomain() + "/sequence/id");
if (ids.size() == 1)
{
urlstring.append("/").append(ids.get(0));
import org.json.simple.parser.JSONParser;
import org.json.simple.parser.ParseException;
+/**
+ * A client for the Ensembl xrefs/symbol REST service;
+ *
+ * @see http://rest.ensembl.org/documentation/info/xref_external
+ * @author gmcarstairs
+ *
+ */
public class EnsemblSymbol extends EnsemblXref
{
/**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblSymbol(String d)
+ {
+ super(d);
+ }
+
+ /**
* Returns the first "id" value in gene identifier format from the JSON
* response, or null if none found
*
protected URL getUrl(String id, Species species)
{
- String url = ENSEMBL_REST + "/xrefs/symbol/" + species.toString() + "/"
+ String url = getDomain() + "/xrefs/symbol/" + species.toString() + "/"
+ id
+ "?content-type=application/json";
try
class EnsemblXref extends EnsemblRestClient
{
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblXref(String d)
+ {
+ super(d);
+ }
+
@Override
public String getDbName()
{
*/
protected URL getUrl(String identifier)
{
- String url = ENSEMBL_REST + "/xrefs/id/" + identifier
+ String url = getDomain() + "/xrefs/id/" + identifier
+ "?content-type=application/json&all_levels=1";
try
{
}
/**
- * Remove the last 3 mapped positions from the given ranges
- *
- * @param ranges
- * @param mappedLength
- */
- public static void unmapStopCodon(List<int[]> ranges,
- int mappedLength)
- {
- if (mappedLength < 3)
- {
- return;
- }
- boolean done = false;
- int targetLength = mappedLength - 3;
- int mapped = 0;
- Iterator<int[]> it = ranges.iterator();
- while (!done && it.hasNext())
- {
- int[] range = it.next();
- int length = Math.abs(range[1] - range[0]) + 1;
- if (mapped + length == targetLength)
- {
- done = true;
- }
- else if (mapped + length < targetLength)
- {
- mapped += length;
- continue;
- }
- else
- {
- /*
- * need just a bit of this range
- */
- int needed = targetLength - mapped;
- int sense = range[1] >= range[0] ? 1 : -1;
- range[1] = range[0] + (sense * (needed - 1));
- done = true;
- }
- }
- /*
- * remove any trailing ranges
- */
- while (it.hasNext())
- {
- it.next();
- it.remove();
- }
- }
-
- /**
* Returns the total length of the supplied ranges
*
* @param ranges
package jalview.ws;
import jalview.ext.ensembl.EnsemblGene;
+import jalview.ext.ensembl.EnsemblGenomes;
import jalview.ws.dbsources.EmblCdsSource;
import jalview.ws.dbsources.EmblSource;
import jalview.ws.dbsources.Pdb;
public SequenceFetcher(boolean addDas)
{
- // addDBRefSourceImpl(EnsemblProtein.class);
- // addDBRefSourceImpl(EnsemblCds.class);
- // addDBRefSourceImpl(EnsemblGenome.class);
addDBRefSourceImpl(EnsemblGene.class);
- // addDBRefSourceImpl(EnsemblCdna.class);
+ addDBRefSourceImpl(EnsemblGenomes.class);
addDBRefSourceImpl(EmblSource.class);
addDBRefSourceImpl(EmblCdsSource.class);
addDBRefSourceImpl(Uniprot.class);
*/
public class EnsemblSeqProxyAdapter extends EnsemblSeqProxy
{
+ /**
+ * Default constructor (to use rest.ensembl.org)
+ */
+ public EnsemblSeqProxyAdapter()
+ {
+ super();
+ }
+
+ /**
+ * Constructor given the target domain to fetch data from
+ *
+ * @param d
+ */
+ public EnsemblSeqProxyAdapter(String d)
+ {
+ super(d);
+ }
@Override
public String getDbName()
import jalview.io.FileParse;
import jalview.io.gff.SequenceOntologyFactory;
import jalview.io.gff.SequenceOntologyLite;
+import jalview.util.MappingUtils;
import java.lang.reflect.Method;
import java.net.MalformedURLException;
import java.net.URL;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
ds.addSequenceFeature(sf);
- List<int[]> ranges = new ArrayList<int[]>();
- int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
- assertEquals(6, mappedLength);
+ List<int[]> ranges = testee.getCdsRanges(dnaSeq);
+ assertEquals(6, MappingUtils.getLength(ranges));
assertEquals(2, ranges.size());
assertEquals(4, ranges.get(0)[0]);
assertEquals(6, ranges.get(0)[1]);
sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
ds.addSequenceFeature(sf);
- List<int[]> ranges = new ArrayList<int[]>();
- int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
+ List<int[]> ranges = testee.getCdsRanges(dnaSeq);
/*
* check the mapping starts with the first complete codon
*/
- assertEquals(6, mappedLength);
+ assertEquals(6, MappingUtils.getLength(ranges));
assertEquals(2, ranges.size());
assertEquals(7, ranges.get(0)[0]);
assertEquals(9, ranges.get(0)[1]);
@Test(groups = "Functional")
public void testIsTranscriptIdentifier()
{
- assertFalse(EnsemblSeqProxy.isTranscriptIdentifier(null));
- assertFalse(EnsemblSeqProxy.isTranscriptIdentifier(""));
- assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENSG00000012345"));
- assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENST00000012345"));
- assertTrue(EnsemblSeqProxy.isTranscriptIdentifier("ENSMUST00000012345"));
- assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("enst00000012345"));
- assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST000000123456"));
- assertFalse(EnsemblSeqProxy.isTranscriptIdentifier("ENST0000001234"));
+ EnsemblSeqProxy testee = new EnsemblGene();
+ assertFalse(testee.isTranscriptIdentifier(null));
+ assertFalse(testee.isTranscriptIdentifier(""));
+ assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
+ assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
+ assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
+ assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
+ assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
+ assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
}
@Test(groups = "Functional")
public void testIsGeneIdentifier()
{
- assertFalse(EnsemblSeqProxy.isGeneIdentifier(null));
- assertFalse(EnsemblSeqProxy.isGeneIdentifier(""));
- assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENST00000012345"));
- assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSG00000012345"));
- assertTrue(EnsemblSeqProxy.isGeneIdentifier("ENSMUSG00000012345"));
- assertFalse(EnsemblSeqProxy.isGeneIdentifier("ensg00000012345"));
- assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG000000123456"));
- assertFalse(EnsemblSeqProxy.isGeneIdentifier("ENSG0000001234"));
+ EnsemblSeqProxy testee = new EnsemblGene();
+ assertFalse(testee.isGeneIdentifier(null));
+ assertFalse(testee.isGeneIdentifier(""));
+ assertFalse(testee.isGeneIdentifier("ENST00000012345"));
+ assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
+ assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
+ assertFalse(testee.isGeneIdentifier("ensg00000012345"));
+ assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
+ assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
}
}
\ No newline at end of file
assertEquals("[5, 10]", Arrays.toString(hidden.get(1)));
}
- /**
- * Tests for the method that removes the trailing stop codon from a mapping
- * range i.e. the last 3 positions (whether split or not)
- */
- @Test(groups = { "Functional" })
- public void testUnmapStopCodon()
- {
- List<int[]> ranges = new ArrayList<int[]>();
-
- // simple case, forward strand:
- ranges.add(new int[] { 1, 3 });
- ranges.add(new int[] { 9, 14 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(2, ranges.size());
- assertArrayEquals(new int[] { 1, 3 }, ranges.get(0));
- assertArrayEquals(new int[] { 9, 11 }, ranges.get(1));
-
- // split stop codon, forward strand:
- ranges.clear();
- ranges.add(new int[] { 1, 8 });
- ranges.add(new int[] { 10, 10 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(1, ranges.size());
- assertArrayEquals(new int[] { 1, 6 }, ranges.get(0));
-
- // very split stop codon, forward strand:
- ranges.clear();
- ranges.add(new int[] { 1, 1 });
- ranges.add(new int[] { 3, 4 });
- ranges.add(new int[] { 6, 6 });
- ranges.add(new int[] { 8, 8 });
- ranges.add(new int[] { 10, 10 });
- MappingUtils.unmapStopCodon(ranges, 6);
- assertEquals(2, ranges.size());
- assertArrayEquals(new int[] { 1, 1 }, ranges.get(0));
- assertArrayEquals(new int[] { 3, 4 }, ranges.get(1));
-
- // simple case, reverse strand:
- ranges.clear();
- ranges.add(new int[] { 12, 10 });
- ranges.add(new int[] { 6, 1 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(2, ranges.size());
- assertArrayEquals(new int[] { 12, 10 }, ranges.get(0));
- assertArrayEquals(new int[] { 6, 4 }, ranges.get(1));
-
- // split stop codon, reverse strand:
- ranges.clear();
- ranges.add(new int[] { 12, 6 });
- ranges.add(new int[] { 4, 3 });
- MappingUtils.unmapStopCodon(ranges, 9);
- assertEquals(1, ranges.size());
- assertArrayEquals(new int[] { 12, 7 }, ranges.get(0));
- }
-
@Test(groups = { "Functional" })
public void testGetLength()
{
git://source.jalview.org / jalview.git / commitdiff