diff --git a/biojava-aa-prop/pom.xml b/biojava-aa-prop/pom.xml index aee8bc50cc..9b2dc58590 100644 --- a/biojava-aa-prop/pom.xml +++ b/biojava-aa-prop/pom.xml @@ -2,7 +2,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 4.0.0 biojava-aa-prop @@ -70,12 +70,12 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 org.biojava biojava-structure - 4.2.10 + 4.2.11 diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml index 272bbe77a2..036c2b90c3 100644 --- a/biojava-alignment/pom.xml +++ b/biojava-alignment/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 biojava-alignment biojava-alignment @@ -46,7 +46,7 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 compile @@ -74,7 +74,7 @@ org.biojava biojava-phylo - 4.2.10 + 4.2.11 diff --git a/biojava-core/pom.xml b/biojava-core/pom.xml index 31e9217495..d79c93e186 100644 --- a/biojava-core/pom.xml +++ b/biojava-core/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 4.0.0 biojava-core diff --git a/biojava-genome/pom.xml b/biojava-genome/pom.xml index 2f865c9f1c..30ab9f5b1f 100644 --- a/biojava-genome/pom.xml +++ b/biojava-genome/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 4.0.0 biojava-genome @@ -85,13 +85,13 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 compile org.biojava biojava-alignment - 4.2.10 + 4.2.11 compile diff --git a/biojava-integrationtest/pom.xml b/biojava-integrationtest/pom.xml index a2c489c21c..b1d1b1b584 100644 --- a/biojava-integrationtest/pom.xml +++ b/biojava-integrationtest/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 biojava-integrationtest jar @@ -32,7 +32,7 @@ org.biojava biojava-structure - 4.2.10 + 4.2.11 diff --git a/biojava-modfinder/pom.xml b/biojava-modfinder/pom.xml index 5b180290a5..485a7496ae 100644 --- a/biojava-modfinder/pom.xml +++ b/biojava-modfinder/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 biojava-modfinder biojava-modfinder @@ -31,7 +31,7 @@ org.biojava biojava-structure - 4.2.10 + 4.2.11 jar compile diff --git a/biojava-ontology/pom.xml b/biojava-ontology/pom.xml index 6ef151037f..e4d1a7e1c6 100644 --- a/biojava-ontology/pom.xml +++ b/biojava-ontology/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.10 + 4.2.11 biojava-ontology diff --git a/biojava-phylo/pom.xml b/biojava-phylo/pom.xml index adc2a88a14..9c84df8c04 100644 --- a/biojava-phylo/pom.xml +++ b/biojava-phylo/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 4.0.0 biojava-phylo @@ -44,7 +44,7 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 compile diff --git a/biojava-protein-disorder/pom.xml b/biojava-protein-disorder/pom.xml index b9ce3e69ea..166af73710 100644 --- a/biojava-protein-disorder/pom.xml +++ b/biojava-protein-disorder/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 biojava-protein-disorder jar @@ -63,7 +63,7 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 diff --git a/biojava-sequencing/pom.xml b/biojava-sequencing/pom.xml index 092c50284c..e688121865 100644 --- a/biojava-sequencing/pom.xml +++ b/biojava-sequencing/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 4.0.0 biojava-sequencing @@ -47,7 +47,7 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 compile diff --git a/biojava-structure-gui/pom.xml b/biojava-structure-gui/pom.xml index 061398727b..b3e8bb6898 100644 --- a/biojava-structure-gui/pom.xml +++ b/biojava-structure-gui/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 4.0.0 biojava-structure-gui @@ -25,13 +25,13 @@ org.biojava biojava-structure - 4.2.10 + 4.2.11 compile org.biojava biojava-core - 4.2.10 + 4.2.11 compile diff --git a/biojava-structure/pom.xml b/biojava-structure/pom.xml index 3c165e33d3..96464b5a83 100644 --- a/biojava-structure/pom.xml +++ b/biojava-structure/pom.xml @@ -4,7 +4,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 biojava-structure biojava-structure @@ -22,13 +22,13 @@ org.biojava biojava-alignment - 4.2.10 + 4.2.11 compile org.biojava biojava-core - 4.2.10 + 4.2.11 compile diff --git a/biojava-survival/pom.xml b/biojava-survival/pom.xml index 058e18519f..68a9daa642 100644 --- a/biojava-survival/pom.xml +++ b/biojava-survival/pom.xml @@ -4,7 +4,7 @@ org.biojava biojava - 4.2.10 + 4.2.11 biojava-survival diff --git a/biojava-ws/pom.xml b/biojava-ws/pom.xml index dd810a38bd..e6359a9cf1 100644 --- a/biojava-ws/pom.xml +++ b/biojava-ws/pom.xml @@ -3,7 +3,7 @@ biojava org.biojava - 4.2.10 + 4.2.11 biojava-ws biojava-ws @@ -19,7 +19,7 @@ org.biojava biojava-core - 4.2.10 + 4.2.11 compile diff --git a/biojava-ws/src/main/java/demo/HmmerDemo.java b/biojava-ws/src/main/java/demo/HmmerDemo.java index 3a94bb73f6..ea44166cd6 100644 --- a/biojava-ws/src/main/java/demo/HmmerDemo.java +++ b/biojava-ws/src/main/java/demo/HmmerDemo.java @@ -30,55 +30,54 @@ import java.util.SortedSet; -/** The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service +/** + * The cookbook recipe for how to request Pfam annotations for a protein sequence using the Hmmer3 service * * @author Andreas Prlic * @since 3.0.3 */ public class HmmerDemo { - public static void main(String[] args){ + public static void main(String[] args) throws Exception { - try { - // first we get a UniProt sequence - String uniProtID = "P08487"; - ProteinSequence seq = getUniprot(uniProtID); + // first we get a UniProt sequence + String uniProtID = "P08487"; + ProteinSequence seq = getUniprot(uniProtID); - // now we submit this sequence to the Hmmer web site - RemoteHmmerScan hmmer = new RemoteHmmerScan(); - SortedSet results = hmmer.scan(seq); + // now we submit this sequence to the Hmmer web site + RemoteHmmerScan hmmer = new RemoteHmmerScan(); - // and now let's print out the obtained annotations + SortedSet results = hmmer.scan(seq); - System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s", - "Domain","ACC", "Start","End","eValue","Description")); + // and now let's print out the obtained annotations - int counter = 0; - for (HmmerResult hmmerResult : results) { - //System.out.println(hmmerResult); + System.out.println(String.format("#\t%15s\t%10s\t%s\t%s\t%8s\t%s", + "Domain","ACC", "Start","End","eValue","Description")); - for ( HmmerDomain domain : hmmerResult.getDomains()) { - counter++; - System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s", - counter, - hmmerResult.getName(), domain.getHmmAcc(), - domain.getSqFrom(),domain.getSqTo(), - domain.getEvalue(), hmmerResult.getDesc() - )); + int counter = 0; + for (HmmerResult hmmerResult : results) { + //System.out.println(hmmerResult); - } + for ( HmmerDomain domain : hmmerResult.getDomains()) { + counter++; + System.out.println(String.format("%d\t%15s\t%10s\t%5d\t%5d\t%.2e\t%s", + counter, + hmmerResult.getName(), domain.getHmmAcc(), + domain.getSqFrom(),domain.getSqTo(), + domain.getEvalue(), hmmerResult.getDesc() + )); } - } catch (Exception e) { - // TODO Auto-generated catch block - e.printStackTrace(); } + + } - /** Fetch a protein sequence from the UniProt web site + /** + * Fetch a protein sequence from the UniProt web site * * @param uniProtID * @return a Protein Sequence diff --git a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java index 586aad785f..1454cf83fd 100644 --- a/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java +++ b/biojava-ws/src/main/java/org/biojava/nbio/ws/hmmer/RemoteHmmerScan.java @@ -43,7 +43,7 @@ public class RemoteHmmerScan implements HmmerScan { private static final Logger LOGGER = LoggerFactory.getLogger(RemoteHmmerScan.class); - public static final String HMMER_SERVICE = "http://www.ebi.ac.uk/Tools/hmmer/search/hmmscan"; + public static final String HMMER_SERVICE = "https://www.ebi.ac.uk/Tools/hmmer/search/hmmscan"; public RemoteHmmerScan(){ diff --git a/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java new file mode 100644 index 0000000000..2bdef898f2 --- /dev/null +++ b/biojava-ws/src/test/java/org/biojava/nbio/ws/hmmer/TestRemoteHmmerScan.java @@ -0,0 +1,42 @@ +package org.biojava.nbio.ws.hmmer; + +import java.util.SortedSet; + +import org.biojava.nbio.core.sequence.ProteinSequence; +import org.junit.Test; +import static org.junit.Assert.*; + +public class TestRemoteHmmerScan { + + /** + * Sequence for UniProt id P30340 (PDB 1SMT) + */ + private static final String TEST_SEQ = "MTKPVLQDGETVVCQGTHAAIASELQAIAPEVAQSLAEFFAVLADPNRLRLLSLLARSEL" + + "CVGDLAQAIGVSESAVSHQLRSLRNLRLVSYRKQGRHVYYQLQDHHIVALYQNALDHLQE" + + "CR"; + + @Test + public void testHmmerWs() throws Exception { + + ProteinSequence seq = new ProteinSequence(TEST_SEQ); + + // now we submit this sequence to the Hmmer web site + RemoteHmmerScan hmmer = new RemoteHmmerScan(); + + SortedSet results = hmmer.scan(seq); + + assertNotNull(results); + // 2 results (domains) for P30340 (PDB 1smt) as of Jan 2018 + assertEquals(2, results.size()); + + boolean gotSh2Domain = false; + + for (HmmerResult hmmerResult : results) { + if (hmmerResult.getName().equals("HTH_5")) { + gotSh2Domain = true; + } + } + + assertTrue("A HTH_5 domain should be present as one of the hmmer scan matches",gotSh2Domain); + } +} diff --git a/pom.xml b/pom.xml index b6dca9f797..0ad241002f 100644 --- a/pom.xml +++ b/pom.xml @@ -12,7 +12,7 @@ org.biojava biojava pom - 4.2.10 + 4.2.11 biojava BioJava is an open-source project dedicated to providing a Java framework for processing biological data. It provides analytical and statistical routines, parsers for common file formats and allows the @@ -44,7 +44,7 @@ scm:git:git@github.com:biojava/biojava.git https://github.com/biojava/biojava - biojava-4.2.10 + biojava-4.2.11