diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
index fd3fffd4f4fb162a6aa1cf53003ff63c0cb70518..353230d43c5489ec9ba375718a3bb09eb79ee202 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/api/v2/sequencedatabases/BlastDatabase.java
@@ -45,6 +45,7 @@ import ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask;
import ch.systemsx.cisd.openbis.dss.generic.shared.api.internal.v2.ISearchDomainService;
import ch.systemsx.cisd.openbis.dss.generic.shared.utils.BlastUtils;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.AlignmentMatch;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.BlastScore;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileBlastSearchResultLocation;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityPropertyBlastSearchResultLocation;
@@ -162,35 +163,21 @@ public class BlastDatabase extends AbstractSearchDomainService
{
Row row = new Row(line);
SearchDomainSearchResult sequenceSearchResult = new SearchDomainSearchResult();
- sequenceSearchResult.setScore(row.bitscore);
- AlignmentMatch alignmentMatch = new AlignmentMatch();
- alignmentMatch.setSequenceStart(row.sstart);
- alignmentMatch.setSequenceEnd(row.send);
- alignmentMatch.setQueryStart(row.qstart);
- alignmentMatch.setQueryEnd(row.qend);
- alignmentMatch.setNumberOfMismatches(row.numberOfMismatchs);
- alignmentMatch.setTotalNumberOfGaps(row.totalNumberOfGaps);
+ sequenceSearchResult.setScore(createBlastScore(row));
+ AlignmentMatch alignmentMatch = createAlignmentMatch(row);
Matcher matcher = STITLE_PATTERN.matcher(row.title);
if (matcher.matches())
{
- DataSetFileBlastSearchResultLocation resultLocation = new DataSetFileBlastSearchResultLocation();
- resultLocation.setIdentifier(matcher.group(1));
- resultLocation.setDataSetCode(matcher.group(2));
- resultLocation.setPathInDataSet(matcher.group(3));
- resultLocation.setAlignmentMatch(alignmentMatch);
- sequenceSearchResult.setResultLocation(resultLocation);
+ sequenceSearchResult.setResultLocation(
+ createDataSetFileBlastSearchResultLocation(matcher, alignmentMatch));
result.add(sequenceSearchResult);
} else
{
matcher = ENTITY_PROPERTY_TITLE_PATTERN.matcher(row.title);
if (matcher.matches())
{
- EntityPropertyBlastSearchResultLocation resultLocation = new EntityPropertyBlastSearchResultLocation();
- resultLocation.setEntityKind(EntityKind.valueOf(matcher.group(1)));
- resultLocation.setPermId(matcher.group(2));
- resultLocation.setPropertyType(matcher.group(3));
- resultLocation.setAlignmentMatch(alignmentMatch);
- sequenceSearchResult.setResultLocation(resultLocation);
+ sequenceSearchResult.setResultLocation(
+ createEntityPropertyBlastSearchResultLocation(matcher, alignmentMatch));
result.add(sequenceSearchResult);
}
}
@@ -201,6 +188,47 @@ public class BlastDatabase extends AbstractSearchDomainService
}
return result;
}
+
+ private EntityPropertyBlastSearchResultLocation createEntityPropertyBlastSearchResultLocation(Matcher matcher, AlignmentMatch alignmentMatch)
+ {
+ EntityPropertyBlastSearchResultLocation resultLocation = new EntityPropertyBlastSearchResultLocation();
+ resultLocation.setEntityKind(EntityKind.valueOf(matcher.group(1)));
+ resultLocation.setPermId(matcher.group(2));
+ resultLocation.setPropertyType(matcher.group(3));
+ resultLocation.setAlignmentMatch(alignmentMatch);
+ return resultLocation;
+ }
+
+ private DataSetFileBlastSearchResultLocation createDataSetFileBlastSearchResultLocation(Matcher matcher, AlignmentMatch alignmentMatch)
+ {
+ DataSetFileBlastSearchResultLocation resultLocation = new DataSetFileBlastSearchResultLocation();
+ resultLocation.setIdentifier(matcher.group(1));
+ resultLocation.setDataSetCode(matcher.group(2));
+ resultLocation.setPathInDataSet(matcher.group(3));
+ resultLocation.setAlignmentMatch(alignmentMatch);
+ return resultLocation;
+ }
+
+ private AlignmentMatch createAlignmentMatch(Row row)
+ {
+ AlignmentMatch alignmentMatch = new AlignmentMatch();
+ alignmentMatch.setSequenceStart(row.sstart);
+ alignmentMatch.setSequenceEnd(row.send);
+ alignmentMatch.setQueryStart(row.qstart);
+ alignmentMatch.setQueryEnd(row.qend);
+ alignmentMatch.setNumberOfMismatches(row.numberOfMismatchs);
+ alignmentMatch.setTotalNumberOfGaps(row.totalNumberOfGaps);
+ return alignmentMatch;
+ }
+
+ private BlastScore createBlastScore(Row row)
+ {
+ BlastScore blastScore = new BlastScore();
+ blastScore.setScore(row.score);
+ blastScore.setBitScore(row.bitscore);
+ blastScore.setEvalue(row.evalue);
+ return blastScore;
+ }
private List<String> createCommand(SequenceType sequenceType, File queryFile, Map<String, String> parameters)
{
@@ -223,7 +251,7 @@ public class BlastDatabase extends AbstractSearchDomainService
command.add("-query");
command.add(queryFile.getAbsolutePath());
command.add("-outfmt");
- command.add("6 stitle bitscore sstart send qstart qend mismatch gaps");
+ command.add("6 stitle bitscore score evalue sstart send qstart qend mismatch gaps");
if (parameters.containsKey("task") == false)
{
parameters.put("task", defaultTask);
@@ -304,6 +332,8 @@ public class BlastDatabase extends AbstractSearchDomainService
{
private String title;
private double bitscore;
+ private double score;
+ private double evalue;
private int sstart;
private int send;
private int qstart;
@@ -317,6 +347,8 @@ public class BlastDatabase extends AbstractSearchDomainService
String[] cells = line.split("\t");
title = cells[len++];
bitscore = asDouble(cells);
+ score = asDouble(cells);
+ evalue = asDouble(cells);
sstart = asInt(cells);
send = asInt(cells);
qstart = asInt(cells);
diff --git a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
index 17e74650929f19f9fef45b640a652b5443fe7a0a..16de68eb33535db333016537fd151099117d9abb 100644
--- a/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
+++ b/openbis/sourceTest/java/ch/systemsx/cisd/openbis/generic/server/business/bo/SearchDomainSearcherTest.java
@@ -34,6 +34,7 @@ import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.AlignmentMatch;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.DataSetFileSearchResultLocation;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityKind;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.EntityPropertyBlastSearchResultLocation;
+import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.ISearchDomainResultScore;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomain;
import ch.systemsx.cisd.openbis.generic.shared.api.v1.dto.SearchDomainSearchResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.IPermIdHolder;
@@ -139,22 +140,22 @@ public class SearchDomainSearcherTest extends AbstractBOTest
createSearcher().searchForEntitiesWithSequences(SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
assertEquals("E1", results.get(0).getEntity().getPermId());
- assertEquals("Search Domain: test-db, Score: 11.5, Result location: "
+ assertEquals("Search Domain: test-db, Score: [11.5], Result location: "
+ "[Experiment perm id: E1, property type: S, alignment in sequence: [42-45], "
+ "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(0).getSearchResult().toString());
assertEquals("S2", results.get(1).getEntity().getPermId());
- assertEquals("Search Domain: test-db, Score: 10.5, Result location: "
+ assertEquals("Search Domain: test-db, Score: [10.5], Result location: "
+ "[Sample perm id: S2, property type: OLIGO, alignment in sequence: [42-45], "
+ "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(1).getSearchResult().toString());
assertEquals("S1", results.get(2).getEntity().getPermId());
- assertEquals("Search Domain: test-db, Score: 9.5, Result location: "
+ assertEquals("Search Domain: test-db, Score: [9.5], Result location: "
+ "[Sample perm id: S1, property type: OLIGO, alignment in sequence: [42-45], "
+ "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(2).getSearchResult().toString());
assertEquals("DS1", results.get(3).getEntity().getPermId());
- assertEquals("Search Domain: test-db, Score: 0.5, Result location: "
+ assertEquals("Search Domain: test-db, Score: [0.5], Result location: "
+ "[Data set perm id: DS1, property type: SEQ, alignment in sequence: [42-45], "
+ "alignment in query: [7-10], number of mismatches: 0, total number of gaps: 0]",
results.get(3).getSearchResult().toString());
@@ -175,22 +176,22 @@ public class SearchDomainSearcherTest extends AbstractBOTest
List<SearchDomainSearchResultWithFullEntity> results =
createSearcher().searchForEntitiesWithSequences(SEQUENCE_DATABASE, SEQUENCE_SNIPPET, OPTIONAL_PARAMETERS);
- assertEquals("Search Domain: test-db, Score: 14.5, Result location: [Data set: ds3, path: ds3/path, "
+ assertEquals("Search Domain: test-db, Score: [14.5], Result location: [Data set: ds3, path: ds3/path, "
+ "identifier: [id-ds3], position: 42]",
results.get(0).getSearchResult().toString());
assertEquals(ds3.getCode(), ((AbstractExternalData) results.get(0).getEntity()).getCode());
assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(0).getEntity()).getExperiment().getIdentifier());
- assertEquals("Search Domain: test-db, Score: 13.5, Result location: [Data set: ds3, path: ds3/path, "
+ assertEquals("Search Domain: test-db, Score: [13.5], Result location: [Data set: ds3, path: ds3/path, "
+ "identifier: [id-ds3], position: 42]",
results.get(1).getSearchResult().toString());
assertEquals(ds3.getCode(), ((AbstractExternalData) results.get(1).getEntity()).getCode());
assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(1).getEntity()).getExperiment().getIdentifier());
- assertEquals("Search Domain: test-db, Score: 1.5, Result location: [Data set: ds2, path: ds2/path, "
+ assertEquals("Search Domain: test-db, Score: [1.5], Result location: [Data set: ds2, path: ds2/path, "
+ "identifier: [id-ds2], position: 42]",
results.get(2).getSearchResult().toString());
assertEquals(ds2.getCode(), ((AbstractExternalData) results.get(2).getEntity()).getCode());
assertEquals("/G1/P1/exp1", ((AbstractExternalData) results.get(2).getEntity()).getExperiment().getIdentifier());
- assertEquals("Search Domain: test-db, Score: 0.5, Result location: [Data set: ds1, path: ds1/path, "
+ assertEquals("Search Domain: test-db, Score: [0.5], Result location: [Data set: ds1, path: ds1/path, "
+ "identifier: [id-ds1], position: 42]",
results.get(3).getSearchResult().toString());
assertEquals(ds1.getCode(), ((AbstractExternalData) results.get(3).getEntity()).getCode());
@@ -241,7 +242,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
SearchDomain searchDomain = new SearchDomain();
searchDomain.setName("test-db");
result.setSearchDomain(searchDomain);
- result.setScore(score++);
+ result.setScore(new SimpleScore(score++));
DataSetFileSearchResultLocation resultLocation = new DataSetFileSearchResultLocation();
resultLocation.setDataSetCode(foundDataSet);
resultLocation.setPathInDataSet(foundDataSet + "/path");
@@ -254,7 +255,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
}
});
}
-
+
private void prepareSearchForEntityPropertiesWithSequences(final DataStorePE dataStore,
final IDataStoreService service, final double initialScore, final String... foundLocations)
{
@@ -271,7 +272,7 @@ public class SearchDomainSearcherTest extends AbstractBOTest
SearchDomain searchDomain = new SearchDomain();
searchDomain.setName("test-db");
result.setSearchDomain(searchDomain);
- result.setScore(score++);
+ result.setScore(new SimpleScore(score++));
EntityPropertyBlastSearchResultLocation resultLocation = new EntityPropertyBlastSearchResultLocation();
String[] splittedLocation = foundLocation.split(":");
resultLocation.setEntityKind(EntityKind.valueOf(splittedLocation[0]));
@@ -392,4 +393,28 @@ public class SearchDomainSearcherTest extends AbstractBOTest
}
return permIds;
}
+
+ private static final class SimpleScore implements ISearchDomainResultScore
+ {
+ private static final long serialVersionUID = 1L;
+ private final double score;
+
+ SimpleScore(double score)
+ {
+ this.score = score;
+ }
+
+ @Override
+ public double getScore()
+ {
+ return score;
+ }
+
+ @Override
+ public String toString()
+ {
+ return Double.toString(score);
+ }
+
+ }
}
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/BlastScore.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/BlastScore.java
new file mode 100644
index 0000000000000000000000000000000000000000..5fc523dbf91a423fe2bdd61f5487a40407409698
--- /dev/null
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/BlastScore.java
@@ -0,0 +1,74 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * Wraps raw score, bit score and evalue of a BLAST search result.
+ *
+ * @author Franz-Josef Elmer
+ */
+@JsonObject("BlastScore")
+public class BlastScore implements ISearchDomainResultScore
+{
+ private static final long serialVersionUID = 1L;
+
+ private double score;
+
+ private double bitScore;
+
+ private double evalue;
+
+ @Override
+ public double getScore()
+ {
+ return score;
+ }
+
+ public void setScore(double score)
+ {
+ this.score = score;
+ }
+
+ public double getBitScore()
+ {
+ return bitScore;
+ }
+
+ public void setBitScore(double bitScore)
+ {
+ this.bitScore = bitScore;
+ }
+
+ public double getEvalue()
+ {
+ return evalue;
+ }
+
+ public void setEvalue(double evalue)
+ {
+ this.evalue = evalue;
+ }
+
+ @Override
+ public String toString()
+ {
+ return "Score: " + score + ", bit score: " + bitScore + ", evalue: " + evalue;
+ }
+
+}
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultScore.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultScore.java
new file mode 100644
index 0000000000000000000000000000000000000000..0629ebe5c52ac3ecce82bb62ee567937a275a24f
--- /dev/null
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultScore.java
@@ -0,0 +1,35 @@
+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.generic.shared.api.v1.dto;
+
+import java.io.Serializable;
+
+import ch.systemsx.cisd.base.annotation.JsonObject;
+
+/**
+ * Basic interface of classes specifying a score of search domain result.
+ *
+ * @author Franz-Josef Elmer
+ */
+@JsonObject("ISearchDomainResultScore")
+public interface ISearchDomainResultScore extends Serializable
+{
+ /**
+ * Returns the score of the result.
+ */
+ public double getScore();
+}
diff --git a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java
index bd0d561554e6f39b1cc6581bcda08a1da3c730e5..92b6ef83612d5cba0f50f71f7af8e3a44b614b41 100644
--- a/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java
+++ b/openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/SearchDomainSearchResult.java
@@ -34,7 +34,7 @@ public class SearchDomainSearchResult implements Serializable, Comparable<Search
private ISearchDomainResultLocation resultLocation;
- private double score;
+ private ISearchDomainResultScore score;
public SearchDomain getSearchDomain()
{
@@ -46,12 +46,12 @@ public class SearchDomainSearchResult implements Serializable, Comparable<Search
this.searchDomain = searchDomain;
}
- public double getScore()
+ public ISearchDomainResultScore getScore()
{
return score;
}
- public void setScore(double score)
+ public void setScore(ISearchDomainResultScore score)
{
this.score = score;
}
@@ -69,14 +69,14 @@ public class SearchDomainSearchResult implements Serializable, Comparable<Search
@Override
public int compareTo(SearchDomainSearchResult searchResult)
{
- return Double.compare(score, searchResult.getScore());
+ return Double.compare(score.getScore(), searchResult.getScore().getScore());
}
@Override
public String toString()
{
- return "Search Domain: " + getSearchDomain() + ", Score: " + score
- + ", Result location: [" + resultLocation + "]";
+ return "Search Domain: " + getSearchDomain() + ", Score: [" + score
+ + "], Result location: [" + resultLocation + "]";
}
}