SSDM-1287: raw score and evalue provided.

SVN: 33013

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);

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);
+        }
+        
+    }
 }

openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/BlastScore.java

+/*
+ * 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;
+    }
+
+}

openbis_api/source/java/ch/systemsx/cisd/openbis/generic/shared/api/v1/dto/ISearchDomainResultScore.java

+/*
+ * 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();
+}

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 + "]";
     }
 
 }