Merge branch 'master' of https://github.com/compomics/colims

colims-core/src/main/java/com/compomics/colims/core/io/fasta/FastaDbParser.java

@@ -1,6 +1,7 @@
 package com.compomics.colims.core.io.fasta;
 
 import com.compomics.colims.model.FastaDb;
+import com.compomics.colims.model.Protein;
 import com.compomics.colims.model.enums.SearchEngineType;
 import com.compomics.util.protein.Header;
 import org.slf4j.Logger;
@@ -42,8 +43,8 @@ public class FastaDbParser {
      * @return the protein sequences map (key: protein accession; value: protein sequence)
      * @throws IOException thrown in case of an input/output related problem
      */
-    public Map<String, String> parse(LinkedHashMap<FastaDb, Path> fastaDbs) throws IOException {
-        Map<String, String> proteinSequences = new HashMap<>();
+    public Map<String, Protein> parse(LinkedHashMap<FastaDb, Path> fastaDbs) throws IOException {
+        Map<String, Protein> proteinSequences = new HashMap<>();
         try {
             for (Map.Entry<FastaDb, Path> entry : fastaDbs.entrySet()) {
                 FastaDb fastaDb = entry.getKey();
@@ -153,7 +154,7 @@ public LinkedHashMap<String, String> testParseRule(Path fastaPath, String parseR
      * @param fastaPath        the FASTA path
      * @throws IOException in case of file reading related problem
      */
-    private void parseWithRule(Map<String, String> proteinSequences, FastaDb fastaDb, Path fastaPath) throws IOException {
+    private void parseWithRule(Map<String, Protein> proteinSequences, FastaDb fastaDb, Path fastaPath) throws IOException {
         try (BufferedReader bufferedReader = Files.newBufferedReader(fastaPath)) {
             //compile the pattern
             Pattern pattern;
@@ -170,11 +171,23 @@ private void parseWithRule(Map<String, String> proteinSequences, FastaDb fastaDb
                 if (line.startsWith(BLOCK_SEPARATOR)) {
                     //add limiting check for protein store to avoid growing
                     if (sequenceBuilder.length() > 0) {
+                        Protein protein = new Protein();
+                        protein.setSequence(sequenceBuilder.toString().trim());
+                        String regex = "(?<!\\\\)" + Pattern.quote("|");
+                        if(fastaHeader.substring(1).split(regex).length > 2){
+                            if(fastaHeader.substring(1).split(regex)[2].split(SPLITTER).length >1){
+                                String description =String.join(SPLITTER, Arrays.copyOfRange(fastaHeader.substring(1).split(regex)[2].split(SPLITTER), 1, fastaHeader.substring(1).split(regex)[2].split(SPLITTER).length));
+                                if(description.contains(" OS=")){
+                                    protein.setDescription(description.substring(0, description.indexOf(" OS=")));
+                                }
+                            }
+
+                        } 
                         Matcher matcher = pattern.matcher(fastaHeader.substring(1));
                         if (matcher.find()) {
-                            proteinSequences.putIfAbsent(matcher.group(1), sequenceBuilder.toString().trim());
+                            proteinSequences.putIfAbsent(matcher.group(1), protein);
                         } else {
-                            proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], sequenceBuilder.toString().trim());
+                            proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], protein);
                         }
                         sequenceBuilder.setLength(0);
                     }
@@ -185,11 +198,19 @@ private void parseWithRule(Map<String, String> proteinSequences, FastaDb fastaDb
             }
             //last line
             if (sequenceBuilder.length() > 0) {
+                Protein protein = new Protein();
+                protein.setSequence(sequenceBuilder.toString().trim());
+                if(fastaHeader.substring(1).split("|").length > 2 && fastaHeader.substring(1).split("|")[2].split(SPLITTER).length >1){
+                    String description = fastaHeader.substring(1).split("|")[2].split(SPLITTER)[1];
+                    if(description.contains(" OS=")){
+                        protein.setDescription(description.substring(0, description.indexOf("OS=")));
+                    } 
+                } 
                 Matcher matcher = pattern.matcher(fastaHeader.substring(1).split(SPLITTER)[0]);
                 if (matcher.find()) {
-                    proteinSequences.putIfAbsent(matcher.group(1), sequenceBuilder.toString().trim());
+                    proteinSequences.putIfAbsent(matcher.group(1), protein);
                 } else {
-                    proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], sequenceBuilder.toString().trim());
+                    proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], protein);
                 }
                 sequenceBuilder.setLength(0);
             }
@@ -203,7 +224,7 @@ private void parseWithRule(Map<String, String> proteinSequences, FastaDb fastaDb
      * @param fastaPath        the FASTA path
      * @throws IOException in case of file reading related problem
      */
-    private void parseWithoutRule(Map<String, String> proteinSequences, Path fastaPath) throws IOException {
+    private void parseWithoutRule(Map<String, Protein> proteinSequences, Path fastaPath) throws IOException {
         try (BufferedReader bufferedReader = Files.newBufferedReader(fastaPath)) {
             //start reading the file
             final StringBuilder sequenceBuilder = new StringBuilder();
@@ -213,7 +234,10 @@ private void parseWithoutRule(Map<String, String> proteinSequences, Path fastaPa
                 if (line.startsWith(BLOCK_SEPARATOR)) {
                     //add limiting check for protein store to avoid growing
                     if (sequenceBuilder.length() > 0) {
-                        proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], sequenceBuilder.toString().trim());
+                        Protein protein = new Protein();
+                        protein.setSequence(sequenceBuilder.toString().trim());
+                      //  protein.setDescription(fastaHeader.substring(1).split(SPLITTER)[1]);
+                        proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], protein);
                         sequenceBuilder.setLength(0);
                     }
                     fastaHeader = line;
@@ -223,7 +247,9 @@ private void parseWithoutRule(Map<String, String> proteinSequences, Path fastaPa
             }
             //last line
             if (sequenceBuilder.length() > 0) {
-                proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], sequenceBuilder.toString().trim());
+                Protein protein = new Protein();
+                protein.setSequence(sequenceBuilder.toString().trim());
+                proteinSequences.putIfAbsent(fastaHeader.substring(1).split(SPLITTER)[0], protein);
                 sequenceBuilder.setLength(0);
             }
         }

colims-core/src/main/java/com/compomics/colims/core/playground/Playground.java

@@ -57,7 +57,7 @@ public static void main(final String[] args) throws IOException, ClassNotFoundEx
         testFastaDb.setDatabaseName("test db");
         LinkedHashMap<FastaDb, Path> fastaDbs = new LinkedHashMap<>();
         fastaDbs.put(testFastaDb, Paths.get(testFastaDb.getFilePath()));
-        Map<String, String> parse = fastaDbParser.parse(fastaDbs);
+  //      Map<String, String> parse = fastaDbParser.parse(fastaDbs);
         System.out.println("=---------------");
 
     }

colims-core/src/main/java/com/compomics/colims/core/service/ProteinService.java

@@ -22,9 +22,10 @@ public interface ProteinService extends GenericService<Protein, Long> {
      * looks for the protein in the cache first before querying the database.
      *
      * @param sequence the protein sequence
+     * @param description the protein description
      * @return the found Protein instance
      */
-    Protein getProtein(String sequence);
+    Protein getProtein(String sequence, String description);
 
     /**
      * Clear the resources used by this resource.

colims-core/src/main/java/com/compomics/colims/core/service/impl/ProteinServiceImpl.java

@@ -67,12 +67,13 @@ public void remove(Protein entity) {
     }
 
     @Override
-    public Protein getProtein(String sequence) {
+    public Protein getProtein(String sequence, String description) {
         Protein targetProtein;
 
         //first, look in the newly added proteins map
         //@todo configure hibernate cache and check performance
         targetProtein = cachedProteins.get(sequence);
+
         if (targetProtein == null) {
             //check if the protein is found in the db
             targetProtein = findBySequence(sequence);
@@ -82,8 +83,13 @@ public Protein getProtein(String sequence) {
                 targetProtein = new Protein(sequence);
 
             }
+            if(targetProtein.getDescription() == null && description != null){
+                targetProtein.setDescription(description);
+            }
             //add to cached proteins
             cachedProteins.put(sequence, targetProtein);
+        }else if(targetProtein.getDescription() == null && description != null){
+            targetProtein.setDescription(description);
         }
         return targetProtein;
     }

colims-core/src/test/java/com/compomics/colims/core/io/fasta/FastaDbParserTest.java

@@ -1,6 +1,7 @@
 package com.compomics.colims.core.io.fasta;
 
 import com.compomics.colims.model.FastaDb;
+import com.compomics.colims.model.Protein;
 import com.compomics.colims.model.enums.SearchEngineType;
 import org.junit.Assert;
 import org.junit.Test;
@@ -52,7 +53,7 @@ public void testParse() throws IOException {
         fastaDbs.put(testFastaDb, Paths.get(testFastaDb.getFilePath()));
         fastaDbs.put(contaminantsFastaDb, Paths.get(contaminantsFastaDb.getFilePath()));
 
-        Map<String, String> parsedFastas = fastaDbParser.parse(fastaDbs);
+        Map<String, Protein> parsedFastas = fastaDbParser.parse(fastaDbs);
 
         Assert.assertFalse(parsedFastas.containsKey(null));
         Assert.assertEquals(20381, parsedFastas.size());
@@ -64,7 +65,8 @@ public void testParse() throws IOException {
         Assert.assertTrue(parsedFastas.containsKey("Q2KJ03"));
         Assert.assertEquals("MEEKTTQSVEGLKQYCLVPEREMKHIERHIHQTGKAGEFKNKPFRQVLQPPNETKLP" +
                 "KIMPEGHGIQNAQRRKQVNEREQMQTKDHQERMIRGRELAEQRLKERILRRSQSQLLTYEKHERVKEIK" +
-                "EFERVIAYLLFQPCSRSRIKVSILMDKSQNGEKVNTIVKPYQRKFLAMPPFLRSQIGKIRD", parsedFastas.get("Q2KJ03"));
+                "EFERVIAYLLFQPCSRSRIKVSILMDKSQNGEKVNTIVKPYQRKFLAMPPFLRSQIGKIRD", parsedFastas.get("Q2KJ03").getSequence());
+        Assert.assertEquals("Putative uncharacterized protein ZNRD1-AS1", parsedFastas.get("Q2KJ03").getDescription());
         //look for 3 contaminants proteins
         Assert.assertTrue(parsedFastas.containsKey("P00761"));
         Assert.assertTrue(parsedFastas.containsKey("Q9TRI1"));
@@ -81,7 +83,9 @@ public void testParse() throws IOException {
                 "DLDSIIAEVRAQYEEIAQRSKAEAEALYQTKVQQLQISVDQHGDNLKNTKSEIAELNRMIQRLRAEIE" +
                 "NIKKQCQTLQVSVADAEQRGENALKDAHSKRVELEAALQQAKEELARMLREYQELMSVKLALDIEIAT" +
                 "YRKLLEGEEYRMSGECQSAVSISVVSGSTSTGGISGGLGSGSGFGLSSGFGSGSGSGFGFGGSVSGSS" +
-                "SSKIISTTTLNKRR", parsedFastas.get("P19013"));
+                "SSKIISTTTLNKRR", parsedFastas.get("P19013").getSequence());
+        Assert.assertEquals("Keratin, type II cytoskeletal 4", parsedFastas.get("P19013").getDescription());
+
     }
 
     @Test

colims-distributed/src/main/java/com/compomics/colims/distributed/io/maxquant/parsers/MaxQuantProteinGroupsParser.java

@@ -52,7 +52,7 @@ public class MaxQuantProteinGroupsParser {
      * The map of parsed protein sequences (key: protein accession; value:
      * protein sequence).
      */
-    private Map<String, String> proteinSequences = new HashMap<>();
+    private Map<String, Protein> proteinSequences = new HashMap<>();
     /**
      * The quantification method.
      */
@@ -165,8 +165,8 @@ private ProteinGroup parseProteinGroup(Map<String, String> proteinGroupsEntry, b
                     strippedAccession = org.apache.commons.lang3.StringUtils.substringAfter(strippedAccession, ProteinGroupHasProtein.CONTAMINANT_PREFIX);
                 }
                 //get the protein sequence by it's accession
-                String sequence = getProteinSequence(strippedAccession);
-                proteinGroup.getProteinGroupHasProteins().add(createProteinGroupHasProtein(sequence, accession, isMainGroup, proteinGroup));
+                Protein protein = getProteinSequence(strippedAccession);
+                proteinGroup.getProteinGroupHasProteins().add(createProteinGroupHasProtein(protein, accession, isMainGroup, proteinGroup));
 
                 if (isMainGroup) {
                     isMainGroup = false;
@@ -208,7 +208,7 @@ private ProteinGroup parseProteinGroup(Map<String, String> proteinGroupsEntry, b
      * @return sequence the found sequence
      * @throws IllegalArgumentException if the accession key is not found
      */
-    private String getProteinSequence(String accession) {
+    private Protein getProteinSequence(String accession) {
         if (proteinSequences.containsKey(accession)) {
             return proteinSequences.get(accession);
         } else {
@@ -224,12 +224,13 @@ private String getProteinSequence(String accession) {
      * @param mainGroup whether this is the main protein of the group
      * @return a ProteinGroupHasProtein object
      */
-    private ProteinGroupHasProtein createProteinGroupHasProtein(String sequence, String accession, boolean mainGroup, ProteinGroup proteinGroup) {
+    private ProteinGroupHasProtein createProteinGroupHasProtein(Protein pr, String accession, boolean mainGroup, ProteinGroup proteinGroup) {
         ProteinGroupHasProtein proteinGroupHasProtein = new ProteinGroupHasProtein();
         proteinGroupHasProtein.setIsMainGroupProtein(mainGroup);
 
         //get protein
-        Protein protein = proteinService.getProtein(sequence);
+        Protein protein = proteinService.getProtein(pr.getSequence(), pr.getDescription());
+        protein.setDescription(pr.getDescription());
 
         //set protein accession
         proteinGroupHasProtein.setProteinAccession(accession);
@@ -262,15 +263,15 @@ private void createProteinGroupQuant(ProteinGroup proteinGroup, AnalyticalRun an
         //set the analytical run
         proteinGroupQuant.setAnalyticalRun(analyticalRun);
         //set the intensity
-        if (intensity != null) {
+        if (intensity != null && !Double.isNaN(Double.parseDouble(intensity))) {
             proteinGroupQuant.setIntensity(Double.parseDouble(intensity));
         }
         //set the LFQ intensity
-        if (lfqIntensity != null) {
+        if (lfqIntensity != null && !Double.isNaN(Double.parseDouble(lfqIntensity))) {
             proteinGroupQuant.setLfqIntensity(Double.parseDouble(lfqIntensity));
         }
         //set the iBAQ
-        if (ibaq != null) {
+        if (ibaq != null && !Double.isNaN(Double.parseDouble(ibaq))) {
             proteinGroupQuant.setIbaq(Double.parseDouble(ibaq));
         }
         //set the MSMS Count

colims-distributed/src/main/java/com/compomics/colims/distributed/io/utilities_to_colims/UtilitiesProteinGroupMapper.java

@@ -67,7 +67,7 @@ public void map(final ProteinMatch proteinMatch, final PSParameter proteinGroupS
                 //get the utilities Protein from SequenceFactory
                 com.compomics.util.experiment.biology.Protein sourceProtein = SequenceFactory.getInstance().getProtein(proteinAccession);
                 //get protein
-                Protein matchedProtein = proteinService.getProtein(sourceProtein.getSequence());
+                Protein matchedProtein = proteinService.getProtein(sourceProtein.getSequence(), null);
 
                 if (proteinAccession.equals(proteinMatch.getMainMatch())) {
                     //set the is main protein group flag to true

colims-model/src/main/java/com/compomics/colims/model/Protein.java

@@ -28,13 +28,17 @@ public class Protein extends DatabaseEntity {
     @Column(name = "protein_sequence", nullable = false)
 //    @Field(index=Index.YES, analyze=Analyze.NO, store=Store.NO)
     private String sequence;
+
+    @Basic(optional = true)
+    @Column(name = "description", nullable = true)
+    private String description;
     /**
-     * The ProteinGroupHasProtein instances from the join table between the protein group and protein tables.
+     * The ProteinGroupHasProtein instances from the join table between the
+     * protein group and protein tables.
      */
     @OneToMany(mappedBy = "protein")
     private List<ProteinGroupHasProtein> proteinGroupHasProteins = new ArrayList<>();
 
-
     /**
      * No-arg constructor.
      */
@@ -58,6 +62,14 @@ public void setSequence(String sequence) {
         this.sequence = sequence;
     }
 
+    public String getDescription() {
+        return description;
+    }
+
+    public void setDescription(String description) {
+        this.description = description;
+    }
+
     public List<ProteinGroupHasProtein> getProteinGroupHasProteins() {
         return proteinGroupHasProteins;
     }
@@ -66,11 +78,14 @@ public void setProteinGroupHasProteins(List<ProteinGroupHasProtein> proteinGroup
         this.proteinGroupHasProteins = proteinGroupHasProteins;
     }
 
-
     @Override
     public boolean equals(Object o) {
-        if (this == o) return true;
-        if (o == null || getClass() != o.getClass()) return false;
+        if (this == o) {
+            return true;
+        }
+        if (o == null || getClass() != o.getClass()) {
+            return false;
+        }
 
         Protein protein = (Protein) o;
 

colims-repository/src/main/resources/setup/colims_db_setup.sql

@@ -243,6 +243,7 @@ create table project_has_user (
 create table protein (
     id bigint not null auto_increment,
     protein_sequence longtext not null,
+    description varchar(200),
     primary key (id)
 );
 

colims-repository/src/main/resources/setup/colims_db_setup_dev.sql

@@ -246,6 +246,7 @@ create table project_has_user (
 create table protein (
     id bigint not null auto_increment,
     protein_sequence longtext not null,
+    description varchar(200),
     primary key (id)
 );