diff --git a/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java b/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java
index 830f04fea218a3cfff8a4c13596c7ad791139e61..4cada4b2655ae107759a322434b949898952cc02 100644
--- a/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/fasta/FastaUtilities.java
@@ -35,17 +35,68 @@ public class FastaUtilities
*/
public static final List<Character> NUCLEIC_ACID_CODES = Arrays.asList('A', 'C', 'G', 'T', 'U', 'R', 'Y',
'K', 'M', 'S', 'W', 'B', 'D', 'H', 'V', 'N', 'X', '-');
-
+
+ public static final List<Character> STRICT_NUCLEIC_ACID_CODES = Arrays.asList('A', 'T', 'U', 'C', 'G');
+
/**
* Amino acid codes as used in FASTA files (see https://en.wikipedia.org/wiki/FASTA_format).
*/
public static final List<Character> AMINO_ACID_CODES = Arrays.asList('A', 'B', 'C', 'D', 'E', 'F', 'G', 'H',
'I', 'J', 'K', 'L', 'M', 'N', 'O', 'P', 'Q', 'R', 'S', 'T', 'U', 'V', 'W', 'Y', 'Z', 'X', '*', '-');
+
+ public static final List<Character> STRICT_AMINO_ACID_CODES = Arrays.asList('A', 'R', 'N', 'D', 'C', 'E',
+ 'Q', 'G', 'H', 'I', 'L', 'K', 'M', 'F', 'P', 'S', 'T', 'W', 'Y', 'V');
private static final Set<Character> NUCLEIC_ACID_CODES_SET = new HashSet<Character>(NUCLEIC_ACID_CODES);
+ private static final Set<Character> STRICT_NUCLEIC_ACID_CODES_SET = new HashSet<Character>(STRICT_NUCLEIC_ACID_CODES);
+
private static final Set<Character> AMINO_ACID_CODES_SET = new HashSet<Character>(AMINO_ACID_CODES);
+ private static final Set<Character> STRICT_AMINO_ACID_CODES_SET = new HashSet<Character>(STRICT_AMINO_ACID_CODES);
+
+ /**
+ * Returns the sequenceType of the specified string or <code>null</code> if undetermined.
+ *
+ * @return {@link SequenceType#PROT} if all characters are from the set STRICT_AMINO_ACID_CODES
+ * and at least one character is not in the set STRICT_NUCLEIC_ACID_CODES. Otherwise
+ * {@link SequenceType#NUCL} is returned if all characters are from the set STRICT_NUCLEIC_ACID_CODES.
+ * If non of these two cases are fulfilled <code>null</code> is returned.
+ */
+ public static SequenceType determineSequenceTypeOrNull(String line)
+ {
+ boolean isAminoAcidSequence = false;
+ int nuclCounter = 0;
+ int aminoCounter = 0;
+ for (char c : line.toUpperCase().toCharArray())
+ {
+ boolean isNucleicAcidCode = STRICT_NUCLEIC_ACID_CODES_SET.contains(c);
+ boolean isAmoniAcidCode = STRICT_AMINO_ACID_CODES_SET.contains(c);
+ if (isNucleicAcidCode == false && isAmoniAcidCode == false)
+ {
+ return null;
+ }
+ if (isNucleicAcidCode)
+ {
+ nuclCounter++;
+ }
+ if (isAmoniAcidCode)
+ {
+ aminoCounter++;
+ if (isNucleicAcidCode == false)
+ {
+ isAminoAcidSequence = true;
+ }
+ }
+ }
+ if (aminoCounter == line.length() && isAminoAcidSequence)
+ {
+ return SequenceType.PROT;
+ }
+ return nuclCounter == line.length() ? SequenceType.NUCL : null;
+ }
+
+
/**
* Determines the sequence type from the specified line of a FASTA file.
*
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java
index 45d67be46a6742d99d5380aa3860d7e965eeca04..ce6d260fdbe02979d529defc2c0d8b0f4ab31d6b 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/fasta/FastaUtilitiesTest.java
@@ -78,5 +78,35 @@ public class FastaUtilitiesTest extends AssertJUnit
{
assertEquals(SequenceType.PROT, FastaUtilities.determineSequenceType("TLI IGGBC"));
}
+
+ @Test
+ public void testDetermineSequenceTypeOrNullForPureU()
+ {
+ assertEquals(SequenceType.NUCL, FastaUtilities.determineSequenceTypeOrNull("UUU"));
+ }
+
+ @Test
+ public void testDetermineSequenceTypeOrNullForPureNuclSequence()
+ {
+ assertEquals(SequenceType.NUCL, FastaUtilities.determineSequenceTypeOrNull("GATTACA"));
+ }
+
+ @Test
+ public void testDetermineSequenceTypeOrNullForProtSequence()
+ {
+ assertEquals(SequenceType.PROT, FastaUtilities.determineSequenceTypeOrNull("ACE"));
+ }
+
+ @Test
+ public void testDetermineSequenceTypeOrNullForMixOfPureNuclCharactersAndPureAminoCharacters()
+ {
+ assertEquals(null, FastaUtilities.determineSequenceTypeOrNull("UV"));
+ }
+
+ @Test
+ public void testDetermineSequenceTypeOrNullForUnknownCharacter()
+ {
+ assertEquals(null, FastaUtilities.determineSequenceTypeOrNull("ABCZ"));
+ }
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java
index f299a4c263c681ea1d0dbd8f03cfd9c4d4e9341d..9d8b97ac8d61b14b70f3eb5874a65dc4d78ec7be 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java
@@ -39,7 +39,6 @@ import java.util.Set;
import java.util.StringTokenizer;
import java.util.TreeSet;
import java.util.regex.Pattern;
-import java.util.regex.PatternSyntaxException;
import org.apache.commons.io.FilenameUtils;
import org.apache.commons.io.IOUtils;
@@ -566,17 +565,21 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
{
if (property.getPropertyType().getCode().equals(propertyType))
{
- String sequence = property.tryGetAsString();
+ String sequence = normalize(property.tryGetAsString());
if (sequence != null)
{
- Sequence seq = new Sequence(entity, propertyType, sequence);
- Sequences sequences = map.get(seq.getSequenceType());
- if (sequences == null)
+ SequenceType sequenceType = FastaUtilities.determineSequenceTypeOrNull(sequence);
+ if (sequenceType != null)
{
- sequences = new Sequences();
- map.put(seq.getSequenceType(), sequences);
+ Sequence seq = new Sequence(entity, propertyType, sequenceType, sequence);
+ Sequences sequences = map.get(seq.getSequenceType());
+ if (sequences == null)
+ {
+ sequences = new Sequences();
+ map.put(seq.getSequenceType(), sequences);
+ }
+ sequences.addSequence(seq);
}
- sequences.addSequence(seq);
}
break;
}
@@ -611,6 +614,24 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
return latestModificationDate;
}
}
+
+ private static String normalize(String sequence)
+ {
+ if (sequence == null)
+ {
+ return null;
+ }
+ StringBuilder builder = new StringBuilder();
+ for (int i = 0; i < sequence.length(); i++)
+ {
+ char c = sequence.charAt(i);
+ if (Character.isWhitespace(c) == false)
+ {
+ builder.append(Character.toUpperCase(c));
+ }
+ }
+ return builder.toString();
+ }
private static final class Sequence
{
@@ -625,10 +646,12 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
private final SequenceType sequenceType;
@SuppressWarnings("rawtypes")
- Sequence(IEntityInformationHolderWithProperties entity, String propertyType, String sequence)
+ Sequence(IEntityInformationHolderWithProperties entity, String propertyType,
+ SequenceType sequenceType, String sequence)
{
this.propertyType = propertyType;
- this.sequence = removeWhiteSpaces(sequence);
+ this.sequenceType = sequenceType;
+ this.sequence = sequence;
permId = entity.getPermId();
Date date = null;
if (entity instanceof CodeWithRegistrationAndModificationDate)
@@ -636,22 +659,6 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
date = ((CodeWithRegistrationAndModificationDate) entity).getModificationDate();
}
modificationDate = date == null ? new Date() : date;
- sequenceType = FastaUtilities.determineSequenceType(this.sequence);
- }
-
- private static String removeWhiteSpaces(String sequence)
- {
- StringBuilder builder = new StringBuilder();
- for (int i = 0; i < sequence.length(); i++)
- {
- char c = sequence.charAt(i);
- if (Character.isWhitespace(c) == false)
- {
- builder.append(c);
- }
- }
- String string = builder.toString();
- return string;
}
String getPermId()