dList = new ArrayList<>();
for(Character c:propertyList){
switch(c){
case '1':
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
index f223eaca23..cecd981223 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Constraints.java
@@ -30,7 +30,7 @@
/**
* This class is used to support the implementation of properties stated in IPeptideProperties.
* It initializes several values that would be needed for the computation of properties such as
- *
+ *
* Molecular weight
* Instability index
* Hydropathy value
@@ -64,14 +64,14 @@ public class Constraints {
public static AminoAcidCompound Y = aaSet.getCompoundForString("Y");
public static AminoAcidCompound V = aaSet.getCompoundForString("V");
- public static Map aa2ExtinctionCoefficient = new HashMap();
- public static Map aa2MolecularWeight = new HashMap();
- public static Map aa2Hydrophathicity = new HashMap();
- public static Map aa2PKa = new HashMap();
- public static Map diAA2Instability = new HashMap();
+ public static Map aa2ExtinctionCoefficient = new HashMap<>();
+ public static Map aa2MolecularWeight = new HashMap<>();
+ public static Map aa2Hydrophathicity = new HashMap<>();
+ public static Map aa2PKa = new HashMap<>();
+ public static Map diAA2Instability = new HashMap<>();
- public static Map aa2NTerminalPka = new HashMap();
- public static Map aa2CTerminalPka = new HashMap();
+ public static Map aa2NTerminalPka = new HashMap<>();
+ public static Map aa2CTerminalPka = new HashMap<>();
static{
initMolecularWeight();
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
index babe1e54d8..5342013b61 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/IPeptideProperties.java
@@ -26,7 +26,7 @@
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
@@ -35,7 +35,7 @@
/**
* An interface to generate some basic physico-chemical properties of protein sequences.
* The following properties could be generated:
- *
+ *
* Molecular weight
* Absorbance
* Extinction coefficient
@@ -258,7 +258,7 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
* Returns the net charge of sequence at pH 7. The sequence argument must be
* a protein sequence consisting of only non-ambiguous characters.
* The net charge will be computed using the approach stated in
- * here
*
* pKa values used will be either
* those used by Expasy which referenced "Electrophoresis 1994, 15, 529-539"
@@ -312,4 +312,14 @@ public AminoAcidCompositionTable obtainAminoAcidCompositionTable(File elementMas
* @see AminoAcidCompound
*/
public Map getAAComposition(ProteinSequence sequence);
+
+ /**
+ * Calculates the aromaticity value of a protein according to Lobry, 1994.
+ * It is simply the relative frequency of Phe+Trp+Tyr.
+ *
+ * @param sequence a protein sequence consisting of non-ambiguous characters only
+ * @return the aromaticity of a protein sequence
+ * @see ProteinSequence
+ */
+ public double getAromaticity(ProteinSequence sequence);
}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
index a46b857314..d14a4d906b 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptideProperties.java
@@ -28,7 +28,7 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Arrays;
@@ -37,7 +37,6 @@
import java.util.Map;
import java.util.Set;
import java.util.stream.Collectors;
-import java.util.stream.Stream;
/**
* This is an adaptor class which enable the ease of generating protein properties.
@@ -533,7 +532,7 @@ public static final Map getAAComposition(String seque
*/
public static final Map getAACompositionString(String sequence){
Map aa2Composition = getAAComposition(sequence);
- Map aaString2Composition = new HashMap();
+ Map aaString2Composition = new HashMap<>();
aaString2Composition = aa2Composition.keySet().stream() .collect(Collectors.toMap(aaCompound -> aaCompound.getShortName(),aaCompound ->aa2Composition.get(aaCompound)));
return aaString2Composition;
}
@@ -551,7 +550,7 @@ public static final Map getAACompositionString(String sequence){
*/
public static final Map getAACompositionChar(String sequence){
Map aa2Composition = getAAComposition(sequence);
- Map aaChar2Composition = new HashMap();
+ Map aaChar2Composition = new HashMap<>();
for(AminoAcidCompound aaCompound:aa2Composition.keySet()){
aaChar2Composition.put(aaCompound.getShortName().charAt(0), aa2Composition.get(aaCompound));
}
@@ -590,4 +589,28 @@ public static final int[] getPolarityOfAminoAcids(String sequence) {
}
return polarity;
}
+
+ /**
+ * An adaptor method to return the aromaticity value of sequence. The sequence argument
+ * must be a protein sequence consisting of only non-ambiguous characters.
+ *
+ * Calculates the aromaticity value of a protein according to Lobry, 1994.
+ * It is simply the relative frequency of Phe+Trp+Tyr.
+ * *
+ *
+ * @param sequence a protein sequence consisting of non-ambiguous characters only
+ * @return the aromaticity value of sequence
+ */
+ public static final double getAromaticity(String sequence) {
+ sequence = Utils.checkSequence(sequence);
+ ProteinSequence pSequence = null;
+ try {
+ pSequence = new ProteinSequence(sequence);
+ } catch (CompoundNotFoundException e) {
+ // the sequence was checked with Utils.checkSequence, this shouldn't happen
+ logger.error("The protein sequence contains invalid characters ({}), this should not happen. This is most likely a bug in Utils.checkSequence()", e.getMessage());
+ }
+ IPeptideProperties pp = new PeptidePropertiesImpl();
+ return pp.getAromaticity(pSequence);
+ }
}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
index 98e14c6a83..ceb0b234ed 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/PeptidePropertiesImpl.java
@@ -29,9 +29,9 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Unmarshaller;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Unmarshaller;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
@@ -210,7 +210,7 @@ private Map getExtinctAACount(ProteinSequence sequen
}
}
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
- Map extinctAA2Count = new HashMap();
+ Map extinctAA2Count = new HashMap<>();
//Ignore Case is always true
extinctAA2Count.put(aaSet.getCompoundForString("W"), numW + smallW);
extinctAA2Count.put(aaSet.getCompoundForString("C"), (int) (numC + smallC));
@@ -532,7 +532,7 @@ private Map getChargedAACount(ProteinSequence sequen
}
}
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
- Map chargedAA2Count = new HashMap();
+ Map chargedAA2Count = new HashMap<>();
chargedAA2Count.put(aaSet.getCompoundForString("K"), numK);
chargedAA2Count.put(aaSet.getCompoundForString("R"), numR);
chargedAA2Count.put(aaSet.getCompoundForString("H"), numH);
@@ -558,7 +558,7 @@ public double getEnrichment(ProteinSequence sequence, AminoAcidCompound aminoAci
@Override
public Map getAAComposition(ProteinSequence sequence) {
int validLength = 0;
- Map aa2Composition = new HashMap();
+ Map aa2Composition = new HashMap<>();
AminoAcidCompoundSet aaSet = new AminoAcidCompoundSet();
for(AminoAcidCompound aa:aaSet.getAllCompounds()){
aa2Composition.put(aa, 0.0);
@@ -582,4 +582,41 @@ public Map getAAComposition(ProteinSequence sequence)
}
return aa2Composition;
}
+
+
+ @Override
+ public double getAromaticity(ProteinSequence sequence) {
+ int validLength = sequence.getSequenceAsString().length();
+
+ if (validLength == 0) {
+ logger.warn("Valid length of sequence is 0, can't divide by 0 to calculate aromaticity: setting aromaticity to 0");
+ return 0.0;
+ }
+
+ //Phe - Phenylalanine
+ int totalF = 0;
+ //Tyr - Tyrosine
+ int totalY = 0;
+ //Trp - Tryptophan
+ int totalW = 0;
+
+ char[] seq = this.getSequence(sequence.toString(), true);
+ for (char aa : seq) {
+ char amino = Character.toUpperCase(aa);
+ switch (amino) {
+ case 'F':
+ totalF++;
+ break;
+ case 'Y':
+ totalY++;
+ break;
+ case 'W':
+ totalW++;
+ break;
+ }
+ }
+
+ return (totalF + totalY + totalW) / (double) (validLength);
+ }
}
+
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
index b66e879d7a..298ad61330 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/Utils.java
@@ -106,7 +106,7 @@ public final static int getNumberOfInvalidChar(String sequence, Set
* a new sequence with all invalid characters being replaced by '-'.
*/
public final static String cleanSequence(String sequence, Set cSet){
- Set invalidCharSet = new HashSet();
+ Set invalidCharSet = new HashSet<>();
StringBuilder cleanSeq = new StringBuilder();
if(cSet == null) cSet = PeptideProperties.standardAASet;
for(char c:sequence.toCharArray()){
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
index 0fab96f94a..7f39fff79e 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/IProfeatProperties.java
@@ -28,7 +28,7 @@ public interface IProfeatProperties {
/**
* Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
* An interface class to generate the properties of a protein sequence based on its converted attributes.
- * The seven different attributes are
+ * The seven different attributes are
* Hydrophobicity (Polar, Neutral, Hydrophobicity)
* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
@@ -103,8 +103,8 @@ public enum DISTRIBUTION {FIRST, FIRST25, FIRST50, FIRST75, ALL};
* Computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
* Example: "1111122222"
* For the above example,
- * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
- * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
+ * position of the GROUPING.GROUP1 & DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
+ * position of the GROUPING.GROUP1 & DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
index d8844476f4..dd0d310439 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatProperties.java
@@ -119,8 +119,8 @@ public static Map> getTransition(String seque
* An adaptor method which computes and return the position with respect to the sequence where the given distribution of the grouping can be found.
* Example: "1111122222"
* For the above example,
- * position of the GROUPING.GROUP1 && DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
- * position of the GROUPING.GROUP1 && DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
+ * position of the GROUPING.GROUP1 & DISTRIBUTION.FIRST = 0/10 (because the first occurrence of '1' is at position 0)
+ * position of the GROUPING.GROUP1 & DISTRIBUTION.ALL = 4/10 (because all occurrences of '1' happens on and before position 4)
*
* @param sequence
* a protein sequence consisting of non-ambiguous characters only
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
index 75b0ff3064..18b63a468b 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/ProfeatPropertiesImpl.java
@@ -125,35 +125,35 @@ private Convertor getConvertor(ATTRIBUTE attribute) throws Exception{
@Override
public Map getComposition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
- Map grouping2Composition = new HashMap();
+ Map grouping2Composition = new HashMap<>();
for(GROUPING group:GROUPING.values()) grouping2Composition.put(group, getComposition(sequence, attribute, group));
return grouping2Composition;
}
@Override
public Map> getComposition(ProteinSequence sequence) throws Exception {
- Map> attribute2Grouping2Composition = new HashMap>();
+ Map> attribute2Grouping2Composition = new HashMap<>();
for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Grouping2Composition.put(attribute, getComposition(sequence, attribute));
return attribute2Grouping2Composition;
}
@Override
public Map getTransition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
- Map transition2Double = new HashMap();
+ Map transition2Double = new HashMap<>();
for(TRANSITION transition:TRANSITION.values()) transition2Double.put(transition, getTransition(sequence, attribute, transition));
return transition2Double;
}
@Override
public Map> getTransition(ProteinSequence sequence) throws Exception {
- Map> attribute2Transition2Double = new HashMap>();
+ Map> attribute2Transition2Double = new HashMap<>();
for(ATTRIBUTE attribute:ATTRIBUTE.values()) attribute2Transition2Double.put(attribute, getTransition(sequence, attribute));
return attribute2Transition2Double;
}
@Override
public Map getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute, GROUPING group) throws Exception {
- Map distribution2Double = new HashMap();
+ Map distribution2Double = new HashMap<>();
for(DISTRIBUTION distribution:DISTRIBUTION.values())
distribution2Double.put(distribution, getDistributionPosition(sequence, attribute, group, distribution));
return distribution2Double;
@@ -161,7 +161,7 @@ public Map getDistributionPosition(ProteinSequence sequenc
@Override
public Map> getDistributionPosition(ProteinSequence sequence, ATTRIBUTE attribute) throws Exception {
- Map> grouping2Distribution2Double = new HashMap>();
+ Map> grouping2Distribution2Double = new HashMap<>();
for(GROUPING group:GROUPING.values())
grouping2Distribution2Double.put(group, getDistributionPosition(sequence, attribute, group));
return grouping2Distribution2Double;
@@ -170,7 +170,7 @@ public Map> getDistributionPosition(ProteinS
@Override
public Map>> getDistributionPosition(ProteinSequence sequence) throws Exception {
Map>> attribute2Grouping2Distribution2Double =
- new HashMap>>();
+ new HashMap<>();
for(ATTRIBUTE attribute:ATTRIBUTE.values())
attribute2Grouping2Distribution2Double.put(attribute, getDistributionPosition(sequence, attribute));
return attribute2Grouping2Distribution2Double;
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
index a88d93add3..e298ab2520 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/Convertor.java
@@ -28,7 +28,7 @@ public abstract class Convertor {
/**
* Based on Table 2 of http://nar.oxfordjournals.org/content/34/suppl_2/W32.full.pdf
* An abstract class to convert a protein sequence into representation of different attribute with each attribute having 3 groups.
- * The seven different attributes are
+ * The seven different attributes are
* Hydrophobicity (Polar, Neutral, Hydrophobicity)
* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
index 22143b53cb..a28076aa41 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/profeat/convertor/package-info.java
@@ -20,7 +20,7 @@
*/
/**
* Set of classes that enable the conversion protein sequences into various attributes.
- * The seven different attributes are
+ * The seven different attributes are
* Hydrophobicity (Polar, Neutral, Hydrophobicity)
* Normalized van der Waals volume (Range 0 - 2.78, 2.95 - 4.0, 4.03 - 8.08)
* Polarity (Value 4.9 - 6.2, 8.0 - 9.2, 10.4 - 13.0)
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java
index 9004426ff5..034df5fb12 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidComposition.java
@@ -20,7 +20,7 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.annotation.*;
+import jakarta.xml.bind.annotation.*;
import java.util.List;
@XmlRootElement(name = "compoundcomposition", namespace ="http://biojava.org")
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
index 4731e90453..b209859600 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/AminoAcidCompositionTable.java
@@ -20,10 +20,10 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlElement;
-import javax.xml.bind.annotation.XmlRootElement;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlRootElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -83,7 +83,7 @@ private void generatesAminoAcidCompoundSet(){
* Stores the mass of elements and isotopes
*/
public void computeMolecularWeight(ElementTable eTable){
- this.aaSymbol2MolecularWeight = new HashMap();
+ this.aaSymbol2MolecularWeight = new HashMap<>();
for(AminoAcidComposition a:aminoacid){
//Check to ensure that the symbol is of single character
if(a.getSymbol().length() != 1){
@@ -132,7 +132,7 @@ public void computeMolecularWeight(ElementTable eTable){
* @throws NullPointerException
* thrown if AminoAcidCompositionTable.computeMolecularWeight(ElementTable) is not called before this method
*/
- public double getMolecularWeight(Character aaSymbol) throws NullPointerException{
+ public double getMolecularWeight(Character aaSymbol) {
if(this.aaSymbol2MolecularWeight == null){
throw new NullPointerException("Please call AminoAcidCompositionTable.computeMolecularWeight(ElementTable) before this method");
}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
index 9b211ab305..7a436d32cd 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/CaseFreeAminoAcidCompoundSet.java
@@ -39,9 +39,9 @@
*/
public class CaseFreeAminoAcidCompoundSet implements CompoundSet {
- private final Map aminoAcidCompoundCache = new HashMap();
+ private final Map aminoAcidCompoundCache = new HashMap<>();
private final Map> equivalentsCache =
- new HashMap>();
+ new HashMap<>();
public CaseFreeAminoAcidCompoundSet() {
aminoAcidCompoundCache.put("A", new AminoAcidCompound(null, "A", "Ala", "Alanine", 71.0788f));
@@ -83,7 +83,7 @@ public CaseFreeAminoAcidCompoundSet() {
//which then does the actual conversion to Pyl.
aminoAcidCompoundCache.put("O", new AminoAcidCompound(null, "O", "Pyl", "Pyrrolysine", 255.3172f));
- Map lowerCaseSet = new HashMap();
+ Map lowerCaseSet = new HashMap<>();
for(String s:this.aminoAcidCompoundCache.keySet()){
lowerCaseSet.put(s.toLowerCase(), this.aminoAcidCompoundCache.get(s));
}
@@ -144,7 +144,7 @@ public Set getEquivalentCompounds(AminoAcidCompound compound)
addAmbiguousEquivalents("I", "L", "J");
// ambiguous gaps
AminoAcidCompound gap1, gap2, gap3;
- Set gaps = new HashSet();
+ Set gaps = new HashSet<>();
gaps.add(gap1 = aminoAcidCompoundCache.get("-"));
gaps.add(gap2 = aminoAcidCompoundCache.get("."));
gaps.add(gap3 = aminoAcidCompoundCache.get("_"));
@@ -162,18 +162,18 @@ private void addAmbiguousEquivalents(String one, String two, String either) {
Set equivalents;
AminoAcidCompound cOne, cTwo, cEither;
- equivalents = new HashSet();
+ equivalents = new HashSet<>();
equivalents.add(cOne = aminoAcidCompoundCache.get(one));
equivalents.add(cTwo = aminoAcidCompoundCache.get(two));
equivalents.add(cEither = aminoAcidCompoundCache.get(either));
equivalentsCache.put(cEither, equivalents);
- equivalents = new HashSet();
+ equivalents = new HashSet<>();
equivalents.add(cOne);
equivalents.add(cEither);
equivalentsCache.put(cOne, equivalents);
- equivalents = new HashSet();
+ equivalents = new HashSet<>();
equivalents.add(cTwo);
equivalents.add(cEither);
equivalentsCache.put(cTwo, equivalents);
@@ -186,7 +186,7 @@ public boolean hasCompound(AminoAcidCompound compound) {
@Override
public List getAllCompounds() {
- return new ArrayList(aminoAcidCompoundCache.values());
+ return new ArrayList<>(aminoAcidCompoundCache.values());
}
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
index b03d15d1ac..c7b9a425fc 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Element.java
@@ -20,10 +20,10 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlElement;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlAttribute;
+import jakarta.xml.bind.annotation.XmlElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -120,7 +120,7 @@ public List getIsotopes() {
public void setIsotopes(List isotopes) {
this.isotope = isotopes;
- this.name2Isotope = new HashMap();
+ this.name2Isotope = new HashMap<>();
if(isotopes != null){
for(Isotope i:isotopes){
name2Isotope.put(i.getName(), i);
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
index efac678f23..e2b30c6211 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ElementTable.java
@@ -20,7 +20,7 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.annotation.XmlRootElement;
+import jakarta.xml.bind.annotation.XmlRootElement;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -58,8 +58,8 @@ public void setElement(List eList){
* Populate the Maps for quick retrieval
*/
public void populateMaps(){
- this.elementName2Element = new HashMap();
- this.isotopeName2Isotope = new HashMap();
+ this.elementName2Element = new HashMap<>();
+ this.isotopeName2Isotope = new HashMap<>();
if(this.element != null){
for(Element e:this.element){
this.elementName2Element.put(e.getName(), e);
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java
index 493bf938a3..cc0682f084 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Isotope.java
@@ -20,10 +20,10 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
-import javax.xml.bind.annotation.XmlType;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlAttribute;
+import jakarta.xml.bind.annotation.XmlType;
@XmlType(name = "Iostope", propOrder = {"name","neutronsNum","mass"})
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
index d9c11c7e66..b1c63e9655 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/ModifiedAminoAcidCompoundSet.java
@@ -28,7 +28,7 @@
public class ModifiedAminoAcidCompoundSet implements CompoundSet {
- private final Map aminoAcidCompoundCache = new HashMap();
+ private final Map aminoAcidCompoundCache = new HashMap<>();
public ModifiedAminoAcidCompoundSet(List aaList, Map aaSymbol2MolecularWeight) {
this.aminoAcidCompoundCache.put("-", new AminoAcidCompound(null, "-", "", "", 0.0f));
@@ -84,7 +84,7 @@ public boolean hasCompound(AminoAcidCompound compound) {
@Override
public List getAllCompounds() {
- return new ArrayList(aminoAcidCompoundCache.values());
+ return new ArrayList<>(aminoAcidCompoundCache.values());
}
@Override
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java
index 2f49bb5c18..9430090436 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/MyValidationEventHandler.java
@@ -23,9 +23,9 @@
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import javax.xml.bind.ValidationEvent;
-import javax.xml.bind.ValidationEventHandler;
-import javax.xml.bind.ValidationEventLocator;
+import jakarta.xml.bind.ValidationEvent;
+import jakarta.xml.bind.ValidationEventHandler;
+import jakarta.xml.bind.ValidationEventLocator;
public class MyValidationEventHandler implements ValidationEventHandler{
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java
index 431cc3e48c..b30e4c6dd2 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/Name2Count.java
@@ -20,9 +20,9 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.annotation.XmlAccessType;
-import javax.xml.bind.annotation.XmlAccessorType;
-import javax.xml.bind.annotation.XmlAttribute;
+import jakarta.xml.bind.annotation.XmlAccessType;
+import jakarta.xml.bind.annotation.XmlAccessorType;
+import jakarta.xml.bind.annotation.XmlAttribute;
@XmlAccessorType(XmlAccessType.FIELD)
public class Name2Count{
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
index 8005bf3bac..5ca2b550ed 100644
--- a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
+++ b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/xml/SchemaGenerator.java
@@ -20,7 +20,7 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import javax.xml.bind.SchemaOutputResolver;
+import jakarta.xml.bind.SchemaOutputResolver;
import javax.xml.transform.Result;
import javax.xml.transform.stream.StreamResult;
import java.io.File;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
index 25ebf3abed..bbde2c1e30 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/CookBookTest.java
@@ -20,13 +20,12 @@
*/
package org.biojava.nbio.aaproperties;
-import org.biojava.nbio.aaproperties.PeptideProperties;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
index 6220ea0b28..8c79e3b078 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/PeptidePropertiesImplTest.java
@@ -20,14 +20,12 @@
*/
package org.biojava.nbio.aaproperties;
-import org.biojava.nbio.aaproperties.PeptideProperties;
-import org.biojava.nbio.aaproperties.Utils;
import org.biojava.nbio.aaproperties.xml.AminoAcidCompositionTable;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import javax.xml.bind.JAXBException;
+import jakarta.xml.bind.JAXBException;
import java.io.File;
import java.io.FileNotFoundException;
import java.util.Map;
@@ -358,4 +356,12 @@ public void testNetCharge(){
public void testNetChargeNull(){
assertEquals(8.6, PeptideProperties.getNetCharge(null), delta);
}
+
+ @Test
+ public void testAromaticity() {
+ assertEquals(1, PeptideProperties.getAromaticity("WWWYYYYFFFWWWYYYYFFF"), 0.001);
+ assertEquals(0.5, PeptideProperties.getAromaticity("WWWYYYYFFFAAAAAAAAAA"), 0.001);
+ assertEquals(0.08, PeptideProperties.getAromaticity(sequence), 0.001);
+ assertEquals(0.0, PeptideProperties.getAromaticity(fullInvalidSequence), 0.001);
+ }
}
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java
deleted file mode 100644
index d1edcef5a9..0000000000
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/ProfeatPropertiesImplTest.java
+++ /dev/null
@@ -1,25 +0,0 @@
-/*
- * BioJava development code
- *
- * This code may be freely distributed and modified under the
- * terms of the GNU Lesser General Public Licence. This should
- * be distributed with the code. If you do not have a copy,
- * see:
- *
- * http://www.gnu.org/copyleft/lesser.html
- *
- * Copyright for this code is held jointly by the individual
- * authors. These should be listed in @author doc comments.
- *
- * For more information on the BioJava project and its aims,
- * or to join the biojava-l mailing list, visit the home page
- * at:
- *
- * http://www.biojava.org/
- *
- */
-package org.biojava.nbio.aaproperties;
-
-public class ProfeatPropertiesImplTest {
-
-}
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
index 528192dcb4..49947c1f50 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/AminoAcidTest.java
@@ -23,10 +23,10 @@
import org.biojava.nbio.aaproperties.PeptideProperties;
import org.junit.Test;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+import jakarta.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
diff --git a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
index 37376b6bd0..26de47bf03 100644
--- a/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
+++ b/biojava-aa-prop/src/test/java/org/biojava/nbio/aaproperties/xml/ElementTest.java
@@ -20,18 +20,14 @@
*/
package org.biojava.nbio.aaproperties.xml;
-import org.biojava.nbio.aaproperties.xml.Element;
-import org.biojava.nbio.aaproperties.xml.ElementTable;
-import org.biojava.nbio.aaproperties.xml.Isotope;
-import org.biojava.nbio.aaproperties.xml.SchemaGenerator;
import org.junit.Test;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBException;
-import javax.xml.bind.Marshaller;
-import javax.xml.bind.Unmarshaller;
+import jakarta.xml.bind.JAXBContext;
+import jakarta.xml.bind.JAXBException;
+import jakarta.xml.bind.Marshaller;
+import jakarta.xml.bind.Unmarshaller;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
diff --git a/biojava-alignment/pom.xml b/biojava-alignment/pom.xml
index f342cebeef..fe75c181c7 100644
--- a/biojava-alignment/pom.xml
+++ b/biojava-alignment/pom.xml
@@ -4,7 +4,7 @@
biojava
org.biojava
- 5.4.0
+ 7.2.3-SNAPSHOT
biojava-alignment
biojava-alignment
@@ -47,7 +47,7 @@
org.biojava
biojava-core
- 5.4.0
+ 7.2.3-SNAPSHOT
compile
@@ -63,7 +63,7 @@
org.apache.logging.log4j
- log4j-slf4j-impl
+ log4j-slf4j2-impl
org.apache.logging.log4j
diff --git a/biojava-alignment/src/main/java/demo/CookbookMSA.java b/biojava-alignment/src/main/java/demo/CookbookMSA.java
index d2952bbeac..c617745539 100644
--- a/biojava-alignment/src/main/java/demo/CookbookMSA.java
+++ b/biojava-alignment/src/main/java/demo/CookbookMSA.java
@@ -43,7 +43,7 @@ public static void main(String[] args) throws Exception {
}
private static void multipleSequenceAlignment(String[] ids) throws Exception {
- List lst = new ArrayList();
+ List lst = new ArrayList<>();
for (String id : ids) {
lst.add(getSequenceForId(id));
}
diff --git a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
index c9f82d39f7..9215fa43dc 100644
--- a/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
+++ b/biojava-alignment/src/main/java/demo/DemoDistanceTree.java
@@ -22,6 +22,7 @@
import java.io.InputStream;
import java.util.LinkedHashMap;
+import java.util.Map;
import org.biojava.nbio.core.alignment.matrices.SubstitutionMatrixHelper;
import org.biojava.nbio.core.alignment.template.SubstitutionMatrix;
@@ -58,19 +59,19 @@ public static void main(String[] args) throws Exception {
.getResourceAsStream("/PF00104_small.fasta");
FastaReader fastaReader =
- new FastaReader(
+ new FastaReader<>(
inStream,
new GenericFastaHeaderParser(),
new ProteinSequenceCreator(AminoAcidCompoundSet
.getAminoAcidCompoundSet()));
- LinkedHashMap proteinSequences =
+ Map proteinSequences =
fastaReader.process();
inStream.close();
MultipleSequenceAlignment msa =
- new MultipleSequenceAlignment();
+ new MultipleSequenceAlignment<>();
for (ProteinSequence proteinSequence : proteinSequences.values()) {
msa.addAlignedSequence(proteinSequence);
diff --git a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
index 4ed72d0979..b389504826 100644
--- a/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
+++ b/biojava-alignment/src/main/java/org/biojava/nbio/alignment/Alignments.java
@@ -122,7 +122,7 @@ private Alignments() { }
* {@link ConcurrencyTools} utility.
*
* @param each {@link Sequence} of an alignment pair is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param sequences the {@link List} of {@link Sequence}s to align
* @param type chosen type from list of pairwise sequence alignment routines
* @param gapPenalty the gap penalties used during alignment
@@ -189,7 +189,7 @@ public static , C extends Compound> Profile getMulti
runPairwiseScorers(scorers);
// stage 2: hierarchical clustering into a guide tree
- GuideTree tree = new GuideTree(sequences, scorers);
+ GuideTree tree = new GuideTree<>(sequences, scorers);
scorers = null;
// stage 3: progressive alignment
@@ -203,7 +203,7 @@ public static , C extends Compound> Profile getMulti
* Factory method which computes a sequence alignment for the given {@link Sequence} pair.
*
* @param each {@link Sequence} of the pair is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param query the first {@link Sequence}s to align
* @param target the second {@link Sequence}s to align
* @param type chosen type from list of pairwise sequence alignment routines
@@ -223,7 +223,7 @@ public static , C extends Compound> SequencePair get
* Factory method which sets up a sequence alignment for all {@link Sequence} pairs in the given {@link List}.
*
* @param each {@link Sequence} of an alignment pair is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param sequences the {@link List} of {@link Sequence}s to align
* @param type chosen type from list of pairwise sequence alignment routines
* @param gapPenalty the gap penalties used during alignment
@@ -233,7 +233,7 @@ public static , C extends Compound> SequencePair get
static , C extends Compound> List> getAllPairsAligners(
List sequences, PairwiseSequenceAlignerType type, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
- List> allPairs = new ArrayList>();
+ List> allPairs = new ArrayList<>();
for (int i = 0; i < sequences.size(); i++) {
for (int j = i+1; j < sequences.size(); j++) {
allPairs.add(getPairwiseAligner(sequences.get(i), sequences.get(j), type, gapPenalty, subMatrix));
@@ -256,7 +256,7 @@ static , C extends Compound> List, C extends Compound> List> getAllPairsScorers(
List sequences, PairwiseSequenceScorerType type, GapPenalty gapPenalty,
SubstitutionMatrix subMatrix) {
- List> allPairs = new ArrayList>();
+ List> allPairs = new ArrayList<>();
for (int i = 0; i < sequences.size(); i++) {
for (int j = i+1; j < sequences.size(); j++) {
allPairs.add(getPairwiseScorer(sequences.get(i), sequences.get(j), type, gapPenalty, subMatrix));
@@ -291,7 +291,7 @@ public static , C extends Compound> double[] getAllPairsSc
* @return calculated elements
*/
static List getListFromFutures(List> futures) {
- List list = new ArrayList();
+ List list = new ArrayList<>();
for (Future f : futures) {
// TODO when added to ConcurrencyTools, log completions and exceptions instead of printing stack traces
try {
@@ -309,7 +309,7 @@ static List getListFromFutures(List> futures) {
* Factory method which constructs a pairwise sequence aligner.
*
* @param each {@link Sequence} of an alignment pair is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param query the first {@link Sequence} to align
* @param target the second {@link Sequence} to align
* @param type chosen type from list of pairwise sequence alignment routines
@@ -326,9 +326,9 @@ public static , C extends Compound> PairwiseSequenceAligne
switch (type) {
default:
case GLOBAL:
- return new NeedlemanWunsch(query, target, gapPenalty, subMatrix);
+ return new NeedlemanWunsch<>(query, target, gapPenalty, subMatrix);
case LOCAL:
- return new SmithWaterman(query, target, gapPenalty, subMatrix);
+ return new SmithWaterman<>(query, target, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case LOCAL_LINEAR_SPACE:
// TODO other alignment options (Myers-Miller, Thompson)
@@ -374,18 +374,18 @@ static , C extends Compound> PairwiseSequenceScorer
case GLOBAL:
return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix);
case GLOBAL_IDENTITIES:
- return new FractionalIdentityScorer(getPairwiseAligner(query, target,
+ return new FractionalIdentityScorer<>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
case GLOBAL_SIMILARITIES:
- return new FractionalSimilarityScorer(getPairwiseAligner(query, target,
+ return new FractionalSimilarityScorer<>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.GLOBAL, gapPenalty, subMatrix));
case LOCAL:
return getPairwiseAligner(query, target, PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix);
case LOCAL_IDENTITIES:
- return new FractionalIdentityScorer(getPairwiseAligner(query, target,
+ return new FractionalIdentityScorer<>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
case LOCAL_SIMILARITIES:
- return new FractionalSimilarityScorer(getPairwiseAligner(query, target,
+ return new FractionalSimilarityScorer<>(getPairwiseAligner(query, target,
PairwiseSequenceAlignerType.LOCAL, gapPenalty, subMatrix));
case KMERS:
case WU_MANBER:
@@ -399,7 +399,7 @@ static , C extends Compound> PairwiseSequenceScorer
* Factory method which constructs a profile-profile aligner.
*
* @param each {@link Sequence} of an alignment profile is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param profile1 the first {@link Profile} to align
* @param profile2 the second {@link Profile} to align
* @param type chosen type from list of profile-profile alignment routines
@@ -413,7 +413,7 @@ static , C extends Compound> ProfileProfileAligner g
switch (type) {
default:
case GLOBAL:
- return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix);
+ return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case GLOBAL_CONSENSUS:
case LOCAL:
@@ -429,7 +429,7 @@ static , C extends Compound> ProfileProfileAligner g
* Factory method which constructs a profile-profile aligner.
*
* @param each {@link Sequence} of an alignment profile is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param profile1 the first {@link Profile} to align
* @param profile2 the second {@link Profile} to align
* @param type chosen type from list of profile-profile alignment routines
@@ -443,7 +443,7 @@ static , C extends Compound> ProfileProfileAligner g
switch (type) {
default:
case GLOBAL:
- return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix);
+ return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case GLOBAL_CONSENSUS:
case LOCAL:
@@ -459,7 +459,7 @@ static , C extends Compound> ProfileProfileAligner g
* Factory method which constructs a profile-profile aligner.
*
* @param each {@link Sequence} of an alignment profile is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param profile1 the first {@link Profile} to align
* @param profile2 the second {@link Profile} to align
* @param type chosen type from list of profile-profile alignment routines
@@ -473,7 +473,7 @@ static , C extends Compound> ProfileProfileAligner g
switch (type) {
default:
case GLOBAL:
- return new SimpleProfileProfileAligner(profile1, profile2, gapPenalty, subMatrix);
+ return new SimpleProfileProfileAligner<>(profile1, profile2, gapPenalty, subMatrix);
case GLOBAL_LINEAR_SPACE:
case GLOBAL_CONSENSUS:
case LOCAL:
@@ -489,7 +489,7 @@ static , C extends Compound> ProfileProfileAligner g
* Factory method which constructs a profile-profile aligner.
*
* @param each {@link Sequence} of an alignment profile is of type S
- * @param each element of an {@link AlignedSequence} is a {@link Compound} of type C
+ * @param each element of a sequence is a {@link Compound} of type C
* @param profile1 the first {@link Profile} to align
* @param profile2 the second {@link Profile} to align
* @param type chosen type from list of profile-profile alignment routines
@@ -503,7 +503,7 @@ static , C extends Compound> ProfileProfileAligner
-[](https://travis-ci.org/biojava/biojava) [](https://github.com/biojava/biojava/releases/tag/biojava-5.3.0) [](https://github.com/biojava/biojava/blob/master/LICENSE) [](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
+
+[](https://github.com/biojava/biojava/releases/tag/biojava-7.2.2) [](https://github.com/biojava/biojava/blob/master/LICENSE) [](https://gitter.im/biojava/biojava?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge&utm_content=badge)
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, reference implementations of popular algorithms, and allows the manipulation of sequences and 3D structures. The goal of the biojava project is to facilitate rapid application development for bioinformatics.
@@ -17,7 +18,7 @@ Full javadocs are available at the [BioJava website](http://biojava.org/docs/api
### Maven Repository
-BioJava release are available from Maven Central. Snapshot builds are distributed using [OSS Sonatype](https://oss.sonatype.org/content/repositories/snapshots/org/biojava)
+BioJava release are available from Maven Central.
### Quick Installation
@@ -28,30 +29,21 @@ If you are using Maven you can add the BioJava repository by adding the followin