refactored code to use java 8 streams

balaji-s · balaji-s · commit a39bd7d8ab9e · 2020-06-11T21:39:09.000+05:30
diff --git a/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java b/biojava-aa-prop/src/main/java/org/biojava/nbio/aaproperties/CommandPrompt.java
@@ -327,9 +327,7 @@ private static void compute(PrintStream output, String header, String sequence,
 			}
 		}
 		output.print(header.replace(delimiter, "_"));
-		for(int i = 0; i < dList.size(); i++){
-			output.print(delimiter + Utils.roundToDecimals(dList.get(i), decimalPlace));
-		}
+		dList.forEach(item -> System.out.print(delimiter + Utils.roundToDecimals(dList.get(item), decimalPlace)));
 		output.println();
 		output.flush();
 	}
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
@@ -31,10 +31,12 @@
 import javax.xml.bind.JAXBException;
 import java.io.File;
 import java.io.FileNotFoundException;
+import java.util.Arrays;
 import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
+import java.util.stream.Collectors;
 
 /**
  * This is an adaptor class which enable the ease of generating protein properties.
@@ -64,8 +66,9 @@ public enum SingleLetterAACode { W, C, M, H, Y, F, Q, N, I, R, D, P, T, K, E, V,
 	 * To initialize the standardAASet
 	 */
 	static{
-		standardAASet = new HashSet<Character>();
-		for(SingleLetterAACode c:SingleLetterAACode.values()) standardAASet.add(c.toString().charAt(0));
+		standardAASet = Arrays.stream(SingleLetterAACode.values())
+                                      .map(singleLetterAACode -> singleLetterAACode.toString().charAt(0))
+                        .             .collect(Collectors.toCollection(HashSet::new));
 	}
 
 	/**
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java b/biojava-core/src/main/java/org/biojava/nbio/core/sequence/template/AbstractNucleotideCompoundSet.java
@@ -23,6 +23,7 @@
 import org.biojava.nbio.core.sequence.compound.NucleotideCompound;
 
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  *
@@ -66,13 +67,10 @@ protected void addNucleotideCompound(String base, String complement, String... e
 	protected void calculateIndirectAmbiguities() {
 		Map<NucleotideCompound, List<NucleotideCompound>> equivalentsMap = new HashMap<NucleotideCompound, List<NucleotideCompound>>();
 
-		List<NucleotideCompound> ambiguousCompounds = new ArrayList<NucleotideCompound>();
-		for(NucleotideCompound compound: getAllCompounds()) {
-			if (!compound.isAmbiguous()) {
-				continue;
-			}
-			ambiguousCompounds.add(compound);
-		}
+		List<NucleotideCompound> ambiguousCompounds = getAllCompounds().stream()		 
+                                                                               .filter(compound -> compound.isAmbiguous())
+                                                                               .collect(Collectors.toCollection(ArrayList::new));
+                        
 
 		for(NucleotideCompound sourceCompound: ambiguousCompounds) {
 			Set<NucleotideCompound> compoundConstituents = sourceCompound.getConstituents();

Original file line number	Diff line number	Diff line change
`@@ -327,9 +327,7 @@ private static void compute(PrintStream output, String header, String sequence,`
`327`	`327`	`}`
`328`	`328`	`}`
`329`	`329`	`output.print(header.replace(delimiter, "_"));`
`330`		`- for(int i = 0; i < dList.size(); i++){`
`331`		`- output.print(delimiter + Utils.roundToDecimals(dList.get(i), decimalPlace));`
`332`		`- }`
	`330`	`+ dList.forEach(item -> System.out.print(delimiter + Utils.roundToDecimals(dList.get(item), decimalPlace)));`
`333`	`331`	`output.println();`
`334`	`332`	`output.flush();`
`335`	`333`	`}`