Cosmetics

josemduarte · josemduarte · commit 747633fc870d · 2019-09-02T15:10:53.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfStructureReader.java
@@ -229,7 +229,7 @@ public void setGroupInfo(String groupName, int groupNumber,
 			group = new HetatomImpl();
 			break;
 		}
-		atomsInGroup = new ArrayList<Atom>();
+		atomsInGroup = new ArrayList<>();
 		ChemComp chemComp = new ChemComp();
 		chemComp.setOne_letter_code(String.valueOf(singleLetterCode));
 		chemComp.setType(chemCompType.toUpperCase());
@@ -243,7 +243,7 @@ public void setGroupInfo(String groupName, int groupNumber,
 			group.setResidueNumber(chain.getName().trim(),
 					groupNumber, insertionCode);
 		}
-		group.setAtoms(new ArrayList<Atom>(atomCount));
+		group.setAtoms(new ArrayList<>(atomCount));
 		if (polymerType==1 || polymerType==2) {
 			MmtfUtils.insertSeqResGroup(chain, group, sequenceIndexId);
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmtf/MmtfUtils.java
@@ -371,7 +371,7 @@ public static int getSecStructType(Group group) {
 	/**
 	 * Get the secondary structure as defined by DSSP.
 	 * @param group the input group to be calculated
-	 * @param the integer index of the group type.
+	 * @param dsspIndex integer index of the group type.
 	 */
 	public static void setSecStructType(Group group, int dsspIndex) {
 		SecStrucType secStrucType = getSecStructTypeFromDsspIndex(dsspIndex);
@@ -508,9 +508,7 @@ public static void addSeqRes(Chain modelChain, String sequence) {
 			
 			char singleLetterCode = sequence.charAt(i);
 			Group group = null;
-			if(seqResGroups.size()<=i){
-			}
-			else{
+			if (seqResGroups.size() > i) {
 				group=seqResGroups.get(i);
 			}
 			if(group!=null){
@@ -525,10 +523,7 @@ public static void addSeqRes(Chain modelChain, String sequence) {
 
 	private static GroupType getChainType(List<Group> groups) {
 		for(Group group : groups) {
-			if(group==null){
-				continue;
-			}
-			else if(group.getType()!=GroupType.HETATM){
+			if(group!=null && group.getType()!=GroupType.HETATM){
 				return group.getType();
 			}
 		}
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/io/mmtf/TestMmtfStructureReader.java
@@ -64,8 +64,6 @@ public void compareMmcif() throws IOException, StructureException {
 		assertEquals(mmcif.getPDBHeader().getExperimentalTechniques(), 
 				mmtf.getPDBHeader().getExperimentalTechniques());
 		
-		
-		
 		// Compare the SEQRES
 		assertEquals(mmcif.getChainByIndex(0).getSeqResSequence(), 
 				mmtf.getChainByIndex(0).getSeqResSequence());

Original file line number	Diff line number	Diff line change
`@@ -229,7 +229,7 @@ public void setGroupInfo(String groupName, int groupNumber,`
`229`	`229`	`group = new HetatomImpl();`
`230`	`230`	`break;`
`231`	`231`	`}`
`232`		`- atomsInGroup = new ArrayList<Atom>();`
	`232`	`+ atomsInGroup = new ArrayList<>();`
`233`	`233`	`ChemComp chemComp = new ChemComp();`
`234`	`234`	`chemComp.setOne_letter_code(String.valueOf(singleLetterCode));`
`235`	`235`	`chemComp.setType(chemCompType.toUpperCase());`
`@@ -243,7 +243,7 @@ public void setGroupInfo(String groupName, int groupNumber,`
`243`	`243`	`group.setResidueNumber(chain.getName().trim(),`
`244`	`244`	`groupNumber, insertionCode);`
`245`	`245`	`}`
`246`		`- group.setAtoms(new ArrayList<Atom>(atomCount));`
	`246`	`+ group.setAtoms(new ArrayList<>(atomCount));`
`247`	`247`	`if (polymerType==1 \|\| polymerType==2) {`
`248`	`248`	`MmtfUtils.insertSeqResGroup(chain, group, sequenceIndexId);`
`249`	`249`	`}`