Merge pull request #1002 from aalhossary/miscellaneous

aalhossary · web-flow · commit c8a3ca3c1bec · 2021-12-06T11:59:43.000+08:00
Miscellaneous
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/alignment/matrices/SubstitutionMatrixTest.java
@@ -54,8 +54,8 @@ void getMatrixReturnsCopy(){
     void matrixToString(){
         String asString = sm.toString();
         // description + 5*2 for ATCGNatcgn + 1 header + 1  for '-'
-        assertEquals(13, asString.split("\n").length);
-        String header = asString.split("\r?\n")[1];
+        assertEquals(13, asString.split("\\n").length);
+        String header = asString.split("\\R")[1];
         assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));
     }
 
@@ -64,8 +64,8 @@ void matrixAsString(){
         String asString = sm.getMatrixAsString();
 
         // 5*2 for ATCGNatcgn + 1 header + 1  for '-'
-        assertEquals(12, asString.split("\n").length);
-        String header = asString.split("\r?\n")[0];
+        assertEquals(12, asString.split("\\n").length);
+        String header = asString.split("\\R")[0];
         assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));
     }
 }
diff --git a/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaGeneWriterTest.java b/biojava-core/src/test/java/org/biojava/nbio/core/sequence/io/FastaGeneWriterTest.java
@@ -58,7 +58,7 @@ void basicGeneWriterTest() throws Exception {
         fastaWriter.process();
 
         String output = new String(os.toByteArray(), "UTF-8");
-        String [] lines =  output.split("\n");
+        String [] lines =  output.split("\\R");
         assertEquals(4,lines.length);
         assertEquals(">gene1", lines[0]);
         assertEquals("ATATATATATaTATAtatat", lines[1]);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/FlipAFPChainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/FlipAFPChainTest.java
@@ -185,10 +185,9 @@ public static void rotateAtoms2(AFPChain afpChain,Atom[] ca2){
 	}
 
 
-	private static final String newline = System.getProperty("line.separator");
 	private void printFirstMismatch(String s1, String s2){
-		String[] spl1 = s1.split(newline);
-		String[] spl2 = s2.split(newline);
+		String[] spl1 = s1.split("\\R");
+		String[] spl2 = s2.split("\\R");
 
 		for (int i = 0 ; i < spl1.length ; i++){
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/FlipAFPChainTest.java
@@ -204,10 +204,9 @@ public static void rotateAtoms2(AFPChain afpChain,Atom[] ca2){
 	}
 
 
-	static final String newline = System.getProperty("line.separator");
 	public void printFirstMismatch(String s1, String s2){
-		String[] spl1 = s1.split(newline);
-		String[] spl2 = s2.split(newline);
+		String[] spl1 = s1.split("\\R");
+		String[] spl2 = s2.split("\\R");
 
 		for (int i = 0 ; i < spl1.length ; i++){
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestOutputStrings.java
@@ -28,8 +28,8 @@ public class TestOutputStrings {
 	private static final String newline = System.getProperty("line.separator");
 
 	public void printFirstMismatch(String s1, String s2){
-		String[] spl1 = s1.split(newline);
-		String[] spl2 = s2.split(newline);
+		String[] spl1 = s1.split("\\R");
+		String[] spl2 = s2.split("\\R");
 
 		for (int i = 0 ; i < spl1.length ; i++){
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/BondImpl.java
@@ -175,9 +175,7 @@ public int getBondOrder() {
 	/**
 	 * Gets the distance between the two atoms of this bond.
 	 * <p>
-	 * This distance is calculated by {@link Calc#getDistance(Atom, Atom)}, but
-	 * this method will suppress the empty threat of a
-	 * {@link StructureException} that method makes.
+	 * This distance is calculated by {@link Calc#getDistance(Atom, Atom)}.
 	 *
 	 * @return the distance between the two atoms of this bond.
 	 */
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/HetatomImpl.java
@@ -168,7 +168,7 @@ public void addAtom(Atom atom){
 				String altLocStr = "";
 				char altLoc = atom.getAltLoc();
 				if (altLoc != ' ') altLocStr = "(alt loc '" + altLoc + "')";
-				logger.warn("An atom with name " + atom.getName() + " " + altLocStr + " is already present in group: " + this.toString() + ". The atom with serial " + atom.getPDBserial() + " will be ignored in look-ups.");
+				logger.warn("An atom with name " + atom.getName() + " " + altLocStr + " is already present in group: " + this.toString() + ". The atom with serial " + existingAtom.getPDBserial() + " will be ignored in look-ups.");
 			}
 		}
 	}

Original file line number	Diff line number	Diff line change
`@@ -54,8 +54,8 @@ void getMatrixReturnsCopy(){`
`54`	`54`	`void matrixToString(){`
`55`	`55`	`String asString = sm.toString();`
`56`	`56`	`// description + 5*2 for ATCGNatcgn + 1 header + 1 for '-'`
`57`		`- assertEquals(13, asString.split("\n").length);`
`58`		`- String header = asString.split("\r?\n")[1];`
	`57`	`+ assertEquals(13, asString.split("\\n").length);`
	`58`	`+ String header = asString.split("\\R")[1];`
`59`	`59`	`assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));`
`60`	`60`	`}`
`61`	`61`
`@@ -64,8 +64,8 @@ void matrixAsString(){`
`64`	`64`	`String asString = sm.getMatrixAsString();`
`65`	`65`
`66`	`66`	`// 5*2 for ATCGNatcgn + 1 header + 1 for '-'`
`67`		`- assertEquals(12, asString.split("\n").length);`
`68`		`- String header = asString.split("\r?\n")[0];`
	`67`	`+ assertEquals(12, asString.split("\\n").length);`
	`68`	`+ String header = asString.split("\\R")[0];`
`69`	`69`	`assertTrue(header.replaceAll(" ","").matches("[ATCGatcgNn-]+"));`
`70`	`70`	`}`
`71`	`71`	`}`
Original file line number	Diff line number	Diff line change
`@@ -185,10 +185,9 @@ public static void rotateAtoms2(AFPChain afpChain,Atom[] ca2){`
`185`	`185`	`}`
`186`	`186`
`187`	`187`
`188`		`- private static final String newline = System.getProperty("line.separator");`
`189`	`188`	`private void printFirstMismatch(String s1, String s2){`
`190`		`- String[] spl1 = s1.split(newline);`
`191`		`- String[] spl2 = s2.split(newline);`
	`189`	`+ String[] spl1 = s1.split("\\R");`
	`190`	`+ String[] spl2 = s2.split("\\R");`
`192`	`191`
`193`	`192`	`for (int i = 0 ; i < spl1.length ; i++){`
`194`	`193`
Original file line number	Diff line number	Diff line change
`@@ -204,10 +204,9 @@ public static void rotateAtoms2(AFPChain afpChain,Atom[] ca2){`
`204`	`204`	`}`
`205`	`205`
`206`	`206`
`207`		`- static final String newline = System.getProperty("line.separator");`
`208`	`207`	`public void printFirstMismatch(String s1, String s2){`
`209`		`- String[] spl1 = s1.split(newline);`
`210`		`- String[] spl2 = s2.split(newline);`
	`208`	`+ String[] spl1 = s1.split("\\R");`
	`209`	`+ String[] spl2 = s2.split("\\R");`
`211`	`210`
`212`	`211`	`for (int i = 0 ; i < spl1.length ; i++){`
`213`	`212`
Original file line number	Diff line number	Diff line change
`@@ -168,7 +168,7 @@ public void addAtom(Atom atom){`
`168`	`168`	`String altLocStr = "";`
`169`	`169`	`char altLoc = atom.getAltLoc();`
`170`	`170`	`if (altLoc != ' ') altLocStr = "(alt loc '" + altLoc + "')";`
`171`		`- logger.warn("An atom with name " + atom.getName() + " " + altLocStr + " is already present in group: " + this.toString() + ". The atom with serial " + atom.getPDBserial() + " will be ignored in look-ups.");`
	`171`	`+ logger.warn("An atom with name " + atom.getName() + " " + altLocStr + " is already present in group: " + this.toString() + ". The atom with serial " + existingAtom.getPDBserial() + " will be ignored in look-ups.");`
`172`	`172`	`}`
`173`	`173`	`}`
`174`	`174`	`}`