biojava#360 improving class and method names

andreasprlic · andreasprlic · commit d4597c48c59e · 2016-01-08T10:58:20.000-08:00
diff --git a/biojava-structure/src/main/java/demo/DemoSecStrucCalc.java b/biojava-structure/src/main/java/demo/DemoSecStrucCalc.java
@@ -27,7 +27,7 @@
 import org.biojava.nbio.structure.StructureException;
 import org.biojava.nbio.structure.align.util.AtomCache;
 import org.biojava.nbio.structure.secstruc.SecStrucElement;
-import org.biojava.nbio.structure.secstruc.SecStrucPred;
+import org.biojava.nbio.structure.secstruc.SecStrucCalc;
 import org.biojava.nbio.structure.secstruc.SecStrucTools;
 
 /**
@@ -38,7 +38,7 @@
  * @author Aleix Lafita
  *
  */
-public class DemoSecStrucPred {
+public class DemoSecStrucCalc {
 
 	public static void main(String[] args) throws IOException,
 			StructureException {
@@ -51,8 +51,8 @@ public static void main(String[] args) throws IOException,
 		Structure s = cache.getStructure(pdbID);
 
 		// Predict and assign the SS of the Structure
-		SecStrucPred ssp = new SecStrucPred();
-		ssp.predict(s, true);
+		SecStrucCalc ssp = new SecStrucCalc();
+		ssp.calculate(s, true);
 
 		// Print the DSSP output
 		System.out.println("******DSSP output: ");
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/secstruc/SecStrucCalc.java
@@ -43,7 +43,7 @@
  * @author Aleix Lafita
  * 
  */
-public class SecStrucPred {
+public class SecStrucCalc {
 	
 	/** 
 	 * DSSP assigns helices one residue shorter at each end, because the
@@ -55,7 +55,7 @@ public class SecStrucPred {
 	private static final boolean DSSP_HELICES = true;
 
 	private static final Logger logger = 
-			LoggerFactory.getLogger(SecStrucPred.class);
+			LoggerFactory.getLogger(SecStrucCalc.class);
 
 	/** min distance between two residues */
 	public static final double MINDIST = 0.5;
@@ -87,7 +87,7 @@ public class SecStrucPred {
 	private List<Ladder> ladders;
 	private List<BetaBridge> bridges;
 
-	public SecStrucPred(){
+	public SecStrucCalc(){
 		ladders = new ArrayList<Ladder>();
 		bridges = new ArrayList<BetaBridge>();
 	}
@@ -100,7 +100,7 @@ public SecStrucPred(){
 	 * @param assign sets the SS information to the Groups of s
 	 * @return a List of SS annotation objects
 	 */
-	public List<SecStrucState> predict(Structure s, boolean assign) 
+	public List<SecStrucState> calculate(Structure s, boolean assign)
 			throws StructureException {
 
 		groups = initGroupArray(s);
@@ -558,9 +558,9 @@ public String printFASTA() {
 	@Override
 	public boolean equals(Object o){
 		
-		if (!(o instanceof SecStrucPred)) return false;
+		if (!(o instanceof SecStrucCalc)) return false;
 		else {
-			SecStrucPred ss = (SecStrucPred) o;
+			SecStrucCalc ss = (SecStrucCalc) o;
 			if (groups.length != ss.groups.length) return false;
 			
 			for (int g=0; g<groups.length; g++){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/symmetry/internal/CeSymm.java
@@ -41,7 +41,7 @@
 import org.biojava.nbio.structure.align.multiple.util.MultipleAlignmentScorer;
 import org.biojava.nbio.structure.align.util.AFPChainScorer;
 import org.biojava.nbio.structure.jama.Matrix;
-import org.biojava.nbio.structure.secstruc.SecStrucPred;
+import org.biojava.nbio.structure.secstruc.SecStrucCalc;
 import org.biojava.nbio.structure.secstruc.SecStrucTools;
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.RefineMethod;
 import org.biojava.nbio.structure.symmetry.internal.CESymmParameters.SymmetryType;
@@ -410,8 +410,8 @@ public MultipleAlignment analyze(Atom[] atoms, CESymmParameters param)
 		if (params.getSSEThreshold() > 0) {
 			Structure s = atoms[0].getGroup().getChain().getStructure();
 			if (SecStrucTools.getSecStrucInfo(s).isEmpty()){
-				SecStrucPred ssp = new SecStrucPred();
-				ssp.predict(s, true);
+				SecStrucCalc ssp = new SecStrucCalc();
+				ssp.calculate(s, true);
 			}
 		}
 		
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestDSSPParser.java
@@ -59,8 +59,8 @@ public void testDSSPParser() throws IOException, StructureException {
 			List<SecStrucState> pdb = DSSPParser.fetch(name, s, false);
 
 			// Test predicting, writting and parsing back
-			SecStrucPred sec = new SecStrucPred();
-			List<SecStrucState> pred = sec.predict(s, false);
+			SecStrucCalc sec = new SecStrucCalc();
+			List<SecStrucState> pred = sec.calculate(s, false);
 
 			List<SecStrucState> parseBack = DSSPParser.parseString(
 					sec.toString(), s, false);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucPred.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/secstruc/TestSecStrucPred.java
@@ -60,8 +60,8 @@ public void testSecStrucPred() throws StructureException, IOException {
 			Structure s = cache.getStructure(name);
 			
 			//Predict with BioJava the SS
-			SecStrucPred sec = new SecStrucPred();
-			List<SecStrucState> biojava = sec.predict(s, true);
+			SecStrucCalc sec = new SecStrucCalc();
+			List<SecStrucState> biojava = sec.calculate(s, true);
 			
 			//Download the original DSSP implementation output
 			List<SecStrucState> dssp = DSSPParser.fetch(name, s, false);
