Removing additional newly deprecated methods

sbliven · sbliven · commit 4e0cdea72c9f · 2015-03-27T16:46:58.000+01:00
Also fixes a minor bug regarding modified amino acids listed as HETATM
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/PDBFileParserTest.java
@@ -505,7 +505,7 @@ public void test4hhbAcceptedAtomNames(){
 			Structure s = cache.getStructure("4HHB");
 
 			//System.out.println(s.toPDB());
-			Atom[] ca = StructureTools.getAtomCAArray(s);
+			Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
 			Atom[] cb = StructureTools.getAtomArray(s, new String[]{StructureTools.CB_ATOM_NAME,});
 
 			// gly does not have cb...
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/StructureToolsTest.java
@@ -89,7 +89,7 @@ protected void setUp() throws IOException
 
 
 	public void testGetCAAtoms(){
-		Atom[] cas = StructureTools.getAtomCAArray(structure);
+		Atom[] cas = StructureTools.getRepresentativeAtomArray(structure);
 		assertEquals("did not find the expected number of Atoms (58), but got " + cas.length,58,cas.length);
 	}
 
@@ -231,13 +231,13 @@ public void testRevisedConvention() throws IOException, StructureException{
 		assertTrue(s.getChains().size() == 1);
 		Chain c = s.getChainByPDB(chainId);
 		assertEquals(c.getChainID(),chainId);
-		Atom[] ca = StructureTools.getAtomCAArray(s);
+		Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
 		assertEquals(83,ca.length);
 
 		String name10 = "4hhb.C_1-83,A_1-10";
 		s = cache.getStructure(name10);
 		assertTrue(s.getChains().size() == 2);
-		ca = StructureTools.getAtomCAArray(s);
+		ca = StructureTools.getRepresentativeAtomArray(s);
 		assertEquals(93, ca.length);
 
 		
@@ -419,8 +419,8 @@ public void testCAmmCIF() throws StructureException {
 			assumeNoException(e);
 		}
 		
-		Atom[] pdbCA = StructureTools.getAtomCAArray(pdb);
-		Atom[] mmcifCA = StructureTools.getAtomCAArray(mmcif);
+		Atom[] pdbCA = StructureTools.getRepresentativeAtomArray(pdb);
+		Atom[] mmcifCA = StructureTools.getRepresentativeAtomArray(mmcif);
 		
 		assertEquals("PDB has wrong length",409,pdbCA.length);
 		assertEquals("PDB has wrong length",409,mmcifCA.length);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/AlignmentToolsTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/AlignmentToolsTest.java
@@ -396,8 +396,8 @@ public void testToConciseAlignmentString() {
 	 */
 	public void testUpdateSuperposition() throws IOException, StructureException {
 		Structure s = StructureTools.getStructure("31BI");
-		Atom[] ca1 = StructureTools.getAtomCAArray(s);
-		Atom[] ca2 = StructureTools.getAtomCAArray(s);
+		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s);
+		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s);
 		StringBuilder sb = new StringBuilder();
 		BufferedReader br = new BufferedReader(new FileReader("src/test/resources/align/31BI_symm_align.xml"));
 		String line = "";
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
@@ -77,8 +77,8 @@ private void flip(String name1, String name2, String algorithmName) throws Struc
 		Structure s1 = cache.getStructure(name1);
 		Structure s2 = cache.getStructure(name2);
 
-		Atom[] ca1 = StructureTools.getAtomCAArray(s1);
-		Atom[] ca2 = StructureTools.getAtomCAArray(s2);
+		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s1);
+		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s2);
 
 		StructureAlignment algorithm = StructureAlignmentFactory.getAlgorithm(algorithmName );
 		AFPChain afpChain = algorithm.align(ca1,ca2);
@@ -138,7 +138,7 @@ private void flip(String name1, String name2, String algorithmName) throws Struc
 	private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2) 
 	throws StructureException {
 
-		Atom[] ca2clone = StructureTools.cloneCAArray(ca2);
+		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
 		rotateAtoms2(afpChain,ca2clone);
 
 		// get only the subset of Atoms that is on structurally equivalent positions
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/ce/OptimalCECPMainTest.java
@@ -249,7 +249,7 @@ public void testPermuteOptAln() throws Exception {
 		Method permuteArray = OptimalCECPMain.class.getDeclaredMethod(
 				"permuteArray", Object[].class, int.class);
 		permuteArray.setAccessible(true);
-		Atom[] ca2p = StructureTools.cloneCAArray(ca2);
+		Atom[] ca2p = StructureTools.cloneAtomArray(ca2);
 		permuteArray.invoke(null, ca2p, 63);
 		
 		AFPChain cpAlignment = ce.align(ca1, ca2);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/AFPChainSerialisationTest.java
@@ -79,8 +79,8 @@ public void testSerialization1a21_1hwg(){
          Structure s2 = getStructure("1hwg","C");
 
 
-         Atom[] ca1 = StructureTools.getAtomCAArray(s1);
-         Atom[] ca2 = StructureTools.getAtomCAArray(s2);
+         Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s1);
+         Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s2);
 
          testAlignment("1a21.A","1hwg.C",ca1,ca2,false);
          testAlignment("1a21.A","1hwg.C",ca1,ca2,true);
@@ -147,7 +147,7 @@ private Structure getStructure(String pdbId, String chainId) throws IOException,
    private void testAlignment(String name1, String name2, Atom[] ca1, Atom[] ca2, boolean doRigid) throws StructureException,IOException{
 
 
-      Atom[] ca3 = StructureTools.cloneCAArray(ca2);
+      Atom[] ca3 = StructureTools.cloneAtomArray(ca2);
 
 
       AFPChain afpChain = doAlign(name1, name2, ca1,ca2,doRigid);
@@ -255,17 +255,17 @@ public void testMulti() throws IOException {
       try {
          Structure s1 = getStructure("5pti","A");
          Structure s2 = getStructure("1znf","A");
-         ca1 = StructureTools.getAtomCAArray(s1);
-         ca2 = StructureTools.getAtomCAArray(s2);
-         ca3 = StructureTools.cloneCAArray(ca2);
+         ca1 = StructureTools.getRepresentativeAtomArray(s1);
+         ca2 = StructureTools.getRepresentativeAtomArray(s2);
+         ca3 = StructureTools.cloneAtomArray(ca2);
 
          result1 = align(name1,name2,ca1, ca2,true);
 
          Structure s3 = getStructure("1hiv","A");
          Structure s4 = getStructure("1a4w","H");
-         ca4 = StructureTools.getAtomCAArray(s3);
-         ca5 = StructureTools.getAtomCAArray(s4);
-         ca6 = StructureTools.cloneCAArray(ca5);
+         ca4 = StructureTools.getRepresentativeAtomArray(s3);
+         ca5 = StructureTools.getRepresentativeAtomArray(s4);
+         ca6 = StructureTools.cloneAtomArray(ca5);
 
          result2 = align(name3,name4,ca4, ca5,true);
 
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
@@ -159,7 +159,7 @@ private void align (StructureAlignment algorithm, String name1, String name2)
 	private double getRMSD(AFPChain afpChain, Atom[] ca1, Atom[] ca2) 
 	throws StructureException {
 		
-		Atom[] ca2clone = StructureTools.cloneCAArray(ca2);
+		Atom[] ca2clone = StructureTools.cloneAtomArray(ca2);
 		rotateAtoms2(afpChain,ca2clone);
 		
 		// get only the subset of Atoms that is on structurally equivalent positions
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/MyTestHelper.java
@@ -82,8 +82,8 @@ public static String compareAlignment(String pdb1, String chain1, String pdb2, S
          Structure s4 = new StructureImpl();
          s4.addChain(c2);
 
-         Atom[] ca1 = StructureTools.getAtomCAArray(s3);
-         Atom[] ca2 = StructureTools.getAtomCAArray(s4);
+         Atom[] ca1 = StructureTools.getRepresentativeAtomArray(s3);
+         Atom[] ca2 = StructureTools.getRepresentativeAtomArray(s4);
 
          // keep an independent copy of them for tests further down..
          Atom[] ca3 = new Atom[ca2.length];
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/align/fatcat/TestFlexibleRotationMatrices.java
@@ -69,10 +69,10 @@ private void compare(String name1, String name2, boolean doRigid){
          Atom[] ca1orig = cache.getAtoms(name1);
          Atom[] ca2orig = cache.getAtoms(name2);
 
-         Atom[] ca1 = StructureTools.cloneCAArray(ca1orig);
-         Atom[] ca2 = StructureTools.cloneCAArray(ca2orig);
+         Atom[] ca1 = StructureTools.cloneAtomArray(ca1orig);
+         Atom[] ca2 = StructureTools.cloneAtomArray(ca2orig);
 
-         Atom[] ca3 = StructureTools.cloneCAArray(ca2);
+         Atom[] ca3 = StructureTools.cloneAtomArray(ca2);
 
          AFPChain afpChain = getAlignment(name1, name2, ca1, ca2, doRigid);
          afpChain.setCalculationTime(-1);
@@ -113,8 +113,8 @@ private void compare(String name1, String name2, boolean doRigid){
             }
 
 
-            Atom[] ca1new = StructureTools.cloneCAArray(ca1orig);
-            Atom[] ca2new = StructureTools.cloneCAArray(ca2orig);
+            Atom[] ca1new = StructureTools.cloneAtomArray(ca1orig);
+            Atom[] ca2new = StructureTools.cloneAtomArray(ca2orig);
 
             compareBlock(x,afpChain, newChain,ca1new,ca2new );
 
@@ -144,9 +144,9 @@ private void compareBlock(int blockNr, AFPChain afpChain, AFPChain newChain,
       
 
 
-      Atom[] ca1Copy = StructureTools.cloneCAArray(ca1);
-      Atom[] ca2Copy = StructureTools.cloneCAArray(ca2);
-      Atom[] ca2Copy2 = StructureTools.cloneCAArray(ca2);
+      Atom[] ca1Copy = StructureTools.cloneAtomArray(ca1);
+      Atom[] ca2Copy = StructureTools.cloneAtomArray(ca2);
+      Atom[] ca2Copy2 = StructureTools.cloneAtomArray(ca2);
 
      // int[][][] blocks1 = afpChain.getOptAln();
       int[][][] blocks2 = newChain.getOptAln();
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/AlignmentCalc.java
@@ -89,8 +89,8 @@ public void run() {
 		//aligner.setDebug(true);
 		try {
 
-			Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
-			Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
+			Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure1);
+			Atom[] ca2 = StructureTools.getRepresentativeAtomArray(structure2);
 
 			//System.out.println("ca1 size:" + ca1.length + " ca2 size: " + ca2.length);
 			AFPChain afpChain = algorithm.align(ca1, ca2);
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/DBResultTable.java
@@ -321,8 +321,8 @@ private void showAlignment( String name1, String name2){
 			Atom[] ca1;
 			Atom[] ca2;
 
-			ca1 = StructureTools.getAtomCAArray(structure1);
-			ca2 = StructureTools.getAtomCAArray(structure2);
+			ca1 = StructureTools.getRepresentativeAtomArray(structure1);
+			ca2 = StructureTools.getRepresentativeAtomArray(structure2);
 
 			AFPChain afpChain;
 
diff --git a/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java b/biojava-structure-gui/src/main/java/org/biojava/nbio/structure/align/gui/jmol/JmolPanel.java
@@ -291,7 +291,7 @@ private void colorByPDP() {
 			return;
 
 		try {
-			Atom[] ca = StructureTools.getAtomCAArray(structure);
+			Atom[] ca = StructureTools.getRepresentativeAtomArray(structure);
 			List<Domain> domains = LocalProteinDomainParser.suggestDomains(ca);
 			int i = -1;
 			for ( Domain dom : domains){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/StructureTools.java
@@ -806,6 +806,7 @@ public static Atom[] getRepresentativeAtomArray(Structure s){
 		for (Chain c: s.getChains()) {
 			for (Group g: c.getAtomGroups()) {
 				switch(g.getType()) {
+				default:
 				case AMINOACID:
 					if (g.hasAtom(CA_ATOM_NAME) && g.getAtom(CA_ATOM_NAME).getElement()==Element.C) {
 						atoms.add(g.getAtom(CA_ATOM_NAME));
@@ -816,8 +817,6 @@ public static Atom[] getRepresentativeAtomArray(Structure s){
 						atoms.add(g.getAtom(NUCLEOTIDE_REPRESENTATIVE));
 					}
 					break;
-				default:
-					// don't add
 				}
 			}
 		}
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/MultiThreadedDBSearch.java
@@ -269,7 +269,7 @@ public void run(){
 
 		ConcurrencyTools.setThreadPoolSize(nrCPUs);
 
-		Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
+		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure1);
 
 		int nrJobs = 0;
 		for (String repre : representatives){
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/align/ce/AbstractUserArgumentProcessor.java
@@ -374,8 +374,8 @@ private void runAlignPairs(AtomCache cache, String alignPairs,
 				Atom[] ca2;
 
 
-				ca1 = StructureTools.getAtomCAArray(structure1);
-				ca2 = StructureTools.getAtomCAArray(structure2);
+				ca1 = StructureTools.getRepresentativeAtomArray(structure1);
+				ca2 = StructureTools.getRepresentativeAtomArray(structure2);
 
 				Object jparams = getParameters();
 
@@ -490,8 +490,8 @@ private void runPairwise() throws ConfigurationException{
 			Atom[] ca1;
 			Atom[] ca2;
 
-			ca1 = StructureTools.getAtomCAArray(structure1);
-			ca2 = StructureTools.getAtomCAArray(structure2);
+			ca1 = StructureTools.getRepresentativeAtomArray(structure1);
+			ca2 = StructureTools.getRepresentativeAtomArray(structure2);
 
 			StructureAlignment algorithm =  getAlgorithm();
 			Object jparams = getParameters();
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/domain/LocalProteinDomainParser.java
@@ -64,7 +64,7 @@ private LocalProteinDomainParser(){
 	 */
 	public static List<Domain> suggestDomains(Structure s) throws StructureException{
 
-		Atom[] ca = StructureTools.getAtomCAArray(s);
+		Atom[] ca = StructureTools.getRepresentativeAtomArray(s);
 
 		return suggestDomains(ca);
 	} 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/FastaAFPChainConverter.java
@@ -137,8 +137,8 @@ public static AFPChain cpFastaToAfpChain(ProteinSequence first, ProteinSequence
 			gappedCpShift++;
 		}
 
-		Atom[] ca1 = StructureTools.getAtomCAArray(structure);
-		Atom[] ca2 =  StructureTools.getAtomCAArray(structure); // can't use cloneCAArray because it doesn't set parent group.chain.structure
+		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure);
+		Atom[] ca2 =  StructureTools.getRepresentativeAtomArray(structure); // can't use cloneCAArray because it doesn't set parent group.chain.structure
 		
 		ProteinSequence antipermuted = null;
 		try {
@@ -283,8 +283,8 @@ public static AFPChain fastaToAfpChain(ProteinSequence sequence1, ProteinSequenc
 			throw new IllegalArgumentException("A sequence is null");
 		}
 
-		Atom[] ca1 = StructureTools.getAtomCAArray(structure1);
-		Atom[] ca2 = StructureTools.getAtomCAArray(structure2);
+		Atom[] ca1 = StructureTools.getRepresentativeAtomArray(structure1);
+		Atom[] ca2 = StructureTools.getRepresentativeAtomArray(structure2);
 
 		ResidueNumber[] residues1 = StructureSequenceMatcher.matchSequenceToStructure(sequence1, structure1);
 		ResidueNumber[] residues2 = StructureSequenceMatcher.matchSequenceToStructure(sequence2, structure2);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestAltLocs.java
@@ -121,7 +121,7 @@ public void test2W72() throws IOException, StructureException{
 		Atom ca7 = lys7.getAtom("CA");			
 		assertNotNull(ca7);
 
-		Atom[] caA = StructureTools.getAtomCAArray(a);
+		Atom[] caA = StructureTools.getRepresentativeAtomArray(a);
 
 		assertEquals(caA.length,141);
 
@@ -253,7 +253,7 @@ public void test3PIUpdb() throws IOException, StructureException{
 
 		assertNotNull(structure);
 
-		Atom[] ca = StructureTools.getAtomCAArray(structure);
+		Atom[] ca = StructureTools.getRepresentativeAtomArray(structure);
 
 		//System.out.println(structure.getPdbId() + " has # CA atoms: " + ca.length);
 
@@ -314,7 +314,7 @@ public void test3PIUmmcif() throws IOException, StructureException{
 
 		assertNotNull(structure);
 
-		Atom[] ca = StructureTools.getAtomCAArray(structure);
+		Atom[] ca = StructureTools.getRepresentativeAtomArray(structure);
 
 		//System.out.println(structure.getPdbId() + " has # CA atoms: " + ca.length);
 
@@ -379,7 +379,7 @@ public void test3U7Tmmcif() throws IOException, StructureException{
 
 		assertNotNull(structure);
 
-		Atom[] ca = StructureTools.getAtomCAArray(structure);
+		Atom[] ca = StructureTools.getRepresentativeAtomArray(structure);
 
 		//System.out.println(structure.getPdbId() + " has # CA atoms: " + ca.length);
 
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/TestParsingCalcium.java
@@ -79,14 +79,14 @@ public void testCAreturnsCalpha() throws IOException, StructureException {
 		AtomCache cache = new AtomCache();
 		Structure s = cache.getStructure(pdbID);
 		
-		Atom[] atoms = StructureTools.getAtomCAArray(s);
+		Atom[] atoms = StructureTools.getRepresentativeAtomArray(s);
 		for (Atom atom:atoms) {
 			assertTrue("atom "+atom.getPDBserial()+" of residue "+atom.getGroup().getResidueNumber()+"-"+atom.getGroup().getPDBName()+
 					" is not a Carbon alpha", atom.getElement()==Element.C);
 		}
 		
 		for (Chain c:s.getChains()) {
-			atoms = StructureTools.getAtomCAArray(c);
+			atoms = StructureTools.getRepresentativeAtomArray(c);
 			for (Atom atom:atoms) {
 				assertTrue("atom "+atom.getPDBserial()+" of residue "+atom.getGroup().getResidueNumber()+"-"+atom.getGroup().getPDBName()+
 						" is not a Carbon alpha", atom.getElement()==Element.C);
diff --git a/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java b/biojava-structure/src/test/java/org/biojava/nbio/structure/contact/TestContactCalc.java
@@ -72,7 +72,7 @@ public void testIntraChainContacts() throws StructureException, IOException {
 				
 				AtomContactSet atomContacts = null;
 				if (cts[i]!=null && cts[i][0].equals("CA")) {
-					atomContacts = StructureTools.getAtomsCAInContact(chain, cutoffs[i]);
+					atomContacts = StructureTools.getRepresentativeAtomsInContact(chain, cutoffs[i]);
 				} else {
 					atomContacts = StructureTools.getAtomsInContact(chain, cts[i], cutoffs[i]);
 				}
