Fix the compile errors - mainly by changin "setChainId" "setChainName"

abradle · abradle · commit a4f87958b9d6 · 2016-05-04T16:56:51.000-07:00
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/Test1o2f.java
@@ -40,9 +40,6 @@ protected void setUp() throws Exception {
 		AtomCache cache = new AtomCache();
 		cache.setUseMmCif(true);
 		cache.setFetchBehavior(FetchBehavior.FETCH_FILES);
-		FileParsingParameters params = cache.getFileParsingParams();
-		params.setUseInternalChainId(true);
-		cache.setFileParsingParams(params);
 		StructureIO.setAtomCache(cache);
 		String pdbId = "1O2F";
 		structure = StructureIO.getStructure(pdbId);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/ecod/EcodParseTest.java
@@ -125,7 +125,7 @@ private static int testVersion(String ecodVersion) throws IOException {
 				try {
 					Integer start = map.getPosition(range.getStart());
 					if(start == null) {
-						Group g = struct.getChainByPDB(range.getStart().getChainId()).getGroupByPDB(range.getStart());
+						Group g = struct.getChainByPDB(range.getStart().getChainName()).getGroupByPDB(range.getStart());
 						if(g!=null) {
 							logger.warn("No CA atom for starting residue "+d.getDomainId()+"_"+range);
 							clean = false;
@@ -143,7 +143,7 @@ private static int testVersion(String ecodVersion) throws IOException {
 					if(end == null) {
 						Group g = null;
 						try {
-							g = struct.getChainByPDB(range.getEnd().getChainId()).getGroupByPDB(range.getEnd());
+							g = struct.getChainByPDB(range.getEnd().getChainName()).getGroupByPDB(range.getEnd());
 						} catch(StructureException e ) {}
 						if(g!=null) {
 							logger.warn("No CA atom for ending residue "+d.getDomainId()+"_"+range);
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test3th3.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test3th3.java
@@ -45,10 +45,6 @@ public class Test3th3 {
 	@Test
 	public void test3th3() throws StructureException, IOException {
 		AtomCache cache = new AtomCache();
-
-		FileParsingParameters params = cache.getFileParsingParams();
-		params.setUseInternalChainId(false);
-		params.setCreateAtomBonds(true);
 		StructureIO.setAtomCache(cache);
 
 		Structure s = StructureIO.getStructure("3th3");
@@ -63,7 +59,7 @@ public void test3th3() throws StructureException, IOException {
 		Chain c = s.getChainByPDB("T");
 
 		ResidueNumber rn = ResidueNumber.fromString("201");
-		rn.setChainId("T");
+		rn.setChainName("T");
 
 		Group g = c.getGroupByPDB(rn);
 
diff --git a/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java b/biojava-integrationtest/src/test/java/org/biojava/nbio/structure/test/io/Test4v5a.java
@@ -46,7 +46,6 @@ public void test4v5a() throws StructureException, IOException {
 		AtomCache cache = new AtomCache();
 
 		FileParsingParameters params = cache.getFileParsingParams();
-		params.setUseInternalChainId(false);
 		params.setCreateAtomBonds(true);
 		StructureIO.setAtomCache(cache);
 
@@ -60,7 +59,6 @@ public void test4v5aInternalChainIds() throws StructureException, IOException {
 		AtomCache cache = new AtomCache();
 
 		FileParsingParameters params = cache.getFileParsingParams();
-		params.setUseInternalChainId(true);
 		params.setCreateAtomBonds(true);
 		StructureIO.setAtomCache(cache);
 
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/io/StructureGroupXMLConverter.java
@@ -52,7 +52,7 @@ public static StructureGroup fromXML(Node n) {
 		String isAminoAcid = getAttribute(n,"isAminoAcid");
 
 		ResidueNumber resNum = new ResidueNumber();
-		resNum.setChainId(chainID);
+		resNum.setChainName(chainID);
 		if ( ( insCode != null) && (! insCode.equals("null")) && insCode.length() == 1)
 		resNum.setInsCode(insCode.charAt(0));
 		resNum.setSeqNum(Integer.parseInt(resN));
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/ProteinModificationIdentifier.java
@@ -402,7 +402,7 @@ private void identifyAdditionalAttachments(ModifiedCompound mc,
 				//	numIns += num.getInsCode();
 				//}
 				ResidueNumber resNum = new ResidueNumber();
-				resNum.setChainId(num.getChainId());
+				resNum.setChainName(num.getChainId());
 				resNum.setSeqNum(num.getResidueNumber());
 				resNum.setInsCode(num.getInsCode());
 				//group = chain.getGroupByPDB(numIns);
diff --git a/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureGroup.java b/biojava-modfinder/src/main/java/org/biojava/nbio/protmod/structure/StructureGroup.java
@@ -62,13 +62,13 @@ public void setPDBResidueNumber(ResidueNumber resNum) {
 		this.resNum = resNum;
 	}
 	public String getChainId() {
-		return resNum.getChainId();
+		return resNum.getChainName();
 	}
 
 	public void setChainId(String chainId){
 		if ( resNum == null)
 			resNum = new ResidueNumber();
-		resNum.setChainId(chainId);
+		resNum.setChainName(chainId);
 	}
 
 	public int getResidueNumber() {
@@ -136,7 +136,7 @@ public String toString() {
 		StringBuilder sb = new StringBuilder();
 		sb.append(pdbName);
 		sb.append('\t');
-		sb.append(resNum.getChainId());
+		sb.append(resNum.getChainName());
 		sb.append('\t');
 		sb.append(resNum.getSeqNum());
 		if (resNum.getInsCode() != null)
diff --git a/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java b/biojava-structure-gui/src/main/java/demo/DemoStructureFromFasta.java
@@ -143,7 +143,7 @@ private static String buildJmolSelection(ResidueNumber[] residues) {
 			if(res != null) {
 				cmd.append(String.format("%d^%s:%s.CA or ", res.getSeqNum(),
 						res.getInsCode()==null?" ":res.getInsCode(),
-								res.getChainId()));
+								res.getChainName()));
 			}
 		}
 		cmd.append("none;");//easier than removing the railing 'or'

Original file line number	Diff line number	Diff line change
`@@ -143,7 +143,7 @@ private static String buildJmolSelection(ResidueNumber[] residues) {`
`143`	`143`	`if(res != null) {`
`144`	`144`	`cmd.append(String.format("%d^%s:%s.CA or ", res.getSeqNum(),`
`145`	`145`	`res.getInsCode()==null?" ":res.getInsCode(),`
`146`		`- res.getChainId()));`
	`146`	`+ res.getChainName()));`
`147`	`147`	`}`
`148`	`148`	`}`
`149`	`149`	`cmd.append("none;");//easier than removing the railing 'or'`