Merge pull request #927 from josemduarte/cif-passparams

josemduarte · web-flow · commit dba397f6b60d · 2021-04-13T18:43:30.000-07:00
Cif reader file parsing parameters fix
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/URLIdentifier.java
@@ -153,7 +153,7 @@ public Structure loadStructure(AtomCache cache) throws StructureException, IOExc
 
 		switch(format) {
 			case CIF: case BCIF:
-				return CifStructureConverter.fromURL(url);
+				return CifStructureConverter.fromURL(url, cache.getFileParsingParams());
 			case MMTF:
 				return MmtfActions.readFromInputStream(url.openStream());
 			default: case PDB:
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConverter.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/cif/CifStructureConverter.java
@@ -57,7 +57,7 @@ public static Structure fromURL(URL url) throws IOException {
      * @return the target
      * @throws IOException thrown when reading fails
      */
-    private static Structure fromURL(URL url, FileParsingParameters parameters) throws IOException {
+    public static Structure fromURL(URL url, FileParsingParameters parameters) throws IOException {
         return fromInputStream(url.openStream(), parameters);
     }
 

Original file line number	Diff line number	Diff line change
`@@ -57,7 +57,7 @@ public static Structure fromURL(URL url) throws IOException {`
`57`	`57`	`* @return the target`
`58`	`58`	`* @throws IOException thrown when reading fails`
`59`	`59`	`*/`
`60`		`- private static Structure fromURL(URL url, FileParsingParameters parameters) throws IOException {`
	`60`	`+ public static Structure fromURL(URL url, FileParsingParameters parameters) throws IOException {`
`61`	`61`	`return fromInputStream(url.openStream(), parameters);`
`62`	`62`	`}`
`63`	`63`