making output less verbose

andreasprlic · andreasprlic · commit 08ed01f6ff06 · 2016-08-18T15:27:29.000-07:00
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/PDBFileParser.java
@@ -1841,13 +1841,13 @@ private void  pdb_ATOM_Handler(String line)	{
 					element = Element.valueOfIgnoreCase(elementSymbol);
 					guessElement = false;
 				}  catch (IllegalArgumentException e){
-					logger.warn("Element {} of atom {} {} was not recognised. Assigning atom element "
+					logger.info("Element {} of atom {} {} was not recognised. Assigning atom element "
 							+ "from Chemical Component Dictionary information", elementSymbol, 
 							fullname.trim(), pdbnumber);
 				}
 			}
 		} else {
-			logger.warn("Missformatted PDB file: element column of atom {} {} is not present. "
+			logger.info("Missformatted PDB file: element column of atom {} {} is not present. "
 					+ "Assigning atom element from Chemical Component Dictionary information",
 					fullname.trim(), pdbnumber);
 		}
@@ -1861,14 +1861,14 @@ private void  pdb_ATOM_Handler(String line)	{
 					}
 				}
 				if (elementSymbol == null) {
-					logger.warn("Atom name {} was not found in the Chemical Component Dictionary information of {}. "
+					logger.info("Atom name {} was not found in the Chemical Component Dictionary information of {}. "
 							+ "Assigning generic element R to it", fullname.trim(), currentGroup.getPDBName());
 				} else {
 					try {
 						element = Element.valueOfIgnoreCase(elementSymbol);
 					} catch (IllegalArgumentException e) {
 						// this can still happen for cases like UNK
-						logger.warn("Element symbol {} found in chemical component dictionary for Atom {} {} could not be recognised as a known element. "
+						logger.info("Element symbol {} found in chemical component dictionary for Atom {} {} could not be recognised as a known element. "
 								+ "Assigning generic element R to it", elementSymbol, fullname.trim(), pdbnumber);
 					}
 				}			
@@ -3552,4 +3552,4 @@ public FileParsingParameters getFileParsingParameters(){
 	}
 
 
-}
+}

Original file line number	Diff line number	Diff line change
`@@ -1841,13 +1841,13 @@ private void pdb_ATOM_Handler(String line) {`
`1841`	`1841`	`element = Element.valueOfIgnoreCase(elementSymbol);`
`1842`	`1842`	`guessElement = false;`
`1843`	`1843`	`} catch (IllegalArgumentException e){`
`1844`		`- logger.warn("Element {} of atom {} {} was not recognised. Assigning atom element "`
	`1844`	`+ logger.info("Element {} of atom {} {} was not recognised. Assigning atom element "`
`1845`	`1845`	`+ "from Chemical Component Dictionary information", elementSymbol,`
`1846`	`1846`	`fullname.trim(), pdbnumber);`
`1847`	`1847`	`}`
`1848`	`1848`	`}`
`1849`	`1849`	`} else {`
`1850`		`- logger.warn("Missformatted PDB file: element column of atom {} {} is not present. "`
	`1850`	`+ logger.info("Missformatted PDB file: element column of atom {} {} is not present. "`
`1851`	`1851`	`+ "Assigning atom element from Chemical Component Dictionary information",`
`1852`	`1852`	`fullname.trim(), pdbnumber);`
`1853`	`1853`	`}`
`@@ -1861,14 +1861,14 @@ private void pdb_ATOM_Handler(String line) {`
`1861`	`1861`	`}`
`1862`	`1862`	`}`
`1863`	`1863`	`if (elementSymbol == null) {`
`1864`		`- logger.warn("Atom name {} was not found in the Chemical Component Dictionary information of {}. "`
	`1864`	`+ logger.info("Atom name {} was not found in the Chemical Component Dictionary information of {}. "`
`1865`	`1865`	`+ "Assigning generic element R to it", fullname.trim(), currentGroup.getPDBName());`
`1866`	`1866`	`} else {`
`1867`	`1867`	`try {`
`1868`	`1868`	`element = Element.valueOfIgnoreCase(elementSymbol);`
`1869`	`1869`	`} catch (IllegalArgumentException e) {`
`1870`	`1870`	`// this can still happen for cases like UNK`
`1871`		`- logger.warn("Element symbol {} found in chemical component dictionary for Atom {} {} could not be recognised as a known element. "`
	`1871`	`+ logger.info("Element symbol {} found in chemical component dictionary for Atom {} {} could not be recognised as a known element. "`
`1872`	`1872`	`+ "Assigning generic element R to it", elementSymbol, fullname.trim(), pdbnumber);`
`1873`	`1873`	`}`
`1874`	`1874`	`}`
`@@ -3552,4 +3552,4 @@ public FileParsingParameters getFileParsingParameters(){`
`3552`	`3552`	`}`
`3553`	`3553`
`3554`	`3554`
`3555`		`-}`
	`3555`	`+}`