A bunch of small fixes, mostly docs and logs

josemduarte · josemduarte · commit 6e6ba98cbace · 2016-01-27T21:01:30.000-08:00
diff --git a/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java b/biojava-core/src/main/java/org/biojava/nbio/core/util/InputStreamProvider.java
@@ -78,8 +78,10 @@ public InputStreamProvider() {
 
    }
 
-   /** get an InputStream for this file 
-    * 
+   /** 
+    * Get an InputStream for given file path.
+    * The caller is responsible for closing the stream or otherwise 
+    * a resource leak can occur.
     * @param pathToFile the path of the file.
     * @return an InputStream for the file located at the path.
     * @throws IOException
@@ -144,8 +146,10 @@ public InputStream getInputStream(URL u)
    }
 
 
-   /** get an InputStream for the file
-    * 
+   /** 
+    * Get an InputStream for the file.
+    * The caller is responsible for closing the stream or otherwise 
+    * a resource leak can occur.
     * @param f a File
     * @return an InputStream for the file
     * @throws IOException
@@ -229,7 +233,8 @@ else if ( fileName.endsWith(".Z")) {
    }
 
 
-   /** Wrapper for new FileInputStream. if System.property biojava.cache.files is set, will try to load files from memory cache.
+   /** 
+    * Wrapper for new FileInputStream. if System.property biojava.cache.files is set, will try to load files from memory cache.
     * 
     * @param f
     * @return
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/contact/Grid.java
@@ -35,7 +35,10 @@
  */
 public class Grid {
 	
-	private static final int SCALE=100; // i.e. we use units of hundreds of Amstrongs (thus cutoffs can be specified with a maximum precision of 0.01A)
+	/**
+	 * The scale: we use units of hundredths of Angstroms (thus cutoffs can be specified with a maximum precision of 0.01A)
+	 */
+	private static final int SCALE=100;
 	
 	private GridCell[][][] cells;
 	
@@ -160,7 +163,6 @@ public void addAtoms(Atom[] atoms, BoundingBox bounds) {
 	 * the 2 grids (i and j) are no more than one cell size apart. If they don't
 	 * overlap then they are too far apart so there's nothing to calculate, we set
 	 * the noOverlap flag and then {@link #getContacts()} will do no calculation at all.
-
 	 */
 	private void fillGrid() {
 
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/DownloadChemCompProvider.java
@@ -212,7 +212,8 @@ private void writeID(StringWriter writer, String currentID) throws IOException{
 
 	}
 
-	/** Loads the definitions for this {@link ChemComp} from a local file and instantiates a new object.
+	/** 
+	 * Loads the definitions for this {@link ChemComp} from a local file and instantiates a new object.
 	 * 
 	 * @param recordName the ID of the {@link ChemComp}
 	 * @return a new {@link ChemComp} definition.
@@ -263,7 +264,8 @@ public  ChemComp getChemComp(String recordName) {
 
 		} catch (IOException e) {
 
-			logger.error("Could not parse chemical component file "+filename, e);
+			logger.error("Could not parse chemical component file {}. Error: {}. "
+					+ "There will be no chemical component info available for {}", filename, e.getMessage(), recordName);
 
 		}
 		finally{
@@ -273,7 +275,7 @@ public  ChemComp getChemComp(String recordName) {
 					inStream.close();
 				} catch (IOException e) {
 					// This would be weird...
-					logger.error("COULD NOT CLOSE CHEMICAL COMPONENT FILE ->>>>> RESOURCE LEAK RESOURCE LEAK. MAYDAY!!!!!!!!! MAYDAY!!!!");
+					logger.error("Could not close chemical component file {}. A resource leak could occur!!", filename);
 				}
 			}
 			
diff --git a/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java b/biojava-structure/src/main/java/org/biojava/nbio/structure/io/mmcif/SimpleMMcifParser.java
@@ -973,9 +973,9 @@ private Object buildObject(String className, List<String> loopFields, List<Strin
 					m.invoke(o, val);
 				}
 			} catch (IllegalAccessException e) {
-				logger.error("Could not invoke setter {} with value {} for class {}", m, val, className);
+				logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);
 			} catch (InvocationTargetException e) {
-				logger.error("Could not invoke setter {} with value {} for class {}", m, val, className);
+				logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);
 			}
 
 		}
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
@@ -464,7 +464,6 @@ private void findBridges() {
 		Collections.sort(outList, new Comparator<Pair<Integer>>() {
 			@Override
 			public int compare(Pair<Integer> o1, Pair<Integer> o2) {
-				// TODO Auto-generated method stub
 				if(o1.getFirst()<o2.getFirst()){
 					return -1;
 				}

Original file line number	Diff line number	Diff line change
`@@ -212,7 +212,8 @@ private void writeID(StringWriter writer, String currentID) throws IOException{`
`212`	`212`
`213`	`213`	`}`
`214`	`214`
`215`		`- /** Loads the definitions for this {@link ChemComp} from a local file and instantiates a new object.`
	`215`	`+ /**`
	`216`	`+ * Loads the definitions for this {@link ChemComp} from a local file and instantiates a new object.`
`216`	`217`	`*`
`217`	`218`	`* @param recordName the ID of the {@link ChemComp}`
`218`	`219`	`* @return a new {@link ChemComp} definition.`
`@@ -263,7 +264,8 @@ public ChemComp getChemComp(String recordName) {`
`263`	`264`
`264`	`265`	`} catch (IOException e) {`
`265`	`266`
`266`		`- logger.error("Could not parse chemical component file "+filename, e);`
	`267`	`+ logger.error("Could not parse chemical component file {}. Error: {}. "`
	`268`	`+ + "There will be no chemical component info available for {}", filename, e.getMessage(), recordName);`
`267`	`269`
`268`	`270`	`}`
`269`	`271`	`finally{`
`@@ -273,7 +275,7 @@ public ChemComp getChemComp(String recordName) {`
`273`	`275`	`inStream.close();`
`274`	`276`	`} catch (IOException e) {`
`275`	`277`	`// This would be weird...`
`276`		`- logger.error("COULD NOT CLOSE CHEMICAL COMPONENT FILE ->>>>> RESOURCE LEAK RESOURCE LEAK. MAYDAY!!!!!!!!! MAYDAY!!!!");`
	`278`	`+ logger.error("Could not close chemical component file {}. A resource leak could occur!!", filename);`
`277`	`279`	`}`
`278`	`280`	`}`
`279`	`281`
Original file line number	Diff line number	Diff line change
`@@ -973,9 +973,9 @@ private Object buildObject(String className, List<String> loopFields, List<Strin`
`973`	`973`	`m.invoke(o, val);`
`974`	`974`	`}`
`975`	`975`	`} catch (IllegalAccessException e) {`
`976`		`- logger.error("Could not invoke setter {} with value {} for class {}", m, val, className);`
	`976`	`+ logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);`
`977`	`977`	`} catch (InvocationTargetException e) {`
`978`		`- logger.error("Could not invoke setter {} with value {} for class {}", m, val, className);`
	`978`	`+ logger.error("Could not invoke setter {} with value {} for class {}", methodName, val, className);`
`979`	`979`	`}`
`980`	`980`
`981`	`981`	`}`
Original file line number	Diff line number	Diff line change
`@@ -464,7 +464,6 @@ private void findBridges() {`
`464`	`464`	`Collections.sort(outList, new Comparator<Pair<Integer>>() {`
`465`	`465`	`@Override`
`466`	`466`	`public int compare(Pair<Integer> o1, Pair<Integer> o2) {`
`467`		`- // TODO Auto-generated method stub`
`468`	`467`	`if(o1.getFirst()<o2.getFirst()){`
`469`	`468`	`return -1;`
`470`	`469`	`}`