use java syntax highlighting

andreasprlic · andreasprlic · commit 62a70b61bc12 · 2013-09-19T19:46:01.000-07:00
diff --git a/structure/caching.md b/structure/caching.md
@@ -8,16 +8,16 @@ The main class that provides this functionality is the [AtomCache](http://www.bi
 
 It is hidden inside the StructureIO class, that we already encountered earlier.
 
-<pre>
+```java
 	Structure structure = StructureIO.getStructure("4hhb");			
-</pre>
+```
 
 is the same as
 
-<pre>
+```java
 	AtomCache cache = new AtomCache();
 	cache.getStructure("4hhb");
-</pre>
+```
 
 
 ## Where are the files getting written to?
@@ -33,11 +33,11 @@ you can configure the AtomCache by setting the PDB_DIR system property
 
 An alternative is to hard-code the path in this way (but setting it as a property is better style)
 
-<pre>
+```java
 	AtomCache cache = new AtomCache();
 
 	cache.setPath("/path/to/pdb/files/");
-</pre>
+```
 
 ## File Parsing Parameters
 
@@ -47,7 +47,7 @@ class is the main place to influence the level of detail and as a consequence th
 
 This example turns on the use of chemical components when loading a structure. (See also the [next chapter](chemcomp.md))
 
-<pre>
+```java
 	AtomCache cache = new AtomCache();
 
 	cache.setPath("/tmp/");
@@ -60,20 +60,20 @@ This example turns on the use of chemical components when loading a structure. (
 
 	Structure structure = StructureIO.getStructure("4hhb");			
 
-</pre>
+```
 
 ## Caching of other SCOP, CATH
 
 The AtomCache not only provides access to PDB, it can also fetch Structure representations of protein domains, as defined by SCOP and CATH.
 
-<pre>
+```java
 	// uses a SCOP domain definition
 	Structure domain1 = StructureIO.getStructure("d4hhba_");
 	
 	// Get a specific protein chain, note: chain IDs are case sensitive, PDB IDs are not.
 	Structure chain1 = StructureIO.getStructure("4HHB.A");
 	
-</pre>
+```
 
 There are quite a number of external database IDs that are supported here. See the 
 <a href="http://www.biojava.org/docs/api/org/biojava/bio/structure/align/util/AtomCache.html#getStructure(java.lang.String)">AtomCache documentation</a> for more details on the supported options.
