use java syntax highlighting

andreasprlic · andreasprlic · commit 7115db2a8870 · 2013-09-19T19:46:40.000-07:00
diff --git a/structure/firststeps.md b/structure/firststeps.md
@@ -5,7 +5,7 @@ First Steps
 
 The simplest way to load a PDB file is by using the [StructureIO](http://www.biojava.org/docs/api/org/biojava3/structure/StructureIO.html) class.
 
-<pre>
+```java
      public static void main(String[] args){
 
         try {
@@ -16,7 +16,7 @@ The simplest way to load a PDB file is by using the [StructureIO](http://www.bio
                 e.printStackTrace();
         }
     }   
-</pre>
+```
 
 BioJava  automatically downloads the PDB file for hemoglobin [4HHB](http://www.rcsb.org/pdb/explore.do?structureId=4HHB) and copies it into a temporary location. Then the PDB file parser loads the data into a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html) object, that provides access to the content in the file. (If you call this a second time, BioJava will automatically re-use the local file.)
 
@@ -53,7 +53,7 @@ Talking about startup properties, it is also good to mention the fact that many
 
 If you have the *biojava-structure-gui* module installed, you can quickly visualise a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html) via this:
 
-<pre>
+```java
     public static void main(String[] args){
     
         try {
@@ -73,7 +73,7 @@ If you have the *biojava-structure-gui* module installed, you can quickly visual
             e.printStackTrace();
         }
     }
-</pre>
+```
 
 This will result in the following view:
 
@@ -92,7 +92,7 @@ This will result in the following view:
 
 By default many people work with the *asymmetric unit* of a protein. However for many studies the correct representation to look at is the *biological assembly* of a protein. You can request it by calling
 
-<pre>
+```java
      public static void main(String[] args){
 
         try {
@@ -103,7 +103,7 @@ By default many people work with the *asymmetric unit* of a protein. However for
                 e.printStackTrace();
         }
     }   
-</pre>
+```
 
 This topic is important, so we dedicated a [whole chapter](bioassembly.md) to it.
 

Original file line number	Diff line number	Diff line change
`@@ -5,7 +5,7 @@ First Steps`
`5`	`5`
`6`	`6`	`The simplest way to load a PDB file is by using the [StructureIO](http://www.biojava.org/docs/api/org/biojava3/structure/StructureIO.html) class.`
`7`	`7`
`8`		`-<pre>`
	`8`	+```java
`9`	`9`	`public static void main(String[] args){`
`10`	`10`
`11`	`11`	`try {`
`@@ -16,7 +16,7 @@ The simplest way to load a PDB file is by using the [StructureIO](http://www.bio`
`16`	`16`	`e.printStackTrace();`
`17`	`17`	`}`
`18`	`18`	`}`
`19`		`-</pre>`
	`19`	+```
`20`	`20`
`21`	`21`	`BioJava automatically downloads the PDB file for hemoglobin [4HHB](http://www.rcsb.org/pdb/explore.do?structureId=4HHB) and copies it into a temporary location. Then the PDB file parser loads the data into a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html) object, that provides access to the content in the file. (If you call this a second time, BioJava will automatically re-use the local file.)`
`22`	`22`
`@@ -53,7 +53,7 @@ Talking about startup properties, it is also good to mention the fact that many`
`53`	`53`
`54`	`54`	`If you have the biojava-structure-gui module installed, you can quickly visualise a [Structure](http://www.biojava.org/docs/api/org/biojava/bio/structure/Structure.html) via this:`
`55`	`55`
`56`		`-<pre>`
	`56`	+```java
`57`	`57`	`public static void main(String[] args){`
`58`	`58`
`59`	`59`	`try {`
`@@ -73,7 +73,7 @@ If you have the biojava-structure-gui module installed, you can quickly visual`
`73`	`73`	`e.printStackTrace();`
`74`	`74`	`}`
`75`	`75`	`}`
`76`		`-</pre>`
	`76`	+```
`77`	`77`
`78`	`78`	`This will result in the following view:`
`79`	`79`
`@@ -92,7 +92,7 @@ This will result in the following view:`
`92`	`92`
`93`	`93`	`By default many people work with the asymmetric unit of a protein. However for many studies the correct representation to look at is the biological assembly of a protein. You can request it by calling`
`94`	`94`
`95`		`-<pre>`
	`95`	+```java
`96`	`96`	`public static void main(String[] args){`
`97`	`97`
`98`	`98`	`try {`
`@@ -103,7 +103,7 @@ By default many people work with the asymmetric unit of a protein. However for`
`103`	`103`	`e.printStackTrace();`
`104`	`104`	`}`
`105`	`105`	`}`
`106`		`-</pre>`
	`106`	+```
`107`	`107`
`108`	`108`	`This topic is important, so we dedicated a [whole chapter](bioassembly.md) to it.`
`109`	`109`