global replace of <java> with markdon formatting and deleting of legacy pages.

Author: andreasprlic

_wikis/Algorithm_Java_port.md

@@ -8,8 +8,7 @@ Possible Java ports of Algorithms
 We would be interested in having Java ports of the following algorithms:
 
 `- Blast`  
-`- Hmmer3`  
-`- Dssp (some parts already available)`
+`- Hmmer3`
 
 ### Couple of tools that might be useful for porting to Java
 

_wikis/Andreas_Prlic.md

@@ -4,16 +4,8 @@ tags:
  - People
 ---
 
-[Andreas Prlic](http://www.spice-3d.org) is Senior Scientist at the
+[Andreas Prlic](http://www.spice-3d.org) is Technical and Scientifc Team Lead at the
 RCSB-PDB database in San Diego, California. Prior to this he worked as a
-PostDoc at the [Wellcome Trust Sanger
-Institute](http://www.sanger.ac.uk/), Cambridge, U.K. Currently he is
-acting as project leader for BioJava. He developed the protein structure
-API. Other projects he was working on include e.g.
-[SPICE](http://www.efamily.org.uk/software/dasclients/spice) a browser
-for protein sequence and structure annotations, based on the
-[Distributed Annotation System](http://www.biodas.org).
-
-[Nightly builds of BioJava](http://www.spice-3d.org/cruise/) can be
-accessed from his CruiseControl page at
-[<http://emmy.rcsb.org:8080/cruisecontrol/>](http://emmy.rcsb.org:8080/cruisecontrol/).
+PostDoc at the [Wellcome Trust Sanger Institute](http://www.sanger.ac.uk/),
+Cambridge, U.K. Currently he is acting as project leader for BioJava. He developed
+the protein structure API as well as many other parts of BioJava.

_wikis/Annotations:List.md

@@ -51,7 +51,7 @@ The following program reads an EMBL file and lists its Annotation
 properties. The output of this program on the above file is listed below
 the program.
 
-<java> import java.io.\*; import java.util.\*;
+```java import java.io.\*; import java.util.\*;
 
 import org.biojava.bio.\*; import org.biojava.bio.seq.\*; import
 org.biojava.bio.seq.io.\*;
@@ -80,7 +80,7 @@ public class ListAnnotations {
 `   }`  
 ` }`
 
-} </java>
+} ```
 
 Program Output
 

_wikis/BioJava3_license.md

@@ -8,7 +8,7 @@ license](BioJava:License "wikilink"): LGPL v 2.1
 Developers: Please include the following javadoc in the header of every
 class you commit:
 
-<java> /\*
+```java /\*
 
 `*                    BioJava development code`  
 `*`  
@@ -32,4 +32,4 @@ class you commit:
 `*`  
 `*/`
 
-</java>
+```