There are several parts of Softparsmap that can be replace in order to
meet more specific needs. The parts are defined by the interfaces
in the package. Here is an example on how to create a new parser and
install it.
Let the java file MyParser.java contain following
lines.
import softparsmap.*;
import ooc.*
public class MyParser extends AbstractTreeParser {
public Node parseIn(String tree) {
// The code for parsing the string 'tree' goes here.
// The method returns the root to the parsed gene tree.
}
public void parseIn(Node tree, String treeInfo) {
// The code for parsing in additional information into the
// tree nodes goes here
}
public String parseOut(Node tree) {
// The code for parsing the gene tree 'tree' to a
// string goes here.
// getting an attribute value
String value = getAttributeString("some_attribute");
// rest of your code
}
}
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Add the parse in and out code and then compile the class by
typing
javac MyParser.java. If it will
not compile, the
CLASSPATH has probably not been
set correctly.
More information on how to set the class path is found at
Solaris or at
Windows.
Since MyParser.java extends the
AbstractTreeParser
it is a good idea to extend the abstract tag defined in def.xml
as well. This is because the abstract tag have some default
attributes which are used by the abstract class. Your property file
will then look something like this.
<?xml version="1.0" encoding="iso-8859-1"?>
<source title="My Project Name">
<!-- Importing package definitions -->
<import source="softparsmap/def.xml" source_context="classpath"/>
<!--
Your tasks, data sources and family groups can be defined here in
which you are using your new parser with did="my_parser"
-->
<!-- Defining my parser -->
<tree_parser did="my_parser" eid="abstract"
class="MyParser"
some_attribute="@@string:=some value"
/>
</source>
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The attribute
class is changed from
AbstractTreeParser to
MyParser
in order to connect the new code to the tag.