This tutorial will guide you through adding a new example command to PhyloNet that can be executed from within the PhyloNet PHYLONET block of a NEXUS file.
Step 1. Prepare Existing Source
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package com.example;
import edu.rice.cs.bioinfo.programs.phylonet.commands.*;
import edu.rice.cs.bioinfo.library.language.pyson._1_0.ir.blockcontents.*;
import edu.rice.cs.bioinfo.library.language.richnewick._1_0.ast.*;
import edu.rice.cs.bioinfo.library.programming.*;
import java.io.*;
import java.util.*;
public class CountNodes extends CommandBase
{
public CountNodes(SyntaxCommand motivatingCommand, ArrayList<Parameter> params,
Map<String,NetworkNonEmpty> sourceIdentToNetwork, Proc3<String, Integer, Integer> errorDetected)
{
super(motivatingCommand, params, sourceIdentToNetwork, errorDetected);
}
...
}
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Your first step should be to provide the illustrated public four argument constructor with corresponding call to super. When your command is encountered in a PhyloNet block, it is this constructor that will be called to create your command.
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protected boolean checkParamsForCommand()
{
int expectedNetworkNameParameterIndex = 0; // network ident should be first parameter in command.
// automatically checks for network existance and reports any errors to this.errorDetected.
NetworkNonEmpty network = this.assertAndGetNetwork(expectedNetworkNameParameterIndex);
if(network == null) // user specified network name is invalid
{
return false;
}
_networkToScan = network; // added field to class to retain network to scan.
return true;
}
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Note that we have added a field to our class _networkToScan to point to the user specified network to scan. This will be useful in our next step.
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protected void executeCommandHelp(Proc<String> displayResult) throws IOException
{
String eNewickNetwork = NetworkTransformer.toENewick(_networkToScan); // convert NEXUS network to extended newick string
/*
* convert extended network string to Network
*/
edu.rice.cs.bioinfo.programs.phylonet.structs.network.io.ExNewickReader<String> enr =
new edu.rice.cs.bioinfo.programs.phylonet.structs.network.io.ExNewickReader<String>(
newStringReader(eNewickNetwork));
edu.rice.cs.bioinfo.programs.phylonet.structs.network.Network<String> net;
try
{
net = enr.readNetwork();
}
catch(Exception e)
{
throw new RuntimeException(e);
}
/*
* count and display number of nodes in network
*/
Iterable<edu.rice.cs.bioinfo.programs.phylonet.structs.network.NetNode<String>> allNodes = net.dfs();
int nodeCount = 0;
for(Object node : net.dfs())
{
nodeCount++;
}
displayResult.execute("\nNetwork contains " + nodeCount + " nodes.");
}
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The next step is to update edu.rice.cs.bioinfo.programs.phylonet.commands.CommandFactory to construct instances of the CountNodes command. When examining the existing structure of the CommandFactory you will discover an if/else if chain within the make method:
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public class CommandFactory { public static Command make(SyntaxCommand directive, Map<String,NetworkNonEmpty> sourceIdentToNetwork, Proc3<String, Integer, Integer> errorDetected, Random rand) { ... if(lowerCommandName.equals("symmetricdifference") || lowerCommandName.equals("rf")) { return new SymmetricDifference(directive, params, sourceIdentToNetwork, errorDetected); } else if(lowerCommandName.equals("lca")) { return new LCA(directive, params, sourceIdentToNetwork, errorDetected); } ... } |
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public class CommandFactory {
public static Command make(SyntaxCommand directive, Map<String,NetworkNonEmpty> sourceIdentToNetwork,
Proc3<String, Integer, Integer> errorDetected, Random rand)
{
...
else if(lowerCommandName.equals("nexus_out"))
{
return new NexusOut(directive, params, sourceIdentToNetwork, errorDetected);
}
else if(lowerCommandName.equals("countnodes"))
{
return new CountNodes(directive, params, sourceIdentToNetwork, errorDetected);
}
...
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At this point inclusion of a new command is complete. After recompiling PhyloNet the new command should be available. For example, the following NEXUS file will now be processed by PhyloNet:
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#NEXUS
BEGIN NETWORKS;
Network net = ((a,(b,(c)x#1)M)N,((x#1,d)J,e)Z)R;
END;
BEGIN PHYLONET;
CountNodes net;
END;
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