Requirements

Genecoder molecular biology software is platform independent and only requires JavaTM 1.6 or later.

applewindowjava

Whats New

  • Multiple Sequence Alignment
  • Align Sanger Trace Files
  • Command line utilities

Program Features

  • Sequence Database
  • Support for a large array of sequence file formats (default: Genbank)
  • Dynamic Restriction Site Analysis of DNA sequences
  • Editable Restriction Enzyme Library
  • Highlight, select, analyze, and save regions of interest
  • Create Linear and Circular Restriction Maps
  • Pairwise and multiple sequence alignments.
  • Plugin API to extend tools, views, and readable file formats.
  • Comprehensive preferences
  • Remote NCBI BLAST and Entrez Queries and downloads
  • View and analyze DNA sequence trace chromatagrams
  • Search for common sequences from an editable database of sequences
  • Analyze oligonucleotides for PCR and/or siRNA
  • And much more...

GeneCoder Plugins

GeneCoder 4.0 provides a plug-in API to customize and/or add functionality to the software. Writing plugins require some knowledge of java programming, and JDK 1.6 or later. Plugins are as simple writing some code, complling into a class file or jar library, and adding the plugin file(s) to the plug-in directory - GeneCoder will automatically load the Plugins on startup.

Overview

The plugin API allows three different types of extensions:

  • View Plugins - Customize how sequences are viewed. These plugins are loaded into the main interface and can be selected using the view type selection.
  • Action Plugins - Add functionality to modify, analyze, or create Sequences. These plugins get loaded into the toolbox, and can be run with the click of a button.
  • IO Plugins - Add different File format parsers to read as many file formats as you wish.

The Java API

Writing a Plugin requires a java class to implement the appropriate interface for the appropriate functionality. These interfaces can be found in the com.algosome.genecoder.plugin package (ISequenceViewPlugin, ISequenceActionPlugin, and IIOPlugin). Three libraries are required on the classpath to compile a plugin: Apache log4j, Algosome Commons, and the GeneCoder plugin API.

Plugins are given access to Sequence objects through the SequenceData interface. All sequences in GeneCoder are represented by an implementation of the Sequence interface (it is advised plugins do NOT attempt to implement this interface - rather if one needs to create or read Sequences use the SequenceFactoryBridge or GeneCoderIOBridge classes, respectively). Sequences are wrapped within two parent container objects - a SequenceModel wraps a Sequence and provides basic access to underlying data and method models such as the EditorModel, RestrictionSiteModel (for DNA sequences), SelectionModel, etc...Instances of SequenceModel are in turn wrapped by a SequenceManager, which is responsible for containing a List of sequences and provides access to underlying data and method models (such as a SelectionModel defining which sequences are selected).

Example

The following class file demonstrates a simple ISequenceActionPlugin, the meat of the code is within the doAction method, and has code examples for retrieving a selected sequence from a SequenceData object, as well as examples for how to create a Sequence using the GeneCoderIOBridge and SequenceFactoryBridge classes.

 

import javax.swing.ImageIcon;
import javax.swing.KeyStroke;

import com.algosome.common.event.IndexSelectionModel;
import com.algosome.genecoder.bio.sequence.SequenceData;
import com.algosome.genecoder.bio.sequence.SequenceManager;
import com.algosome.genecoder.bio.sequence.SequenceModel;
import com.algosome.genecoder.bio.sequence.SequenceFactoryBridge;
import com.algosome.genecoder.plugin.DefinedTypes;
import com.algosome.genecoder.plugin.ISequenceActionPlugin;
import com.algosome.genecoder.plugin.PluginListener;
import com.algosome.genecoder.plugin.SequenceCount;
import com.algosome.genecoder.plugin.DefinedTypes.Option;
import com.algosome.genecoder.io.GeneCoderIOBridge;

/**
 * An example implementation of an Action plugin which 
 * @author Greg Cope
 *
 */
class ExamplePlugin implements ISequenceActionPlugin{

	private SequenceData sequenceData = null;
	
	@Override
	public SequenceCount getRequiredSequenceCount() {
		return SequenceCount.ONE;//operates on only one sequence
	}

	@Override
	public void setSequenceData(SequenceData seq) {
		sequenceData = seq;
	}

	@Override
	public void breakDown() {
		//break down anything necessary - nothing with this Plugin
	}

	@Override
	public void doStart() {
		//perform any setup here - nothing with this plugin
	}

	@Override
	public String getDescription() {
		return "An example plugin";
	}

	@Override
	public String getName() {
		return "Example Action";
	}

	@Override
	public Option getType() {
		return DefinedTypes.Option.DNA;
	}

	@Override
	public void doAction(PluginListener listener) throws Exception {
		/*
		 * Given this Plugin is defined with SequenceCount.ONE, only one sequence
		 * should be selected and operated on. The following code operates on this assumption
		 * be retrieving the SelectionModels and getting the selected Sequence.
		 */
		IndexSelectionModel model = sequenceData.getSequenceManagerContainer().getSelectionModel();
		int selection = model.getSelectedIndex();
		assert selection != -1 : "The selection should NOT be -1";
		SequenceManager sequenceManager = sequenceData.getSequenceManagerContainer().getSequenceManagers().get(selection);
		IndexSelectionModel smModel = sequenceManager.getSelectionModel();
		int selectedSequenceIndex = smModel.getSelectedIndex();
		assert selectedSequenceIndex != -1 : "The selection should NOT be -1";
		SequenceModel sequenceModel = sequenceManager.getSequences().get(selectedSequenceIndex);
		System.out.println(sequenceModel.getSequence().getSequenceName());
		/*
		 * Do Manipulation here
		 */
		
		System.out.println("Constructing sequence");
        Sequence seq = SequenceFactoryBridge.getInstance().constructSequence("AGCTAAAAGGGGACCCTA", Sequence.SEQUENCE_TYPE_DNA);//construct a new DNA sequence
		System.out.println(seq.getSequence());
		/*
		List seqs = GeneCoderIOBridge.getGeneCoderIOBridge().readSequence(new File(""));//enter absolute File path to read a File.
		System.out.println(seqs.get(0).getSequence());
		*/
		System.out.println(GeneCoderIOBridge.getGeneCoderIOBridge().convertToGenbank(seq))
        
	}

	@Override
	public ImageIcon getImageIcon() {
		return null;
	}

	@Override
	public KeyStroke getShortcut() {
		return null;
	}

	@Override
	public void stopAction() {
		//do nothing.
	}
	
}
        

References

Required API's to compile Plugins

© 2008-2017 Greg Cope