[Biojava-dev] WeightMatrixAnnotator

[Schreiber, Mark]

Hi -

These additional methods have been added to CVS. Thanks Tanya.

- Mark


> -----Original Message-----
> From: Tanya Vavouri [mailto:tvavouri at hotmail.com] 
> Sent: Wednesday, 3 December 2003 1:04 a.m.
> To: biojava-dev at biojava.org
> Subject: [Biojava-dev] WeightMatrixAnnotator
> 
> 
> Hi,
> 
> I've made some really simple changes to the latest 
> WeightMatrixAnnotator 
> that have allowed me to annotate sequences with multiple 
> weight matrices. 
> Basically, I've just added an extra variable the String wmID, 
> a constructor 
> that initialises with a user specified weight matrix ID and a 
> getter/setter 
> for the weight matrix ID.
> 
> The changes are really simple but below is the code if anyone 
> is interested 
> to use it or add it to biojava.
> 
> Thanks
> Tanya Vavouri
> 
> package org.biojava.bio.dp;
> 
> import java.io.Serializable;
> 
> import org.biojava.bio.BioException;
> import org.biojava.bio.SimpleAnnotation;
> import org.biojava.bio.seq.Feature;
> import org.biojava.bio.seq.Sequence;
> import org.biojava.bio.seq.SequenceAnnotator;
> import org.biojava.bio.seq.impl.ViewSequence;
> import org.biojava.bio.symbol.IllegalAlphabetException;
> import org.biojava.bio.symbol.RangeLocation;
> import org.biojava.utils.ChangeVetoException;
> 
> /**
> * Annotates a sequence with hits to a weight-matrix.
> *
> * <p>
> * This SequenceAnnotator implementation returns a new
> * ViewSequence wrapping the underlying Sequence
> * </p>
> *
> * @author Matthew Pocock
> * @author Thomas Down
> */
> public class WeightMatrixAnnotator implements SequenceAnnotator, 
> Serializable {
>     private WeightMatrix matrix;
>     private double threshold;
>     private final ScoreType scoreType;
>     private String wmID;
> 
>     public Sequence annotate(Sequence seq)
> 	throws IllegalAlphabetException, BioException, 
> ChangeVetoException
>     {
> 	seq = new ViewSequence(seq);
> 
> 	int cols = matrix.columns();
> 	Feature.Template template = new Feature.Template();
> 	template.source = "WeightMatrixAnnotator";
> 	template.type = wmID;
> 	for(int offset = 1;
> 	    offset <= seq.length() - cols + 1;
> 	    offset++) {
> 	    double score = DP.scoreWeightMatrix(matrix, seq, 
> scoreType,  offset);
> 	    double q = Math.exp(score);
> 	    if(q >= threshold) {
> 		template.location = new RangeLocation(offset, 
> offset+cols-1);
> 		SimpleAnnotation ann = new SimpleAnnotation();
> 		ann.setProperty("score", new Double(q));
> 		ann.setProperty("weightMatrix", matrix);
> 		template.annotation = ann;
> 		seq.createFeature(template);
> 	    }
> 	}
> 	return seq;
>     }
> 
>   /**
>    * Create a new annotator that uses the PROBABILITY score 
> type and an ID 
> for the weight matrix.
>    *
>    * @param wm        the weight matrix
>    * @param threshold the threshold
>    * @param wmID the weight matrix ID
>    */
>     public WeightMatrixAnnotator(WeightMatrix wm, ScoreType 
> scoreType, 
> double threshold, String wmID) {
> 	this.matrix = wm;
> 	this.threshold = threshold;
> 	this.scoreType = ScoreType.PROBABILITY;
> 	this.wmID = wmID;
>     }
> 
>     /**
>      * Create a new annotator that uses PROBABILITY score type.
>      *
>      * @param wm a <code>WeightMatrix</code> value
>      * @param threshold a <code>double</code> value
>      */
>     public WeightMatrixAnnotator(WeightMatrix wm, double threshold) {
> 	this(wm, ScoreType.PROBABILITY, threshold, "hit");
>     }
> 
>     /**
>      * Create a new annotator that uses a specific score type.
>      *
>      * @param wm        the weigth matrix
>      * @param scoreType the score type
>      * @param threshold the threshold
>      * @since 1.4
>      */
>     public WeightMatrixAnnotator(WeightMatrix wm, ScoreType 
> scoreType, 
> double threshold) {
> 	this.matrix = wm;
> 	this.scoreType = scoreType;
> 	this.threshold = threshold;
>         this.wmID = "hit";
>     }
> 
>     /**
>      * Get the value of the weight matrix id.
>      * @return value of the weight matrix id.
>      */
>     public String getWmID() {
> 	return wmID;
>     }
> 
>     /**
>      * Set the weight matrix id.
>      * @param v  Value to assign to the weight matrix id.
>      */
>     public void setWmID(String  v) {
> 	this.wmID = v;
>     }
> 
> 
> }
> 
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