src/org/gel/mauve/format/GenbankEmblFormat.java

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package org.gel.mauve.format;

import java.awt.BasicStroke;
import java.awt.Color;
import java.util.StringTokenizer;
import java.util.Iterator;
import java.util.Set;

import org.biojava.bio.Annotation;
import org.biojava.bio.gui.sequence.RectangularBeadRenderer;
import org.biojava.bio.seq.Feature;
import org.biojava.bio.seq.FeatureFilter;
import org.biojava.bio.seq.FeatureHolder;
import org.biojava.bio.seq.Sequence;
import org.biojava.bio.seq.StrandedFeature;
import org.biojava.utils.ChangeVetoException;
import org.biojavax.Note;
import org.biojavax.RichObjectFactory;
import org.biojavax.bio.seq.RichFeature;
import org.biojavax.bio.seq.RichSequence;
import org.biojavax.bio.taxa.NCBITaxon;
import org.biojavax.ontology.ComparableTerm;
import org.gel.mauve.FilterCacheSpec;
import org.gel.mauve.MauveConstants;
import org.gel.mauve.gui.navigation.AnnotationContainsFilter;
import org.gel.mauve.gui.sequence.ZiggyRectangularBeadRenderer;

public abstract class GenbankEmblFormat extends BaseFormat {
        private static FilterCacheSpec [] specs = new FilterCacheSpec [11];
        static {
                RectangularBeadRenderer renderer = null;
                ZiggyRectangularBeadRenderer zrenderer;
                try {
                        zrenderer = new ZiggyRectangularBeadRenderer (10.0, 0.0,
                                        Color.BLACK, Color.WHITE, new BasicStroke ());
                        specs[0] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("CDS"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.POSITIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        zrenderer);

                        renderer = new RectangularBeadRenderer (10.0, 0.0, Color.BLACK,
                                        Color.RED, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[1] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("rRNA"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.POSITIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);

                        renderer = new RectangularBeadRenderer (10.0, 0.0, Color.BLACK,
                                        Color.GREEN, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[2] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("tRNA"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.POSITIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);

                        renderer = new RectangularBeadRenderer (10.0, 0.0, Color.BLACK,
                                        Color.BLUE, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[3] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("misc_RNA"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.POSITIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);

                        zrenderer = new ZiggyRectangularBeadRenderer (10.0, 10.0,
                                        Color.BLACK, Color.WHITE, new BasicStroke ());
                        specs[4] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("CDS"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.NEGATIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        zrenderer);

                        renderer = new RectangularBeadRenderer (10.0, 10.0, Color.BLACK,
                                        Color.RED, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[5] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("rRNA"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.NEGATIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);

                        renderer = new RectangularBeadRenderer (10.0, 10.0, Color.BLACK,
                                        Color.GREEN, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[6] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("tRNA"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.NEGATIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);

                        renderer = new RectangularBeadRenderer (10.0, 10.0, Color.BLACK,
                                        Color.BLUE, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[7] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("misc_RNA"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.NEGATIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);

                        // for repeats
                        renderer = new RectangularBeadRenderer (6.0, 26.0, Color.BLACK,
                                        Color.PINK, new BasicStroke ());
                        renderer.setHeightScaling (false);
                        specs[8] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("repeat_region"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.NEGATIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);
                        renderer.setHeightScaling (false);
                        renderer = new RectangularBeadRenderer (6.0, 20.0, Color.BLACK,
                                        Color.PINK, new BasicStroke ());
                        specs[9] = new FilterCacheSpec (new FeatureFilter.And (
                                        new FeatureFilter.ByType ("repeat_region"),
                                        new FeatureFilter.StrandFilter (StrandedFeature.POSITIVE)),
                                        new String [] {"gene", "locus_tag", "product", "db_xref"},
                                        renderer);
                        renderer.setHeightScaling (false);
                        specs[10] = new FilterCacheSpec (
                                        new FeatureFilter.ByType ("source"),
                                        new String [] {FilterCacheSpec.ALL_ANNOTATIONS});
                } catch (ChangeVetoException e) {
                        e.printStackTrace ();
                }
        }

        public String getChromosomeName (Sequence s) {
                FeatureHolder fh = s.filter(new FeatureFilter.ByType("source"));
        String name = null;
        Annotation a = null;
        if (fh.countFeatures() != 0)
        {
            Feature f2 = (Feature) fh.features().next();
            a = f2.getAnnotation();
        }
        if (a != null) {
            if (a.containsProperty("chromosome"))
            {
                name = (String) a.getProperty("chromosome");
            }
            else if (a.containsProperty("biojavax:chromosome"))
            {
                name = (String) a.getProperty("biojavax:chromosome");
            }
            else if (a.containsProperty("plasmid"))
            {
                name = (String) a.getProperty("plasmid");
            }
            else if (a.containsProperty("biojavax:plasmid"))
            {
                name = (String) a.getProperty("biojavax:plasmid");
            }
                }
        if (name != null) {
                name = name.trim();
                if (name.length() == 0)
                        name = null;
        }
        if (name == null && s.getAnnotation() != null) {
                name = (String) s.getName();
        }
        if (name == null && 
                        AnnotationContainsFilter.getKeyIgnoreCase ("definition",
                                s.getAnnotation()) != null) {
                        name = getChromNameFromDescription (s);
                }
                return name;
        }

        public String getChromNameFromDescription (Sequence seq) {
                String desc = ((String) AnnotationContainsFilter.getValueIgnoreCase (
                                "definition", seq.getAnnotation ()));
        if(desc == null) {
            return null;
        } else {
            desc = desc.toLowerCase();
        }

                int ind = desc.indexOf ("contig");
                if (ind > -1) {
                        ind = desc.lastIndexOf (" ", ind);
                        if (ind < 0)
                                ind = 0;
                        int ind2 = desc.indexOf (" ", ind + 1);
                        if (ind2 < 0)
                                ind2 = desc.length ();
                        desc = desc.substring (ind, ind2);
                }
                else if (desc.indexOf("chromosome") > 0)
                        desc = "chromosome";
                else if (desc.indexOf("plasmid") > 0)
                        desc = "plasmid";
                /*else {
                        StringTokenizer toke = new StringTokenizer (getSequenceName (seq));
                        while (toke.hasMoreTokens ()) {
                                String [] pieces = desc.split (toke.nextToken ().toLowerCase ());
                                desc = "";
                                for (int i = 0; i < pieces.length; i++)
                                        desc += pieces[i].trim () + " ";
                                desc = desc.trim ();
                        }
                }*/
                return desc;
        }

        public String getSequenceName (Sequence s) {
                FeatureHolder fh = s.filter (new FeatureFilter.ByType ("source"));
                if (fh.countFeatures () != 0) {
                        Feature f2 = (Feature) fh.features ().next ();
                        Annotation a = f2.getAnnotation ();
                        String name = "";
                        String add = null;
                        if (a.containsProperty ("organism")) {
                                name += a.getProperty ("organism") + " ";
                        }
                        if (a.containsProperty ("serovar")) {
                                add = a.getProperty ("serovar").toString ();
                                if (name.indexOf (add) == -1)
                                        name += add + " ";
                        }
                        if (a.containsProperty ("strain")) {
                                add = a.getProperty ("strain").toString ();
                                if (name.indexOf (add) == -1)
                                        name += add + " ";
                        }
                        if (name != "")
                                return name.trim ();
                }
                // if a source feature didn't exist
                // try getting the source from the headers
                try {
                        Object source = s.getAnnotation ().getProperty ("SOURCE");
                        if (source != null) {
                                return (String) source;
                        }
                } catch (Exception e) {
                }
                return null;
        }

        public FilterCacheSpec [] getFilterCacheSpecs () {
                return specs;
        }

}

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