src/org/gel/mauve/summary/output/IslandFeatureWriter.java

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package org.gel.mauve.summary.output;

import java.util.Hashtable;
import java.util.Vector;

import org.gel.air.util.GroupHelpers;
import org.gel.mauve.MauveConstants;
import org.gel.mauve.MauveHelperFunctions;
import org.gel.mauve.analysis.Segment;
import org.gel.mauve.gui.sequence.FlatFileFeatureConstants;

public class IslandFeatureWriter extends AbstractIslandWriter implements
                MauveConstants, FlatFileFeatureConstants {

        public static final int MULTIPLICITY_INDEX = 6;
        public static final String ISLAND = "island";

        protected IslandFeatureWriter (SegmentDataProcessor processor) {
                super (MauveHelperFunctions.getSeqPartOfFile (processor) + "islands", processor);
        }
        
        protected IslandFeatureWriter (String file, SegmentDataProcessor processor) {
                super (file, processor);
        }

        protected void initSubClassParticulars (Hashtable args) {
                seq_index = ((Integer) args.get (SEQUENCE_INDEX)).intValue ();
                super.initSubClassParticulars (args);
        }

        public void printIslands () {
                printHeaders ();
                printData (BY_ONE_GENOME);
        }

        protected String getData (int column, int row) {
                long value = 0;
                switch (column) {
                        case TYPE:
                                return ISLAND;
                        case LABEL:
                                return current.typed_id;
                        case CONTIG:
                                return contig_handler.getContigName (seq_index, current.left [seq_index]);
                        case STRAND:
                                return current.reverse [seq_index] ? COMPLEMENT : FORWARD;
                        case LEFT:
                                value = current.left [seq_index];
                                break;
                        case RIGHT:
                                value = current.right [seq_index];
                                break;
                        case MULTIPLICITY_INDEX:
                                return MauveHelperFunctions.getReadableMultiplicity (current);
                        default:
                                return null;
                }
                return adjustForContigs (seq_index, value) + "";
        }

        public Vector setColumnHeaders () {
                String [] cols = new String [] {TYPE_STRING, LABEL_STRING,
                                CONTIG_STRING, STRAND_STRING, LEFT_STRING, RIGHT_STRING,
                                Segment.MULTIPLICITY_STRING};
                Vector vect = new Vector ();
                GroupHelpers.arrayToCollection (vect, cols);
                return vect;
        }

        public static void printIslandsAsFeatures (SegmentDataProcessor processor) {
                int count = ((Object []) processor.get (FIRSTS)).length;
                for (int i = 0; i < count; i++) {
                        processor.put (SEQUENCE_INDEX, new Integer (i));
                        new IslandFeatureWriter (processor);
                }
        }

        public boolean shouldPrintRow (int row) {
                long cur = current.multiplicityType ();
                return (cur & multiplicity) == multiplicity && cur != all_seq_multiplicity &&
                                current.getSegmentLength (seq_index) > island_min;
        }

}

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