edu.vt.vbi.patric.jbrowse.CRResultSet.java Source code

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Here is the source code for edu.vt.vbi.patric.jbrowse.CRResultSet.java

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/*******************************************************************************
 * Copyright 2014 Virginia Polytechnic Institute and State University
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 ******************************************************************************/
package edu.vt.vbi.patric.jbrowse;

import edu.vt.vbi.patric.common.StringHelper;
import org.apache.commons.lang.StringUtils;
import org.json.simple.JSONArray;
import org.json.simple.JSONObject;
import org.json.simple.parser.JSONParser;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

import java.io.BufferedReader;
import java.io.Serializable;
import java.util.*;

public class CRResultSet implements Serializable {

    private static final long serialVersionUID = 4687109777629511114L;

    private static final Logger LOGGER = LoggerFactory.getLogger(CRResultSet.class);

    private String pinStrand;

    private String pinGenome;

    private Set<String> genomeNames;

    private Set<String> genomeIds;

    private List<String> defaultTracks;

    private Map<Integer, CRTrack> trackMap;

    public CRResultSet(String pin, BufferedReader br) {
        pinGenome = pin.replace("fig|", "").split(".peg.[0-9]*")[0];

        try {
            if (br != null) {
                JSONObject res = (JSONObject) (new JSONParser()).parse(br);

                LOGGER.trace("CompareRegionViewer result: {}", res.toJSONString());

                JSONArray tracks = (JSONArray) res.get(pin);
                genomeNames = new HashSet<>();
                genomeIds = new HashSet<>();
                defaultTracks = new ArrayList<>();
                trackMap = new HashMap<>();

                for (Object track : tracks) {
                    JSONObject tr = (JSONObject) track;

                    if (((JSONArray) tr.get("features")).size() > 0) {
                        CRTrack crTrk = new CRTrack(tr);
                        trackMap.put(crTrk.getRowID(), crTrk);
                        genomeNames.add(crTrk.getGenomeName());
                        genomeIds.add(crTrk.getGenomeID());
                        if (pinGenome.equals(crTrk.getGenomeID())) {
                            pinStrand = crTrk.findFeature(pin).getStrand();
                        }
                    }
                }
            } else {
                LOGGER.error("BufferedReader is null");
            }
        } catch (Exception e) {
            LOGGER.error(e.getMessage(), e);
        }
    }

    public String getPinStrand() {
        return pinStrand;
    }

    public Set<String> getGenomeNames() {
        return genomeNames;
    }

    public Set<String> getGenomeIds() {
        return genomeIds;
    }

    public void addToDefaultTracks(CRTrack crTrk) {
        if (pinGenome.equals(crTrk.getGenomeID())) {
            ArrayList<String> newTrack = new ArrayList<String>();
            newTrack.add("CR" + crTrk.getRowID());
            newTrack.addAll(defaultTracks);
            defaultTracks = newTrack;
        } else {
            defaultTracks.add("CR" + crTrk.getRowID());
        }
    }

    public String getDefaultTracks() {
        return StringUtils.join(defaultTracks, ",");
    }

    public Map<Integer, CRTrack> getTrackMap() {
        return trackMap;
    }

    public void setTrackMap(Map<Integer, CRTrack> map) {
        this.trackMap = map;
    }
}