<commit_before>package org.intermine.bio.web.struts;

/*
 * Copyright (C) 2002-2011 FlyMine
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  See the LICENSE file for more
 * information or http://www.gnu.org/copyleft/lesser.html.
 *
 */

import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;

import org.apache.commons.collections.keyvalue.MultiKey;
import org.apache.log4j.Logger;
import org.apache.struts.action.Action;
import org.apache.struts.action.ActionForm;
import org.apache.struts.action.ActionForward;
import org.apache.struts.action.ActionMapping;
import org.intermine.api.InterMineAPI;
import org.intermine.api.profile.InterMineBag;
import org.intermine.api.profile.Profile;
import org.intermine.api.query.WebResultsExecutor;
import org.intermine.api.results.WebResults;
import org.intermine.api.util.NameUtil;
import org.intermine.bio.web.export.GenomicRegionSequenceExporter;
import org.intermine.bio.web.logic.GenomicRegionSearchService;
import org.intermine.bio.web.logic.GenomicRegionSearchUtil;
import org.intermine.bio.web.model.GenomicRegion;
import org.intermine.bio.web.model.GenomicRegionSearchConstraint;
import org.intermine.objectstore.ObjectStoreException;
import org.intermine.pathquery.PathQuery;
import org.intermine.util.StringUtil;
import org.intermine.web.logic.config.WebConfig;
import org.intermine.web.logic.export.ResponseUtil;
import org.intermine.web.logic.export.http.HttpExportUtil;
import org.intermine.web.logic.export.http.TableExporterFactory;
import org.intermine.web.logic.export.http.TableHttpExporter;
import org.intermine.web.logic.export.rowformatters.CSVRowFormatter;
import org.intermine.web.logic.export.rowformatters.TabRowFormatter;
import org.intermine.web.logic.export.string.StringTableExporter;
import org.intermine.web.logic.results.PagedTable;
import org.intermine.web.logic.session.SessionMethods;
import org.intermine.web.struts.TableExportForm;

/**
 * Genomic region search ajax calls.
 *
 * @author <NAME>
 */
public class GenomicRegionSearchAjaxAction extends Action
{
    @SuppressWarnings("unused")
    private static final Logger LOG = Logger
            .getLogger(GenomicRegionSearchAjaxAction.class);

    private String spanUUIDString;
    private GenomicRegionSearchService grsService;
    private Map<String, Map<GenomicRegion, List<List<String>>>> spanOverlapFullResultMap;
    private Map<String, Map<GenomicRegion, Map<String, Integer>>> spanOverlapFullStatMap;
    private Map<GenomicRegionSearchConstraint, String> spanConstraintMap;
    private HttpSession session;
    private WebConfig webConfig;
    private Profile profile;
    private InterMineAPI api;
    private static Map<MultiKey, String> chromosomeSequenceMap = new HashMap<MultiKey, String>();<commit_msg>removed unused class import<commit_after>package org.intermine.bio.web.struts;

/*
 * Copyright (C) 2002-2011 FlyMine
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  See the LICENSE file for more
 * information or http://www.gnu.org/copyleft/lesser.html.
 *
 */

import java.io.IOException;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;

import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpSession;

import org.apache.log4j.Logger;
import org.apache.struts.action.Action;
import org.apache.struts.action.ActionForm;
import org.apache.struts.action.ActionForward;
import org.apache.struts.action.ActionMapping;
import org.intermine.api.InterMineAPI;
import org.intermine.api.profile.InterMineBag;
import org.intermine.api.profile.Profile;
import org.intermine.api.query.WebResultsExecutor;
import org.intermine.api.results.WebResults;
import org.intermine.api.util.NameUtil;
import org.intermine.bio.web.export.GenomicRegionSequenceExporter;
import org.intermine.bio.web.logic.GenomicRegionSearchService;
import org.intermine.bio.web.logic.GenomicRegionSearchUtil;
import org.intermine.bio.web.model.GenomicRegion;
import org.intermine.bio.web.model.GenomicRegionSearchConstraint;
import org.intermine.objectstore.ObjectStoreException;
import org.intermine.pathquery.PathQuery;
import org.intermine.util.StringUtil;
import org.intermine.web.logic.config.WebConfig;
import org.intermine.web.logic.export.ResponseUtil;
import org.intermine.web.logic.export.http.HttpExportUtil;
import org.intermine.web.logic.export.http.TableExporterFactory;
import org.intermine.web.logic.export.http.TableHttpExporter;
import org.intermine.web.logic.export.rowformatters.CSVRowFormatter;
import org.intermine.web.logic.export.rowformatters.TabRowFormatter;
import org.intermine.web.logic.export.string.StringTableExporter;
import org.intermine.web.logic.results.PagedTable;
import org.intermine.web.logic.session.SessionMethods;
import org.intermine.web.struts.TableExportForm;

/**
 * Genomic region search ajax calls.
 *
 * @author <NAME>
 */
public class GenomicRegionSearchAjaxAction extends Action
{
    @SuppressWarnings("unused")
    private static final Logger LOG = Logger
            .getLogger(GenomicRegionSearchAjaxAction.class);

    private String spanUUIDString;
    private GenomicRegionSearchService grsService;
    private Map<String, Map<GenomicRegion, List<List<String>>>> spanOverlapFullResultMap;
    private Map<String, Map<GenomicRegion, Map<String, Integer>>> spanOverlapFullStatMap;
    private Map<GenomicRegionSearchConstraint, String> spanConstraintMap;
    private HttpSession session;
    private WebConfig webConfig;
    private Profile profile;
    private InterMineAPI api;
{'fraction_non_alphanumeric': 0.09744634184552718, 'fraction_numerical': 0.0028199906000313333, 'mean_word_length': 5.677824267782427, 'pattern_counts': {'":': 0, '<': 23, '<?xml version=': 0, '>': 23, 'https://': 0, 'lorem ipsum': 0, 'www.': 2, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '6819219', 'n_tokens_mistral': 1932, 'n_tokens_neox': 1900, 'n_words': 378}