/*
 *  The MIT License (MIT)
 *
 * Copyright (c) 2016 University of California San Diego
 *
 * Permission is hereby granted, free of charge, to any person obtaining a copy
 * of this software and associated documentation files (the "Software"), to deal
 * in the Software without restriction, including without limitation the rights
 * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the Software is
 * furnished to do so, subject to the following conditions:
 *
 * The above copyright notice and this permission notice shall be included in
 * all copies or substantial portions of the Software.
 *
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
 * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
 * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
 * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
 *  LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
 * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
 * THE SOFTWARE.
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package org.broad.igv.sam;

import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.prefs.PreferencesManager;

import java.util.*;

import static org.broad.igv.prefs.Constants.SAM_HIDE_SMALL_INDEL;
import static org.broad.igv.prefs.Constants.SAM_SMALL_INDEL_BP_THRESHOLD;

/**
 * Created by jrobinso on 12/22/16.
 * <p>
 * Experimental class to test strategies for drawing insertions
 */
public class InsertionManager {

    private static InsertionManager theInstance = new InsertionManager();

    private Map<String, Map<Integer, InsertionMarker>> insertionMaps;
    private Map<String, List<Integer>> positionsMap;
    private Map<String, Integer> selectedInsertions;

    public static synchronized InsertionManager getInstance() {
        return theInstance;
    }

    private InsertionManager() {
        this.insertionMaps = Collections.synchronizedMap(new HashMap<>(100));
        this.positionsMap = Collections.synchronizedMap(new HashMap<>(100));
        this.selectedInsertions = Collections.synchronizedMap(new HashMap<>(100));
    }

    public void clear() {
        this.insertionMaps.clear();
        this.positionsMap.clear();
        this.selectedInsertions.clear();;
    }

    public synchronized List<InsertionMarker> getInsertions(String chrName, double start, double end) {


        Map<Integer, InsertionMarker> insertionMap = insertionMaps.get(chrName);
        List<Integer> positions = positionsMap.get(chrName);
        if(insertionMap == null || positions == null) return null;

        List<InsertionMarker> insertionMarkers = new ArrayList<>();
        for (int i = 0; i < positions.size(); i++) {
            final Integer key = positions.get(i);
            if (key > end) break;
            if (key >= start) {
                final InsertionMarker insertionMarker = insertionMap.get(key);
                insertionMarkers.add(insertionMarker);
            }
        }
        return insertionMarkers;

    }

    public void setSelected(String chrName, int position) {
        this.selectedInsertions.put(chrName, position);
    }

    public void clearSelected() {
        this.selectedInsertions.clear();
    }

    public InsertionMarker getSelectedInsertion(String chrName) {
        Integer selectedInsertion = selectedInsertions.get(chrName);
        Map<Integer, InsertionMarker> insertionMap = insertionMaps.get(chrName);
        return (selectedInsertion == null  || insertionMap == null) ? null : insertionMap.get(selectedInsertion);
    }


    public void processAlignments(String chr, List<Alignment> alignments) {


        Genome genome = GenomeManager.getInstance().getCurrentGenome();
        chr = genome == null ? chr : genome.getCanonicalChrName(chr);

        Map<Integer, InsertionMarker> insertionMap = insertionMaps.get(chr);
        if(insertionMap == null) {
            insertionMap =  Collections.synchronizedMap(new HashMap<>());
            insertionMaps.put(chr, insertionMap);
        }
        List<Integer> positions = positionsMap.get(chr);
        if(positions == null) {
            positions = new ArrayList<>();
            positionsMap.put(chr, positions);
        }

        int minLength = 0;
        if (PreferencesManager.getPreferences().getAsBoolean(SAM_HIDE_SMALL_INDEL)) {
            minLength = PreferencesManager.getPreferences().getAsInt(SAM_SMALL_INDEL_BP_THRESHOLD);
        }

        for (Alignment a : alignments) {
            AlignmentBlock[] blocks = a.getInsertions();
            if (blocks != null) {
                for (AlignmentBlock block : blocks) {

                    if (block.getBases().length < minLength) continue;

                    Integer key = block.getStart();
                    InsertionMarker insertionMarker = insertionMap.get(key);
                    if (insertionMarker == null) {
                        insertionMarker = new InsertionMarker(block.getStart(), block.getLength());
                        insertionMap.put(key, insertionMarker);
                        positions.add(block.getStart());
                    } else {
                        insertionMarker.size = Math.max(insertionMarker.size, block.getLength());
                    }
                }
            }
        }


        positions.addAll(insertionMap.keySet());
        positions.sort((o1, o2) -> o1 - o2);
    }


}

@@ -3715,24 +3715,28 @@
 on);%0A    %7D%0A%0A
+    
 %0A    public 
@@ -3731,24 +3731,37 @@
 %0A    public 
+synchronized 
 void process

Synchronize alignment processing in InsertionManager