/*
 * Copyright 2015-2020 OpenCB
 *
 * 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 org.opencb.opencga.core.models.sample;

import org.opencb.biodata.models.clinical.ClinicalComment;

import java.io.Serializable;
import java.util.ArrayList;
import java.util.List;

public class SampleQualityControl implements Serializable {

    List<String> fileIds;
    List<ClinicalComment> comments;
    List<SampleAlignmentQualityControlMetrics> alignmentMetrics;
    SampleVariantQualityControlMetrics variantMetrics;


    public SampleQualityControl() {
        this(new ArrayList<>(), new ArrayList<>(), new ArrayList<>(), null);
    }

    public SampleQualityControl(List<String> fileIds, List<ClinicalComment> comments,
                                List<SampleAlignmentQualityControlMetrics> alignmentMetrics,
                                SampleVariantQualityControlMetrics variantMetrics) {
        this.fileIds = fileIds;
        this.comments = comments;
        this.alignmentMetrics = alignmentMetrics;
        this.variantMetrics = variantMetrics;
    }

    @Override
    public String toString() {
        final StringBuilder sb = new StringBuilder("SampleQualityControl{");
        sb.append("fileIds=").append(fileIds);
        sb.append(", comments=").append(comments);
        sb.append(", alignmentMetrics=").append(alignmentMetrics);
        sb.append(", variantMetrics=").append(variantMetrics);
        sb.append('}');
        return sb.toString();
    }

    public List<String> getFileIds() {
        return fileIds;
    }

    public SampleQualityControl setFileIds(List<String> fileIds) {
        this.fileIds = fileIds;
        return this;
    }

    public List<ClinicalComment> getComments() {
        return comments;
    }

    public SampleQualityControl setComments(List<ClinicalComment> comments) {
        this.comments = comments;
        return this;
    }

    public List<SampleAlignmentQualityControlMetrics> getAlignmentMetrics() {
        return alignmentMetrics;
    }

    public SampleQualityControl setAlignmentMetrics(List<SampleAlignmentQualityControlMetrics> alignmentMetrics) {
        this.alignmentMetrics = alignmentMetrics;
        return this;
    }

    public SampleVariantQualityControlMetrics getVariantMetrics() {
        return variantMetrics;
    }

    public SampleQualityControl setVariantMetrics(SampleVariantQualityControlMetrics variantMetrics) {
        this.variantMetrics = variantMetrics;
        return this;
    }
}

@@ -839,24 +839,32 @@
 able %7B%0A%0A    
+private 
 List%3CString%3E
@@ -873,24 +873,32 @@
 ileIds;%0A    
+private 
 List%3CClinica
@@ -917,24 +917,32 @@
 mments;%0A    
+private 
 List%3CSampleA
@@ -990,24 +990,32 @@
 etrics;%0A    
+private 
 SampleVarian
@@ -1054,17 +1054,16 @@
 trics;%0A%0A
-%0A
     publ

make private some Sample QC fields