ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject.java Source code

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Here is the source code for ubic.gemma.model.expression.experiment.ExperimentalFactorValueObject.java

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/*
 * The Gemma project
 *
 * Copyright (c) 2007 University of British Columbia
 *
 * 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 ubic.gemma.model.expression.experiment;

import org.apache.commons.lang3.StringUtils;
import ubic.gemma.model.IdentifiableValueObject;
import ubic.gemma.model.common.description.Characteristic;

import java.io.Serializable;
import java.util.Collection;
import java.util.HashSet;
import java.util.Objects;

/**
 * @author luke
 * @author keshav
 */
@SuppressWarnings({ "unused", "WeakerAccess" }) // Used in frontend
public class ExperimentalFactorValueObject extends IdentifiableValueObject<ExperimentalFactor>
        implements Serializable {

    private static final long serialVersionUID = -2615804031123874251L;

    private String category;
    private String categoryUri;

    private String description;

    private String factorValues;

    private String name;
    private Integer numValues = 0;
    private String type = "categorical"; // continuous or categorical.
    private Collection<FactorValueValueObject> values;

    /**
     * Required when using the class as a spring bean.
     */
    public ExperimentalFactorValueObject() {
    }

    public ExperimentalFactorValueObject(Long id) {
        super(id);
    }

    public ExperimentalFactorValueObject(ExperimentalFactor factor) {
        super(factor.getId());
        this.setName(factor.getName());
        this.setDescription(factor.getDescription());

        if (factor.getCategory() != null)
            this.setCategory(factor.getCategory().getCategory());

        this.setCategoryUri(this.getCategoryUri(factor.getCategory()));

        /*
         * Note: this code copied from the ExperimentalDesignController.
         */
        Collection<FactorValueValueObject> vals = new HashSet<>();

        if (factor.getType() != null) {
            this.type = factor.getType().equals(FactorType.CATEGORICAL) ? "categorical" : "continuous";
        } else {
            // Backwards compatibility: for old entries created prior to introduction of 'type' field in
            // ExperimentalFactor entity.
            // We have to take a guess.
            if (factor.getFactorValues().isEmpty()) {
                this.type = "categorical";
            } else {
                // Just use first factor value to make our guess.
                if (factor.getFactorValues().iterator().next().getMeasurement() != null) {
                    this.type = "continuous";
                } else {
                    this.type = "categorical";
                }
            }
        }

        if (factor.getFactorValues() == null || factor.getFactorValues().isEmpty()) {
            return;
        }

        Collection<FactorValue> fvs = factor.getFactorValues();
        StringBuilder factorValuesAsString = new StringBuilder(StringUtils.EMPTY);
        for (FactorValue fv : fvs) {
            String fvName = fv.toString();
            if (StringUtils.isNotBlank(fvName)) {
                factorValuesAsString.append(fvName).append(", ");
            }
        }
        /* clean up the start and end of the string */
        factorValuesAsString = new StringBuilder(
                StringUtils.remove(factorValuesAsString.toString(), factor.getName() + ":"));
        factorValuesAsString = new StringBuilder(StringUtils.removeEnd(factorValuesAsString.toString(), ", "));

        this.setFactorValues(factorValuesAsString.toString());

        this.numValues = factor.getFactorValues().size();
        Characteristic c = factor.getCategory();
        /*
         * NOTE this replaces code that previously made no sense. PP
         */
        for (FactorValue value : factor.getFactorValues()) {
            vals.add(new FactorValueValueObject(value, c));
        }

        this.setValues(vals);
    }

    @Override
    public boolean equals(Object obj) {
        if (this == obj)
            return true;
        if (obj == null)
            return false;
        if (this.getClass() != obj.getClass())
            return false;
        ExperimentalFactorValueObject other = (ExperimentalFactorValueObject) obj;
        return Objects.equals(id, other.id);
    }

    public String getCategory() {
        return category;
    }

    public void setCategory(String category) {
        this.category = category;
    }

    public String getCategoryUri() {
        return categoryUri;
    }

    public void setCategoryUri(String categoryUri) {
        this.categoryUri = categoryUri;
    }

    public String getDescription() {
        return description;
    }

    public void setDescription(String description) {
        this.description = description;
    }

    public String getFactorValues() {
        return factorValues;
    }

    /**
     * @param factorValues Set a string which describes (in summary) the factor values
     */
    public void setFactorValues(String factorValues) {
        this.factorValues = factorValues;
    }

    @Override
    public int hashCode() {
        final int prime = 31;
        int result = 1;
        result = prime * result + (int) (id ^ (id >>> 32));
        return result;
    }

    public String getName() {
        return name;
    }

    public void setName(String name) {
        this.name = name;
    }

    /**
     * @return the numValues
     */
    public Integer getNumValues() {
        return this.numValues;
    }

    /**
     * @param numValues the numValues to set
     */
    public void setNumValues(Integer numValues) {
        this.numValues = numValues;
    }

    public String getType() {
        return type;
    }

    public void setType(String type) {
        this.type = type;
    }

    public Collection<FactorValueValueObject> getValues() {
        return values;
    }

    public void setValues(Collection<FactorValueValueObject> values) {
        this.values = values;
    }

    private String getCategoryUri(Characteristic c) {
        return c.getCategoryUri();

    }

}