lphy.base.function.alignment.MetaDataOptions Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of lphy-base Show documentation

The standard library of LPhy, which contains the required generative distributions and basic functions.

The newest version!

package lphy.base.function.alignment;

import lphy.base.function.io.ReadFasta;
import lphy.base.function.io.ReadNexus;
import lphy.core.model.Value;

import java.util.Map;

/**
 * For example, {@link #AGE_DIRECTION} and {@link #AGE_REGEX}.
 * @author Walter Xie
 * @see ReadNexus
 * @see ReadFasta
 */
public final class MetaDataOptions {

    protected static final String AGE_DIRECTION = "ageDirection";
    protected static final String AGE_REGEX = "ageRegex";

    protected static final String SPECIESE_REGEX = "speciesRegex";

    public static final String OPT_DESC = "the map containing optional arguments and their values for reuse, " +
            "                          such as " + AGE_DIRECTION + " and " + AGE_REGEX + ".";

    public static String getAgeDirectionStr(Value> optionsVal) {
        Map options = optionsVal == null ? null : optionsVal.value();
        return options == null ? null : options.get(AGE_DIRECTION);
    }

    /**
     * @param optionsVal
     * @return The string of regex to extract ages from taxa labels.
     */
    public static String getAgeRegxStr(Value> optionsVal) {
        Map options = optionsVal == null ? null : optionsVal.value();
        return options == null ? null : options.get(AGE_REGEX);
    }

    public static String getSpecieseRegex(Value> optionsVal) {
        Map options = optionsVal == null ? null : optionsVal.value();
        return options == null ? null : options.get( SPECIESE_REGEX );
    }

    public static boolean isSame(Map options1, Map options2) {
        if (options1 == options2) return true; // include null == null
        if (options1 == null || options2 == null) return false;
        for (Map.Entry entry : options1.entrySet()) {
            // no key
            if (!options2.containsKey(entry.getKey())) return false;
            // not same value
            String opt2Val = options2.get(entry.getKey());
            if (!entry.getValue().equals(opt2Val)) return false;
        }
        return true;
    }


}