QuantitationUtilities.java

/*
 * Copyright (c) 2003-2012 Fred Hutchinson Cancer Research Center
 *
 * 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.fhcrc.cpl.toolbox.proteomics;

import org.apache.log4j.Logger;
import org.fhcrc.cpl.toolbox.proteomics.feature.Feature;
import org.fhcrc.cpl.toolbox.proteomics.feature.extraInfo.MS2ExtraInfoDef;


/**
 * Utilities for working with quantitation
 */
public class QuantitationUtilities
{
    protected static Logger _log = Logger.getLogger(QuantitationUtilities.class);

    public static final float SILAC_LABEL_MASSDIFF_PERRESIDUE = 6.020129f;
    public static final String ALGORITHM_Q3 = "Q3";
    public static final String ALGORITHM_XPRESS = "XPRESS";

    public static final float ACRYLAMIDE_LABEL_LIGHTMASS = 174.0458f;
    public static final float ACRYLAMIDE_LABEL_HEAVYMASS = 177.05591f;

    public static final float SILAC_LABEL_MASS = 134.115092f;
    public static final float ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE =
            ACRYLAMIDE_LABEL_HEAVYMASS - ACRYLAMIDE_LABEL_LIGHTMASS;

    //internal integer codes representing all known isotopic label types
    public static final int LABEL_ACRYLAMIDE = 0;
    public static final int LABEL_LYCINE = 1;
    public static final int LABEL_LYCINE_ARGININE = 2;


    //codes representing all known isotopic label types.
//    public static final String LABEL_ACRYLAMIDE_CODE = "acrylamide";
//    public static final String LABEL_LYCINE_CODE = "silac";

    //Human-readable explanations representing all known isotopic label types.
//    public static final String LABEL_ACRYLAMIDE_EXPLANATION = "Acrylamide (3.0106Da on C)";
//    public static final String LABEL_LYCINE_EXPLANATION = "SILAC Lycine labeling (134.115092 on K, i.e. 6Da SILAC)";

    //Array with codes representing all known isotopic label types.
    //All of these should be defined as string constants
    // When adding to this, add to ALL_LABEL_EXPLANATIONS, in same order
//    public static final String[] ALL_LABEL_CODES = new String[]
//            {
//                    LABEL_ACRYLAMIDE_CODE,
//                    LABEL_LYCINE_CODE
//            };

    //human-readable explanations of isotopic label types
//    public static final String[] ALL_LABEL_EXPLANATIONS = new String[]
//            {
//                    LABEL_ACRYLAMIDE_EXPLANATION,
//                    LABEL_LYCINE_EXPLANATION
//            };


    /**
     * Calculate the difference between heavy and light masses of a completely heavy and completely light
     * labeled version of this peptide
     * @param peptide
     * @param labelType
     * @return
     */
//    public static float calcHeavyLightMassDiff(String peptide, int labelType)
//    {
//        String residue = "";
//        switch(labelType)
//        {
//            case LABEL_ACRYLAMIDE:
//                residue = "C";
//                break;
//            case LABEL_LYCINE:
//                residue = "K";
//                break;
//        }
//        int numLabels = 0;
//        for (int i=0; i<peptide.length(); i++)
//        {
//            if (residue.equals("" + peptide.charAt(i)))
//                numLabels++;
//        }
//
//        return numLabels * (labelType == LABEL_ACRYLAMIDE ? ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE :
//                SILAC_LABEL_MASSDIFF_PERRESIDUE);
//    }

    /**
     * Infer a label type by its residue and mass diff.  If can't, return -1;
     * @param residue
     * @param massDiff
     * @return
     */
//    public static int inferLabelType(String residue, float massDiff)
//    {
//        float slop = 0.1f;
//        if (residue.equalsIgnoreCase("C"))
//        {
//            if (Math.abs(ACRYLAMIDE_LABEL_MASSDIFF_PERRESIDUE - massDiff) < slop)
//                return LABEL_ACRYLAMIDE;
//        }
//        else if (residue.equalsIgnoreCase("K"))
//        {
//            if (Math.abs(SILAC_LABEL_MASSDIFF_PERRESIDUE - massDiff) < slop)
//                return LABEL_LYCINE;
//        }
//        return -1;
//    }
}