// Path: scala/org/broad/igv/WindowFunction.java
// public enum WindowFunction {
// 
//     mean("Mean"),
//     median("Median"),
//     min("Minimum"),
//     max("Maximum"),
//     percentile2("2nd Percentile"),
//     percentile10("10th Percentile"),
//     percentile90("90th Percentile"),
//     percentile98("98th Percentile"),
// //    stddev("Standard Deviation"),
//     count("Count");
// //    density("Density");
// 
//     private String displayName = "";
// 
//     WindowFunction(String displayName) {
//         this.displayName = displayName;
//     }
// 
//     public String getDisplayName() {
//         return displayName;
//     }
// 
//     static public WindowFunction getWindowFunction(String name) {
// 
//         WindowFunction windowFunction = null;
//         if (WindowFunction.mean.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.mean;
//         } else if (WindowFunction.median.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.median;
//         } else if (WindowFunction.min.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.min;
//         } else if (WindowFunction.max.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.max;
//         } else if (WindowFunction.percentile10.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.percentile10;
//         } else if (WindowFunction.percentile90.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.percentile90;
//         } else if (WindowFunction.percentile98.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.percentile98;
// //        } else if (WindowFunction.stddev.name().equals(name)) {
// //            windowFunction = WindowFunction.stddev;
//         } else if (WindowFunction.count.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.count;
// //        } else if (WindowFunction.density.name().equals(name)) {
// //            windowFunction = WindowFunction.density;
//         }
//         return windowFunction;
//     }
// }


import org.broad.igv.WindowFunction;
import org.broad.tribble.Feature;
/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package org.broad.igv;


/**
 * @author jrobinso
 */
public interface LocusScore  extends Feature {

    //public int getStart();

   // public int getEnd();
    
    public void setStart(int start);

    public void setEnd(int end);

    public float getScore();

    public void setConfidence(float confidence);

    public float getConfidence();

    public LocusScore copy();

    /**
     * Return a string to be used for popup text.   The WindowFunction is passed
     * in so it can be used t annotate the value.  The LocusScore object itself
     * does not "know" from what window function it was derived
     *
     * @param windowFunction
     * @return
     */
// Path: scala/org/broad/igv/WindowFunction.java
// public enum WindowFunction {
// 
//     mean("Mean"),
//     median("Median"),
//     min("Minimum"),
//     max("Maximum"),
//     percentile2("2nd Percentile"),
//     percentile10("10th Percentile"),
//     percentile90("90th Percentile"),
//     percentile98("98th Percentile"),
// //    stddev("Standard Deviation"),
//     count("Count");
// //    density("Density");
// 
//     private String displayName = "";
// 
//     WindowFunction(String displayName) {
//         this.displayName = displayName;
//     }
// 
//     public String getDisplayName() {
//         return displayName;
//     }
// 
//     static public WindowFunction getWindowFunction(String name) {
// 
//         WindowFunction windowFunction = null;
//         if (WindowFunction.mean.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.mean;
//         } else if (WindowFunction.median.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.median;
//         } else if (WindowFunction.min.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.min;
//         } else if (WindowFunction.max.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.max;
//         } else if (WindowFunction.percentile10.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.percentile10;
//         } else if (WindowFunction.percentile90.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.percentile90;
//         } else if (WindowFunction.percentile98.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.percentile98;
// //        } else if (WindowFunction.stddev.name().equals(name)) {
// //            windowFunction = WindowFunction.stddev;
//         } else if (WindowFunction.count.name().equalsIgnoreCase(name)) {
//             windowFunction = WindowFunction.count;
// //        } else if (WindowFunction.density.name().equals(name)) {
// //            windowFunction = WindowFunction.density;
//         }
//         return windowFunction;
//     }
// }


// Path: scala/org/broad/igv/LocusScore.java
import org.broad.igv.WindowFunction;
import org.broad.tribble.Feature;

/*
 * Copyright (c) 2007-2010 by The Broad Institute, Inc. and the Massachusetts Institute of Technology.
 * All Rights Reserved.
 *
 * This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which
 * is available at http://www.opensource.org/licenses/lgpl-2.1.php.
 *
 * THE SOFTWARE IS PROVIDED "AS IS." THE BROAD AND MIT MAKE NO REPRESENTATIONS OR WARRANTIES OF
 * ANY KIND CONCERNING THE SOFTWARE, EXPRESS OR IMPLIED, INCLUDING, WITHOUT LIMITATION, WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE, NONINFRINGEMENT, OR THE ABSENCE OF LATENT
 * OR OTHER DEFECTS, WHETHER OR NOT DISCOVERABLE.  IN NO EVENT SHALL THE BROAD OR MIT, OR THEIR
 * RESPECTIVE TRUSTEES, DIRECTORS, OFFICERS, EMPLOYEES, AND AFFILIATES BE LIABLE FOR ANY DAMAGES OF
 * ANY KIND, INCLUDING, WITHOUT LIMITATION, INCIDENTAL OR CONSEQUENTIAL DAMAGES, ECONOMIC
 * DAMAGES OR INJURY TO PROPERTY AND LOST PROFITS, REGARDLESS OF WHETHER THE BROAD OR MIT SHALL
 * BE ADVISED, SHALL HAVE OTHER REASON TO KNOW, OR IN FACT SHALL KNOW OF THE POSSIBILITY OF THE
 * FOREGOING.
 */

/*
 * To change this template, choose Tools | Templates
 * and open the template in the editor.
 */
package org.broad.igv;


/**
 * @author jrobinso
 */
public interface LocusScore  extends Feature {

    //public int getStart();

   // public int getEnd();
    
    public void setStart(int start);

    public void setEnd(int end);

    public float getScore();

    public void setConfidence(float confidence);

    public float getConfidence();

    public LocusScore copy();

    /**
     * Return a string to be used for popup text.   The WindowFunction is passed
     * in so it can be used t annotate the value.  The LocusScore object itself
     * does not "know" from what window function it was derived
     *
     * @param windowFunction
     * @return
     */
    public String getValueString(double position, WindowFunction windowFunction);