// Path: scala/org/broad/igv/LocusScore.java
// 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);
// }
// 
// 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 java.util.Collection;
import java.util.List;
import org.broad.igv.LocusScore;
import org.broad.igv.WindowFunction;
/*
 * 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 DataSource {

	double getDataMax();

	double getDataMin();

	List<LocusScore> getSummaryScoresForRange(String chr, int startLocation, int endLocation, int zoom);

	void setWindowFunction(WindowFunction statType);

	boolean isLogNormalized();

	void refreshData(long timestamp);

// Path: scala/org/broad/igv/LocusScore.java
// 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);
// }
// 
// 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/DataSource.java
import java.util.Collection;
import java.util.List;
import org.broad.igv.LocusScore;
import org.broad.igv.WindowFunction;

/*
 * 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 DataSource {

	double getDataMax();

	double getDataMin();

	List<LocusScore> getSummaryScoresForRange(String chr, int startLocation, int endLocation, int zoom);

	void setWindowFunction(WindowFunction statType);

	boolean isLogNormalized();

	void refreshData(long timestamp);

	public WindowFunction getWindowFunction();