/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
package org.broad.igv.track;
//~--- JDK imports ------------------------------------------------------------
import org.apache.log4j.Logger;
import org.broad.igv.util.ParsingUtils;
import java.awt.*;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
/**
* This class is based on the UCSC track configuration parameters
*
* @author jrobinso
*/
public class TrackProperties {
private static Logger log = Logger.getLogger(TrackProperties.class);
private String trackLine;
public enum BaseCoord {
ZERO, ONE, UNSPECIFIED
}
private Track.DisplayMode displayMode;
/**
* Base coordinate system, either 0 or 1
*/
private BaseCoord baseCoord = BaseCoord.UNSPECIFIED;
/**
* The track name. Will be displayed to the left of the track.
*/
private String name;
/**
* The track description. The description, when supplied, will appear in popup text
* when hovering over the track. May optionally be displayed centered over the track
* on certain chart types (currently scatter plot and barchart).
*/
private String description;
/**
* A url to an web page associated with this track. This is currently not used.
*/
private String url;
/**
* The track height in pixels
*/
private int height;
private int minHeight;
private boolean gffTags = false;
/**
* The default color for the track. This can be overridden by individual feature lines in
* certain formats, notably BED.
*/
private Color color;
/**
* An alternate color. The use of this color depends on the particular graph type (renderer)
* being displayed. See documentation for specific renderes for details.
*/
private Color altColor;
private Color midColor;
private String genome;
private int offset;
private boolean autoScaleFlag = false;
private float minValue = Float.NaN;
private float maxValue = Float.NaN;
private float midValue = Float.NaN;
private float neutralFromValue = Float.NaN;
private float neutralToValue = Float.NaN;
private boolean drawYLine = false;
private Class rendererClass;
private WindowFunction windowingFunction;
private int smoothingWindow;
private boolean itemRGB = true;
private boolean useScore = false;
private int featureVisibilityWindow = -1;
private boolean logScale;
private float yLine;
private boolean sortable = true;
private boolean alternateExonColor = false;
private String dataURL;
private String indexURL;
private String coverageURL;
/**
* Track attributes (meta data)
*/
private Map<String, String> attributes;
public TrackProperties() {
}
public void setTrackLine(String trackLine) {
this.trackLine = trackLine;
}
public String getTrackLine() {
return this.trackLine;
}
public boolean isSortable() {
return sortable;
}
public void setSortable(boolean sortable) {
this.sortable = sortable;
}
public boolean isLogScale() {
return logScale;
}
public void setLogScale(boolean logScale) {
this.logScale = logScale;
}
public int getFeatureVisibilityWindow() {
return featureVisibilityWindow;
}
public void setFeatureVisibilityWindow(int featureVisibilityWindow) {
this.featureVisibilityWindow = featureVisibilityWindow;
}
public boolean isUseScore() {
return useScore;
}
public void setUseScore(boolean useScore) {
this.useScore = useScore;
}
public boolean isItemRGB() {
return itemRGB;
}
public void setItemRGB(boolean itemRGB) {
this.itemRGB = itemRGB;
}
/**
* Method description
*
* @return
*/
public int getOffset() {
return offset;
}
public void setOffset(int offset) {
this.offset = offset;
}
public String getName() {
return name;
}
public void setName(String name) {
this.name = name;
}
public String getDescription() {
return description;
}
public void setDescription(String description) {
this.description = description;
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public int getHeight() {
return height;
}
public void setHeight(int height) {
this.height = height;
}
public Color getColor() {
return color;
}
public void setColor(Color color) {
this.color = color;
}
public Color getAltColor() {
return altColor;
}
public void setAltColor(Color altColor) {
this.altColor = altColor;
}
public boolean isAutoScale() {
return autoScaleFlag || Float.isNaN(minValue) || Float.isNaN(maxValue);
}
public boolean getAutoScale() {
return this.autoScaleFlag;
}
public String getGenome() {
return genome;
}
public void setGenome(String genome) {
this.genome = genome;
}
public float getMinValue() {
return minValue;
}
public void setMinValue(float minValue) {
this.minValue = minValue;
}
public float getMaxValue() {
return maxValue;
}
public void setMaxValue(float maxValue) {
this.maxValue = maxValue;
}
public WindowFunction getWindowingFunction() {
return windowingFunction;
}
public void setWindowingFunction(WindowFunction windowingFunction) {
this.windowingFunction = windowingFunction;
}
public int getSmoothingWindow() {
return smoothingWindow;
}
public void setSmoothingWindow(int smoothingWindow) {
this.smoothingWindow = smoothingWindow;
}
public Class getRendererClass() {
return rendererClass;
}
public void setRendererClass(Class rendererClass) {
this.rendererClass = rendererClass;
}
public void setAutoScale(boolean autoScale) {
this.autoScaleFlag = autoScale;
}
public float getMidValue() {
return midValue;
}
public void setMidValue(float midValue) {
this.midValue = midValue;
}
public Color getMidColor() {
return midColor;
}
public void setMidColor(Color midColor) {
this.midColor = midColor;
}
public boolean isDrawYLine() {
return drawYLine;
}
public void setDrawYLine(boolean drawYLine) {
this.drawYLine = drawYLine;
}
public int getMinHeight() {
return minHeight;
}
public void setMinHeight(int minHeight) {
this.minHeight = minHeight;
}
public BaseCoord getBaseCoord() {
return baseCoord;
}
public void setBaseCoord(BaseCoord baseCoord) {
this.baseCoord = baseCoord;
}
public float getNeutralFromValue() {
return neutralFromValue;
}
public void setNeutralFromValue(float neutralFromValue) {
this.neutralFromValue = neutralFromValue;
}
public float getNeutralToValue() {
return neutralToValue;
}
public void setNeutralToValue(float neutralToValue) {
this.neutralToValue = neutralToValue;
}
public float getyLine() {
return yLine;
}
public void setyLine(float yLine) {
this.yLine = yLine;
}
public void setGffTags(boolean gffTags) {
this.gffTags = gffTags;
}
public boolean isGffTags() {
return gffTags;
}
public boolean isAlternateExonColor() {
return alternateExonColor;
}
public void setAlternateExonColor(boolean alternateExonColor) {
this.alternateExonColor = alternateExonColor;
}
public void setDisplayMode(Track.DisplayMode displayMode) {
this.displayMode = displayMode;
}
public Track.DisplayMode getDisplayMode() {
return displayMode;
}
public String getDataURL() {
return dataURL;
}
public String getIndexURL() {
return indexURL;
}
public String getCoverageURL() {
return coverageURL;
}
public void setDataURL(String dataURL) {
this.dataURL = dataURL;
}
public void setIndexURL(String indexURL) {
this.indexURL = indexURL;
}
public void setCoverageURL(String coverageURL) {
this.coverageURL = coverageURL;
}
public Map<String,String> getAttributes() {
return attributes;
}
/**
* example:
* Library=DNA_Lib 1387;Sample=NH-Osteoblast;Antibody=H3K4me3
*
* @param value
*/
public void setMetaData(String value) {
if (attributes == null) {
attributes = new LinkedHashMap<String, String>(); // <= maintain order
}
String[] attStrings = ParsingUtils.SEMI_COLON_PATTERN.split(value);
for (String att : attStrings) {
String[] kv = ParsingUtils.EQ_PATTERN.split(att, 2);
if (kv.length == 2) {
attributes.put(kv[0], kv[1]);
} else {
log.info("Skipping meta value: " + value + ". Missing '=' token?");
}
}
}
}