/*
* 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;
//~--- non-JDK imports --------------------------------------------------------
import htsjdk.tribble.Feature;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.event.IGVEventBus;
import org.broad.igv.event.IGVEventObserver;
import org.broad.igv.gwas.GWASTrack;
import org.broad.igv.prefs.PreferencesManager;
import org.broad.igv.renderer.*;
import org.broad.igv.sam.AlignmentTrack;
import org.broad.igv.sam.CoverageTrack;
import org.broad.igv.session.IGVSessionReader;
import org.broad.igv.session.SessionXmlAdapters;
import org.broad.igv.session.SubtlyImportant;
import org.broad.igv.ui.FontManager;
import org.broad.igv.ui.IGV;
import org.broad.igv.ui.TooltipTextFrame;
import org.broad.igv.ui.UIConstants;
import org.broad.igv.ui.panel.AttributeHeaderPanel;
import org.broad.igv.ui.panel.IGVPopupMenu;
import org.broad.igv.ui.panel.MouseableRegion;
import org.broad.igv.ui.panel.ReferenceFrame;
import org.broad.igv.ui.util.UIUtilities;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.Utilities;
import org.w3c.dom.Node;
import javax.xml.bind.JAXBException;
import javax.xml.bind.annotation.*;
import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
import java.awt.*;
import java.awt.event.MouseEvent;
import java.util.*;
import java.util.List;
import static org.broad.igv.prefs.Constants.*;
/**
* @author jrobinso
*/
@XmlType(factoryClass = IGVSessionReader.class, factoryMethod = "getNextTrack")
@XmlAccessorType(XmlAccessType.NONE)
@XmlSeeAlso({CNFreqTrack.class, CoverageTrack.class, AlignmentTrack.class, DataSourceTrack.class, GWASTrack.class, FeatureTrack.class, MergedTracks.class})
public abstract class AbstractTrack implements Track {
private static Logger log = Logger.getLogger(AbstractTrack.class);
/**
* Classes which we have tried to marshal/unmarshal
* and have failed. Since we just use exception catching (slow),
* we don't want to repeat failures
*/
public static final Set<Class> knownUnknownTrackClasses = new HashSet<Class>();
public static final Class defaultTrackClass = AbstractTrack.class;
/**
* Set default renderer classes by track type.
*/
private static Class defaultRendererClass = BarChartRenderer.class;
private static Map<TrackType, Class> defaultRendererMap = new HashMap();
static {
defaultRendererMap.put(TrackType.RNAI, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.COPY_NUMBER, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.CNV, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.ALLELE_SPECIFIC_COPY_NUMBER, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.GENE_EXPRESSION, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.DNA_METHYLATION, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.LOH, HeatmapRenderer.class);
defaultRendererMap.put(TrackType.OTHER, BarChartRenderer.class);
defaultRendererMap.put(TrackType.CHIP_CHIP, HeatmapRenderer.class);
}
@XmlAttribute
private String id;
@XmlAttribute
private String name;
private String url;
private boolean itemRGB = true;
private boolean useScore;
private float viewLimitMin = Float.NaN; // From UCSC track line
private float viewLimitMax = Float.NaN; // From UCSC track line
@XmlAttribute
protected int fontSize = PreferencesManager.getPreferences().getAsInt(DEFAULT_FONT_SIZE);
private boolean showDataRange = true;
private String sampleId;
private ResourceLocator resourceLocator;
private int top;
protected int minimumHeight = -1;
protected int maximumHeight = 1000;
private TrackType trackType = TrackType.OTHER;
private boolean selected = false;
@XmlAttribute
private boolean visible = true;
@XmlAttribute
private boolean sortable = true;
boolean overlaid;
boolean drawYLine = false;
float yLine = 0;
// Map to store attributes specific to this track. Attributes shared by multiple
private Map<String, String> attributes = new HashMap();
// Scale for heatmaps
@XmlJavaTypeAdapter(SessionXmlAdapters.ContinuousColorScale.class)
@XmlAttribute
private ContinuousColorScale colorScale;
//TODO Only write it out for applicable tracks
//Not applicable to all tracks.
@XmlAttribute
protected boolean autoScale;
@XmlJavaTypeAdapter(SessionXmlAdapters.Color.class)
@XmlAttribute(name = "color")
protected Color posColor = Color.blue.darker();
@XmlJavaTypeAdapter(SessionXmlAdapters.Color.class)
@XmlAttribute
protected Color altColor = posColor;
@XmlAttribute(name = "featureVisibilityWindow")
protected int visibilityWindow = -1;
@XmlAttribute
private DisplayMode displayMode = DisplayMode.COLLAPSED;
@XmlJavaTypeAdapter(SessionXmlAdapters.Height.class)
@XmlAttribute
protected Integer height = -1;
@XmlElement(name = "DataRange")
protected DataRange dataRange;
@SubtlyImportant
protected AbstractTrack() {
}
public AbstractTrack(
ResourceLocator dataResourceLocator,
String id,
String name) {
this.resourceLocator = dataResourceLocator;
this.id = id;
this.name = name;
init();
}
public AbstractTrack(ResourceLocator dataResourceLocator, String id) {
this(dataResourceLocator, id, dataResourceLocator.getTrackName());
}
public AbstractTrack(ResourceLocator locator) {
this(locator, locator != null ? locator.getPath() : null, locator != null ? locator.getTrackName() : null);
}
public AbstractTrack(String id) {
this(null, id, id);
}
public AbstractTrack(String id, String name) {
this(null, id, name);
}
private void init() {
showDataRange = PreferencesManager.getPreferences().getAsBoolean(CHART_SHOW_DATA_RANGE);
if (PreferencesManager.getPreferences().getAsBoolean(EXPAND_FEAUTRE_TRACKS)) {
displayMode = DisplayMode.EXPANDED;
}
}
public void setRendererClass(Class rc) {
// Ignore by default
}
public String getUrl() {
return url;
}
public void setUrl(String url) {
this.url = url;
}
public void setUseScore(boolean useScore) {
this.useScore = useScore;
}
public String getId() {
return id;
}
public void setName(String name) {
this.name = name;
}
public String getName() {
return name;
}
private String getDisplayName() {
String sampleKey = IGV.getInstance().getSession().getTrackAttributeName();
if (sampleKey != null && sampleKey.trim().length() > 0) {
String name = getAttributeValue(sampleKey.trim());
if (name != null) {
return name;
}
}
return getName();
}
public void setSampleId(String sampleId) {
this.sampleId = sampleId;
}
@Override
public boolean isFilterable() {
return true; // True by default
}
public void renderName(Graphics2D g2D, Rectangle trackRectangle, Rectangle visibleRectangle) {
Rectangle rect = getDisplayableRect(trackRectangle, visibleRectangle);
String trackName = getDisplayName();
if ((trackName != null)) {
if (rect.getHeight() > 3) {
// Calculate fontsize
int gap = Math.min(4, rect.height / 3);
int fs = Math.min(fontSize, rect.height - gap);
Font font = FontManager.getFont(fs);
g2D.setFont(font);
GraphicUtils.drawWrappedText(trackName, rect, g2D, false);
//g2D.dispose();
}
}
}
public void renderAttributes(Graphics2D graphics, Rectangle trackRectangle, Rectangle visibleRect,
List<String> names, List<MouseableRegion> mouseRegions) {
int x = trackRectangle.x;
for (String name : names) {
String key = name.toUpperCase();
String attributeValue = getAttributeValue(key);
if (attributeValue != null) {
Rectangle rect = new Rectangle(x, trackRectangle.y, AttributeHeaderPanel.ATTRIBUTE_COLUMN_WIDTH,
trackRectangle.height);
graphics.setColor(AttributeManager.getInstance().getColor(key, attributeValue));
graphics.fill(rect);
mouseRegions.add(new MouseableRegion(rect, key, attributeValue));
// Border
// graphics.setColor(Color.lightGray);
// graphics.fillRect(x + AttributeHeaderPanel.ATTRIBUTE_COLUMN_WIDTH, trackRectangle.y,
// AttributeHeaderPanel.COLUMN_BORDER_WIDTH, trackRectangle.height);
}
x += AttributeHeaderPanel.ATTRIBUTE_COLUMN_WIDTH + AttributeHeaderPanel.COLUMN_BORDER_WIDTH;
}
}
private Rectangle getDisplayableRect(Rectangle trackRectangle, Rectangle visibleRect) {
Rectangle rect = null;
if (visibleRect != null) {
Rectangle intersectedRect = trackRectangle.intersection(visibleRect);
if (intersectedRect.height > 15) {
rect = intersectedRect;
} else {
rect = new Rectangle(trackRectangle);
}
}
return rect;
}
/**
* Called to overlay a track on another, presumably previously rendered,
* track. The default behavior is to do nothing.
*
* @param context
* @param rect
*/
public void overlay(RenderContext context, Rectangle rect) {
}
public Color getColor() {
return posColor;
}
public Color getAltColor() {
return altColor;
}
public ResourceLocator getResourceLocator() {
return resourceLocator;
}
public Collection<ResourceLocator> getResourceLocators() {
return Arrays.asList(getResourceLocator());
}
/**
* Add an attribute to this track and register the key with the attribute panel.
* <p/>
* Note: Attribute keys are case insensitive. Currently this is implemented
* by forcing all keys to upper case
*
* @param name
* @param value
*/
public void setAttributeValue(String name, String value) {
String key = name.toUpperCase();
attributes.put(key, value);
AttributeManager.getInstance().addAttribute(getSample(), name, value);
}
public void removeAttribute(String name) {
String key = name.toUpperCase();
attributes.remove(key);
AttributeManager.getInstance().removeAttribute(getSample(), name);
}
/**
* Return the attribute value. Attribute lookup occurs in the following order, if all fail null is returned.
* <p/>
* (1) the track attribute table
* (2) by sampleId, as set in the Resource element of a session or load-from-server menu
* (3) by track name, the visible display name
* (4) by full path to the file associated with this track
*
* @param attributeName
* @return
*/
public String getAttributeValue(String attributeName) {
String key = attributeName.toUpperCase();
String value = attributes.get(key);
final AttributeManager attributeManager = AttributeManager.getInstance();
if (value == null && getSample() != null) {
value = attributeManager.getAttribute(getSample(), key);
}
if (value == null) {
value = attributeManager.getAttribute(getName(), key);
}
if (value == null && getResourceLocator() != null && getResourceLocator().getPath() != null) {
value = attributeManager.getAttribute(getResourceLocator().getPath(), key);
}
return value;
}
public String getSample() {
if (sampleId != null) {
return sampleId;
}
// String sample = AttributeManager.getInstance().getSampleFor(getName());
// return sample != null ? sample : getName();
sampleId = AttributeManager.getInstance().getSampleFor(getName());
return sampleId != null ? sampleId : getName();
}
/**
* Returns the default height based on the default renderer for the data
* type, as opposed to the actual renderer in use. This is done to prevent
* the track size from changing if renderer is changed.
*
* @return
*/
private int getDefaultHeight() {
if (XYPlotRenderer.class.isAssignableFrom(getDefaultRendererClass())) {
return PreferencesManager.getPreferences().getAsInt(CHART_TRACK_HEIGHT_KEY);
} else {
return PreferencesManager.getPreferences().getAsInt(TRACK_HEIGHT_KEY);
}
}
/**
* Returns the default minimum height based on the actual renderer for this track. Heatmaps default
* to 1, all other renderers to 5.
*
* @return
*/
public int getDefaultMinimumHeight() {
Renderer r = getRenderer();
if (r != null && HeatmapRenderer.class.isAssignableFrom(r.getClass())) {
return 1;
} else {
return 10;
}
}
public void setMinimumHeight(int minimumHeight) {
this.minimumHeight = minimumHeight;
}
public void setMaximumHeight(int maximumHeight) {
this.maximumHeight = maximumHeight;
}
/**
* Return the actual minimum height if one has been set, otherwise get the default for the current renderer.
*
* @return
*/
public int getMinimumHeight() {
return minimumHeight < 0 ? getDefaultMinimumHeight() : minimumHeight;
}
public int getMaximumHeight() {
return maximumHeight;
}
public void setTrackType(TrackType type) {
this.trackType = type;
}
public TrackType getTrackType() {
return trackType;
}
public boolean isVisible() {
if (visible && getTrackType() == TrackType.MUTATION) {
// Special rules for mutations. If display as overlays == true, only show if not overlaid on another
// track and "show orphaned" is true
boolean displayOverlays = IGV.getInstance().getSession().getOverlayMutationTracks();
if (displayOverlays) {
if (overlaid) {
return false;
} else {
return PreferencesManager.getPreferences().getAsBoolean(SHOW_ORPHANED_MUTATIONS);
}
}
}
return visible;
}
public void setColor(Color color) {
this.posColor = color;
}
public void setAltColor(Color color) {
altColor = color;
}
public void setVisible(boolean isVisible) {
this.visible = isVisible;
}
public void setOverlayed(boolean bool) {
this.overlaid = bool;
}
public void setSelected(boolean selected) {
this.selected = selected;
}
public boolean isSelected() {
return selected;
}
public void setHeight(int height) {
setHeight(height, false);
}
@Override
public void setHeight(int preferredHeight, boolean force) {
if (height < getHeight()) {
if ((this.getDisplayMode() == DisplayMode.EXPANDED) && (getTrackType() != TrackType.GENE)) {
this.setDisplayMode(DisplayMode.SQUISHED);
}
}
if (force) {
this.height = preferredHeight;
} else {
this.height = Math.min(Math.max(getMinimumHeight(), preferredHeight), getMaximumHeight());
}
}
public int getHeight() {
return (height < 0) ? getDefaultHeight() : height;
}
public boolean hasDataRange() {
return dataRange != null;
}
public DataRange getDataRange() {
if (dataRange == null) {
// Use the color scale if there is one
float min = (float) (colorScale == null ? 0 : colorScale.getMinimum());
float max = (float) (colorScale == null ? 10 : colorScale.getMaximum());
float baseline = (float) (colorScale == null ? 0 : (colorScale.getNegStart() + colorScale.getPosStart()) / 2);
setDataRange(new DataRange(min, baseline, max));
}
return dataRange;
}
public void setDataRange(DataRange axisDefinition) {
this.dataRange = axisDefinition;
}
protected Class getDefaultRendererClass() {
Class def = defaultRendererMap.get(getTrackType());
return (def == null) ? defaultRendererClass : def;
}
public Collection<WindowFunction> getAvailableWindowFunctions() {
return new ArrayList();
}
public boolean handleDataClick(TrackClickEvent te) {
if (IGV.getInstance().isShowDetailsOnClick()) {
return openTooltipWindow(te);
}
return false;
}
protected boolean openTooltipWindow(TrackClickEvent e) {
ReferenceFrame frame = e.getFrame();
final MouseEvent me = e.getMouseEvent();
String popupText = getValueStringAt(frame.getChrName(), e.getChromosomePosition(), e.getMouseEvent().getX(), e.getMouseEvent().getY(), frame);
if (popupText != null) {
final TooltipTextFrame tf = new TooltipTextFrame(getName(), popupText);
Point p = me.getComponent().getLocationOnScreen();
tf.setLocation(Math.max(0, p.x + me.getX() - 150), Math.max(0, p.y + me.getY() - 150));
UIUtilities.invokeOnEventThread(new Runnable() {
public void run() {
tf.setVisible(true);
}
});
return true;
}
return false;
}
public void handleNameClick(MouseEvent e) {
// Do nothing
}
@Override
public void setAutoScale(boolean autoScale) {
this.autoScale = autoScale;
}
/**
* Set some properties of this track, usually from a "track line" specification.
* <p/>
* TODO -- keep the properties object, rather than copy all the values.
*
* @param properties
*/
public void setProperties(TrackProperties properties) {
this.itemRGB = properties.isItemRGB();
this.useScore = properties.isUseScore();
this.viewLimitMin = properties.getMinValue();
this.viewLimitMax = properties.getMaxValue();
this.yLine = properties.getyLine();
this.drawYLine = properties.isDrawYLine();
this.sortable = properties.isSortable();
// If view limits are explicitly set turn off autoscale
if (!Float.isNaN(viewLimitMin) && !Float.isNaN(viewLimitMax)) {
this.setAutoScale(false);
} else {
this.setAutoScale(properties.isAutoScale());
}
// Color scale properties
if (!properties.isAutoScale()) {
float min = properties.getMinValue();
float max = properties.getMaxValue();
float mid = properties.getMidValue();
if (Float.isNaN(mid)) {
if (min >= 0) {
mid = Math.max(min, 0);
} else {
mid = Math.min(max, 0);
}
}
DataRange dr = new DataRange(min, mid, max);
setDataRange(dr);
if (properties.isLogScale()) {
dr.setType(DataRange.Type.LOG);
}
// If the user has explicity set a data range and colors apply to heatmap as well
Color maxColor = properties.getColor();
Color minColor = properties.getAltColor();
if (maxColor != null && minColor != null) {
float tmp = properties.getNeutralFromValue();
float neutralFrom = Float.isNaN(tmp) ? mid : tmp;
tmp = properties.getNeutralToValue();
float neutralTo = Float.isNaN(tmp) ? mid : tmp;
Color midColor = properties.getMidColor();
if (midColor == null) {
midColor = Color.white;
}
colorScale = new ContinuousColorScale(neutralFrom, min, neutralTo, max, minColor, midColor, maxColor);
}
}
if (properties.getDisplayMode() != null) {
this.setDisplayMode(properties.getDisplayMode());
}
if (properties.getName() != null) {
name = properties.getName();
}
if (properties.getColor() != null) {
setColor(properties.getColor());
}
if (properties.getAltColor() != null) {
setAltColor(properties.getAltColor());
}
if (properties.getMidColor() != null) {
//setMidColor(trackProperties.getMidColor());
}
if (properties.getHeight() > 0) {
setHeight(properties.getHeight());
}
if (properties.getMinHeight() > 0) {
setMinimumHeight(properties.getMinHeight());
}
if (properties.getRendererClass() != null) {
setRendererClass(properties.getRendererClass());
if(properties.getRendererClass() == PointsRenderer.class) {
setWindowFunction(WindowFunction.none);
}
}
if (properties.getWindowingFunction() != null) {
setWindowFunction(properties.getWindowingFunction());
}
if (properties.getUrl() != null) {
setUrl(properties.getUrl());
}
Map<String, String> attributes = properties.getAttributes();
if (attributes != null) {
for (Map.Entry<String, String> entry : attributes.entrySet()) {
this.setAttributeValue(entry.getKey(), entry.getValue());
}
}
// Start of Roche-Tessella modification
this.autoScale = properties.getAutoScale();
// End of Roche-Tessella modification
}
/**
* @return the top
*/
public int getY() {
return top;
}
public void setColorScale(ContinuousColorScale colorScale) {
this.colorScale = colorScale;
}
/**
* @param top the top to set
*/
public void setY(int top) {
this.top = top;
}
/**
* Return the color scale for this track. If a specific scale exists for this data type
* use that. Otherwise create one using the track color and data range.
*
* @return
*/
public ContinuousColorScale getColorScale() {
if (colorScale == null) {
if (IGV.hasInstance()) {
ContinuousColorScale defaultScale = IGV.getInstance().getSession().getColorScale(trackType);
if (defaultScale != null) {
colorScale = defaultScale;
return defaultScale;
}
}
double min = dataRange == null ? 0 : dataRange.getMinimum();
double max = dataRange == null ? 10 : dataRange.getMaximum();
Color c = getColor();
Color minColor = Color.white;
if (min < 0) {
minColor = altColor == null ? oppositeColor(minColor) : altColor;
colorScale = new ContinuousColorScale(min, 0, max, minColor, Color.white, c);
} else {
colorScale = new ContinuousColorScale(min, max, minColor, c);
}
colorScale.setNoDataColor(UIConstants.NO_DATA_COLOR);
}
return colorScale;
}
private Color oppositeColor(Color c) {
float[] rgb = new float[4];
c.getRGBComponents(rgb);
rgb[0] = Math.abs(rgb[0] - 255);
rgb[1] = Math.abs(rgb[1] - 255);
rgb[2] = Math.abs(rgb[2] - 255);
return Color.getHSBColor(rgb[0], rgb[1], rgb[2]);
}
/**
* Return the current state of this object as map of key-value pairs. Used to store session state.
* Only those attributes not already annotated in AbstractTrack need to be included here
*
* @return
* @see #restorePersistentState
*/
public Map<String, String> getPersistentState() {
return new HashMap<String, String>();
}
/**
* Restore from XML node. Default implementation just turns attributes
* into a map
*
* @param node
*/
public void restorePersistentState(Node node, int version) throws JAXBException {
Map<String, String> attributes = Utilities.getAttributes(node);
restorePersistentState(attributes, version);
}
/**
* Restore attributes from track tag, no children
* Only those attributes not unmarshalled (meaning not part of AbstractTrack)
* need to be restored
*
* @param attributes
* @see #getPersistentState
*/
public void restorePersistentState(Map<String, String> attributes, int version) {
String displayName = attributes.get(IGVSessionReader.SessionAttribute.DISPLAY_NAME.getText());
String name = attributes.get(IGVSessionReader.SessionAttribute.NAME.getText());
if (name != null && name.length() > 0) {
setName(name);
} else if (displayName != null && displayName.length() > 0) {
setName(displayName);
}
if(attributes.containsKey("visible")) {
this.setVisible(Boolean.parseBoolean(attributes.get("visible")));
}
// Set DataRange -- legacy (pre V3 sessions)
if(version <= 3){
String scale = attributes.get(IGVSessionReader.SessionAttribute.SCALE.getText());
if (scale != null) {
String[] axis = scale.split(",");
float minimum = Float.parseFloat(axis[0]);
float baseline = Float.parseFloat(axis[1]);
float maximum = Float.parseFloat(axis[2]);
setDataRange(new DataRange(minimum, baseline, maximum));
}
}
}
public boolean isItemRGB() {
return itemRGB;
}
public boolean isUseScore() {
return useScore;
}
public float getViewLimitMin() {
return viewLimitMin;
}
public float getViewLimitMax() {
return viewLimitMax;
}
public int getFontSize() {
return fontSize;
}
public void setFontSize(int fontSize) {
this.fontSize = fontSize;
}
public boolean isShowDataRange() {
return showDataRange;
}
public void setShowDataRange(boolean showDataRange) {
this.showDataRange = showDataRange;
}
/**
* Overriden by subclasses
*
* @param e
* @return
*/
public Feature getFeatureAtMousePosition(TrackClickEvent e) {
return null;
}
/**
* Special normalization function for linear (non logged) copy number data
*
* @param value
* @param norm
* @return
*/
public static float getLogNormalizedValue(float value, double norm) {
if (norm == 0) {
return Float.NaN;
} else {
return (float) (Math.log(Math.max(Float.MIN_VALUE, value) / norm) / Globals.log2);
}
}
public float logScaleData(float dataY) {
// Special case for copy # -- centers data around 2 copies (1 for allele
// specific) and log normalizes
if (((getTrackType() == TrackType.COPY_NUMBER) ||
(getTrackType() == TrackType.ALLELE_SPECIFIC_COPY_NUMBER) ||
(getTrackType() == TrackType.CNV)) &&
!isLogNormalized()) {
double centerValue = (getTrackType() == TrackType.ALLELE_SPECIFIC_COPY_NUMBER)
? 1.0 : 2.0;
dataY = getLogNormalizedValue(dataY, centerValue);
}
return dataY;
}
public boolean isRegionScoreType(RegionScoreType type) {
return (getTrackType() == TrackType.GENE_EXPRESSION && type == RegionScoreType.EXPRESSION) ||
((getTrackType() == TrackType.COPY_NUMBER || getTrackType() == TrackType.CNV ||
getTrackType() == TrackType.ALLELE_SPECIFIC_COPY_NUMBER) &&
(type == RegionScoreType.AMPLIFICATION ||
type == RegionScoreType.DELETION ||
type == RegionScoreType.FLUX)) ||
(type == RegionScoreType.MUTATION_COUNT) ||
(type == RegionScoreType.SCORE);
}
public void setVisibilityWindow(int i) {
this.visibilityWindow = i;
}
public int getVisibilityWindow() {
return visibilityWindow;
}
/**
* Override to return a specialized popup menu
*
* @return
*/
public IGVPopupMenu getPopupMenu(final TrackClickEvent te) {
return null;
}
public DisplayMode getDisplayMode() {
return displayMode;
}
public void setDisplayMode(DisplayMode mode) {
this.displayMode = mode;
}
public String getNameValueString(int y) {
StringBuffer buffer = new StringBuffer();
buffer.append("<html>" + getName());
if(resourceLocator != null && resourceLocator.getPath() != null) {
buffer.append("<br>" + this.resourceLocator.getPath());
}
return buffer.toString();
}
/**
* Return a value string for the tooltip window at the given location, or null to signal there is no value
* at that location
*
* @param chr
* @param position
* @param mouseX
*@param frame @return
*/
public String getValueStringAt(String chr, double position, int mouseX, int mouseY, ReferenceFrame frame) {
return null;
}
public void setWindowFunction(WindowFunction type) {
// Required method for track interface, ignore
}
@XmlAttribute(name = "windowFunction")
public WindowFunction getWindowFunction() {
return null;
}
public float getRegionScore(String chr, int start, int end, int zoom, RegionScoreType type, String frameName) {
// Required method for track interface, ignore
return getRegionScore(chr, start, end, zoom, type, frameName, null);
}
/**
* @param chr
* @param start
* @param end
* @param zoom
* @param type
* @param frameName
* @param tracks
* @return
*/
public float getRegionScore(String chr, int start, int end, int zoom, RegionScoreType type, String frameName, List<Track> tracks) {
// Required method for track interface, ignore
return 0;
}
public boolean isLogNormalized() {
// Required method for track interface, ignore
return true;
}
public boolean isSortable() {
return sortable;
}
public void setSortable(boolean sortable) {
this.sortable = sortable;
}
public boolean isDrawYLine() {
return drawYLine;
}
public float getYLine() {
return yLine;
}
@Override
public void dispose() {
if(this instanceof IGVEventObserver) {
IGVEventBus.getInstance().unsubscribe((IGVEventObserver) this);
}
}
protected void setRenderer(Renderer renderer) {
//Here as setter for corresponding getter, subclasses should override
}
@XmlJavaTypeAdapter(SessionXmlAdapters.Renderer.class)
@XmlAttribute(name = "renderer")
@Override
public Renderer getRenderer() {
return null;
}
// Start of Roche-Tessella modification
public boolean getAutoScale() {
return this.autoScale;
}
// End of Roche-Tessella modification
}