Filter tracks

src/main/java/org/broad/igv/Globals.java

@@ -46,9 +46,6 @@ public class Globals {
     public static final String DEFAULT_GENOME = "hg38";
 
     public static final String CHR_ALL = "All";
-    public static final String TRACK_NAME_ATTRIBUTE = "NAME";
-    public static final String TRACK_DATA_FILE_ATTRIBUTE = "DATA FILE";
-    public static final String TRACK_DATA_TYPE_ATTRIBUTE = "DATA TYPE";
 
     private static boolean headless = false;
     private static boolean suppressMessages = false;

src/main/java/org/broad/igv/event/IGVEvent.java

@@ -6,18 +6,8 @@
 import org.broad.igv.ui.panel.FrameManager;
 
 public sealed interface IGVEvent
-        permits
-        AlignmentTrackEvent,
-        DataLoadedEvent,
-        GenomeChangeEvent,
-        GenomeResetEvent,
-        RefreshEvent,
-        StopEvent,
-        TrackGroupEvent,
-        ViewChange,
-        OAuthProvider.AuthStateEvent,
-        PreferencesChangeEvent,
-        InsertionSelectionEvent,
-        FrameManager.ChangeEvent {
+        permits AlignmentTrackEvent, DataLoadedEvent, GenomeChangeEvent, GenomeResetEvent, RefreshEvent, StopEvent,
+        TrackFilterEvent, TrackGroupEvent, ViewChange, OAuthProvider.AuthStateEvent, PreferencesChangeEvent,
+        InsertionSelectionEvent, FrameManager.ChangeEvent {
 
 }

src/main/java/org/broad/igv/event/TrackFilterEvent.java

@@ -0,0 +1,16 @@
+package org.broad.igv.event;
+
+import org.broad.igv.util.Filter;
+
+public final class TrackFilterEvent implements IGVEvent {
+
+    private Filter filter;
+
+    public TrackFilterEvent(Filter filter) {
+        this.filter = filter;
+    }
+
+    public Filter getFilter() {
+        return filter;
+    }
+}

src/main/java/org/broad/igv/feature/genome/GenomeManager.java

@@ -245,9 +245,6 @@ public void restoreGenomeTracks(Genome genome) {
         // Fetch the gene track, defined by .genome files.  In this format the genome data is encoded in the .genome file
         FeatureTrack geneFeatureTrack = genome.getGeneTrack();   // Used for .genome and .gbk formats.  Otherwise null
         if (geneFeatureTrack != null) {
-            geneFeatureTrack.setAttributeValue(Globals.TRACK_NAME_ATTRIBUTE, geneFeatureTrack.getName());
-            geneFeatureTrack.setAttributeValue(Globals.TRACK_DATA_FILE_ATTRIBUTE, "");
-            geneFeatureTrack.setAttributeValue(Globals.TRACK_DATA_TYPE_ATTRIBUTE, geneFeatureTrack.getTrackType().toString());
             IGV.getInstance().addTrack(geneFeatureTrack, PanelName.ANNOTATION_PANEL.getName());
         }
 
@@ -283,9 +280,6 @@ public void restoreGenomeTracks(Genome genome) {
                             fn = fn.substring(lastSlashIdx + 1);
                         }
                     }
-                    track.setAttributeValue(Globals.TRACK_NAME_ATTRIBUTE, track.getName());
-                    track.setAttributeValue(Globals.TRACK_DATA_FILE_ATTRIBUTE, fn);
-                    track.setAttributeValue(Globals.TRACK_DATA_TYPE_ATTRIBUTE, track.getTrackType().toString());
                 }
             }
         }

src/main/java/org/broad/igv/session/IGVSessionReader.java

@@ -50,8 +50,6 @@
 import org.broad.igv.sam.SpliceJunctionTrack;
 import org.broad.igv.track.*;
 import org.broad.igv.ui.IGV;
-import org.broad.igv.ui.TrackFilter;
-import org.broad.igv.ui.TrackFilterElement;
 import org.broad.igv.ui.color.ColorUtilities;
 import org.broad.igv.ui.panel.FrameManager;
 import org.broad.igv.ui.panel.ReferenceFrame;
@@ -89,15 +87,15 @@ public class IGVSessionReader implements SessionReader {
     private Collection<ResourceLocator> dataFiles;
     private Collection<ResourceLocator> missingDataFiles;
     private boolean panelElementPresent = false;    // Flag indicating if "Panel" sections are present
-    private TrackFilter filter;  // There is a single TrackFilter object per session, usually null
 
     /**
      * List of combined data source tracks.  Processing of combined data sources has to be deferred until all tracks
      * are loaded
      */
     private final List<Pair<CombinedDataTrack, Element>> combinedDataSourceTracks = new ArrayList<>();
 
-    private Set<Track> allocatedToPanel = new LinkedHashSet<>();;  // List of tracks allocated to panels, if Panel elements are present.
+    private Set<Track> allocatedToPanel = new LinkedHashSet<>();
+    ;  // List of tracks allocated to panels, if Panel elements are present.
 
     /**
      * Map of id -> track, for second pass through when tracks reference each other
@@ -108,12 +106,6 @@ public class IGVSessionReader implements SessionReader {
 
     private boolean hasTrackElments;
 
-    static {
-        attributeSynonymMap.put("DATA FILE", "DATA SET");
-        attributeSynonymMap.put("TRACK NAME", "NAME");
-    }
-
-
     public IGVSessionReader(IGV igv) {
         this.igv = igv;
         currentReader = new WeakReference<IGVSessionReader>(this);
@@ -159,7 +151,7 @@ public void loadSession(InputStream inputStream, Session session, String session
         List<Track> unallocatedTracks = new ArrayList<>();
         for (List<Track> tracks : allTracks.values()) {
             for (Track t : tracks) {
-                if (allocatedToPanel == null ||!allocatedToPanel.contains(t)) {
+                if (allocatedToPanel == null || !allocatedToPanel.contains(t)) {
                     unallocatedTracks.add(t);
                 }
             }
@@ -307,8 +299,6 @@ private void process(Session session, Node element, String sessionPath) {
             processGeneList(session, (Element) element);
         } else if (nodeName.equalsIgnoreCase(SessionElement.FILTER)) {
             processFilter(session, (Element) element, sessionPath);
-        } else if (nodeName.equalsIgnoreCase(SessionElement.FILTER_ELEMENT)) {
-            processFilterElement(session, (Element) element, sessionPath);
         } else if (nodeName.equalsIgnoreCase(SessionElement.COLOR_SCALES)) {
             processColorScales(session, (Element) element, sessionPath);
         } else if (nodeName.equalsIgnoreCase(SessionElement.COLOR_SCALE)) {
@@ -692,47 +682,34 @@ private void processFilter(Session session, Element element, String sessionPath)
         String showAllTracks = getAttribute(element, SessionAttribute.FILTER_SHOW_ALL_TRACKS);
 
         String filterName = getAttribute(element, SessionAttribute.NAME);
-        filter = new TrackFilter(filterName, null);
+        boolean matchAll = "all".equalsIgnoreCase(match);
+        boolean showAll = "true".equalsIgnoreCase(showAllTracks);
 
         NodeList elements = element.getChildNodes();
-        process(session, elements, sessionPath);
 
-        // Save the filter
+        List<FilterElement> filterElements = new ArrayList();
+        for (int i = 0; i < elements.getLength(); i++) {
+            Node childNode = elements.item(i);
+            if (childNode.getNodeName().equalsIgnoreCase(SessionElement.FILTER_ELEMENT)) {
+                filterElements.add(processFilterElement((Element) childNode));
+            } else {
+                // Unrecognized child element
+                log.warn("Unrecognized child element in <Filter>: " + childNode.getNodeName());
+            }
+        }
+
+        Filter filter = new Filter(showAll, matchAll,  filterElements);
         session.setFilter(filter);
 
-        // Update UI elements -- the matchAll and showAll state is kept in the UI, not the Filter object.  This seems wrong.  TODO
-        if ("all".equalsIgnoreCase(match)) {
-            igv.setFilterMatchAll(true);
-        } else if ("any".equalsIgnoreCase(match)) {
-            igv.setFilterMatchAll(false);
-        }
-        if ("true".equalsIgnoreCase(showAllTracks)) {
-            igv.setFilterShowAllTracks(true);
-        } else {
-            igv.setFilterShowAllTracks(false);
-        }
     }
 
-    private void processFilterElement(Session session, Element element,
-                                      String sessionPath) {
-
-        if (filter == null) {
-            throw new RuntimeException("Filter elements defined before filter");
-        }
+    private FilterElement processFilterElement(Element element) {
 
         String item = getAttribute(element, SessionAttribute.ITEM);
         String operator = getAttribute(element, SessionAttribute.OPERATOR);
         String value = getAttribute(element, SessionAttribute.VALUE);
-        String booleanOperator = getAttribute(element, SessionAttribute.BOOLEAN_OPERATOR);
-
         Operator opEnum = CollUtils.findValueOf(Operator.class, operator);
-        BooleanOperator boolEnum = BooleanOperator.valueOf(booleanOperator.toUpperCase());
-        TrackFilterElement trackFilterElement = new TrackFilterElement(filter, item,
-                opEnum, value, boolEnum);
-        filter.add(trackFilterElement);
-
-        NodeList elements = element.getChildNodes();
-        process(session, elements, sessionPath);
+        return new FilterElement(item, opEnum, value);
     }
 
     /**

src/main/java/org/broad/igv/session/Session.java

@@ -39,12 +39,11 @@
 import org.broad.igv.prefs.PreferencesManager;
 import org.broad.igv.renderer.ContinuousColorScale;
 import org.broad.igv.sam.InsertionManager;
-import org.broad.igv.track.AttributeManager;
 import org.broad.igv.track.TrackType;
 import org.broad.igv.ui.IGV;
-import org.broad.igv.ui.TrackFilter;
 import org.broad.igv.ui.panel.FrameManager;
 import org.broad.igv.ui.panel.ReferenceFrame;
+import org.broad.igv.util.Filter;
 import org.broad.igv.util.ObservableForObject;
 
 import java.util.*;
@@ -69,7 +68,7 @@ public enum GeneListMode {
     public boolean expandInsertions = false; //false;
     private int nextAutoscaleGroup;
     private ReferenceFrame referenceFrame = FrameManager.getDefaultFrame();
-    private TrackFilter filter;
+    private Filter filter;
     private HashMap<String, String> preferences;
     private HashMap<TrackType, ContinuousColorScale> colorScales;
     private boolean removeEmptyPanels = false;
@@ -304,11 +303,11 @@ public String getLocus() {
         return locus;
     }
 
-    public TrackFilter getFilter() {
+    public Filter getFilter() {
         return filter;
     }
 
-    public void setFilter(TrackFilter filter) {
+    public void setFilter(Filter filter) {
         this.filter = filter;
     }
 
@@ -444,13 +443,8 @@ public int getNextAutoscaleGroup() {
      * @return
      */
     public Set<String> getHiddenAttributes() {
-        if (hiddenAttributes == null) {
-            return (PreferencesManager.getPreferences().getAsBoolean(SHOW_DEFAULT_TRACK_ATTRIBUTES))  ?
-                    Collections.emptySet() :
-                    new HashSet<>(AttributeManager.defaultTrackAttributes);
-        } else {
             return hiddenAttributes;
-        }
+
     }
 
     public void setHiddenAttributes(Set<String> attributes) {

src/main/java/org/broad/igv/session/SessionWriter.java

@@ -35,14 +35,10 @@
 import org.broad.igv.track.AttributeManager;
 import org.broad.igv.track.Track;
 import org.broad.igv.ui.IGV;
-import org.broad.igv.ui.TrackFilter;
-import org.broad.igv.ui.TrackFilterElement;
 import org.broad.igv.ui.panel.FrameManager;
 import org.broad.igv.ui.panel.ReferenceFrame;
 import org.broad.igv.ui.panel.TrackPanel;
-import org.broad.igv.util.FileUtils;
-import org.broad.igv.util.ResourceLocator;
-import org.broad.igv.util.Utilities;
+import org.broad.igv.util.*;
 import org.w3c.dom.DOMException;
 import org.w3c.dom.Document;
 import org.w3c.dom.Element;
@@ -182,16 +178,12 @@ public String createXmlFromSession(Session session, File outputFile) throws Runt
 
 
     private void writeFilters(Session session, Element globalElement, Document document) {
-        TrackFilter trackFilter = session.getFilter();
+        Filter trackFilter = session.getFilter();
         if (trackFilter != null) {
 
             Element filter = document.createElement(SessionElement.FILTER);
 
-            filter.setAttribute(SessionAttribute.NAME, trackFilter.getName());
-
-            if (IGV.getInstance().isFilterMatchAll()) {
-                filter.setAttribute(SessionAttribute.FILTER_MATCH, "all");
-            } else if (!IGV.getInstance().isFilterMatchAll()) {
+            if (!IGV.getInstance().isFilterMatchAll()) {
                 filter.setAttribute(SessionAttribute.FILTER_MATCH, "any");
             } else {    // Defaults to match all
                 filter.setAttribute(SessionAttribute.FILTER_MATCH, "all");
@@ -208,20 +200,18 @@ private void writeFilters(Session session, Element globalElement, Document docum
             Iterator iterator = session.getFilter().getFilterElements();
             while (iterator.hasNext()) {
 
-                TrackFilterElement trackFilterElement = (TrackFilterElement) iterator.next();
+                FilterElement trackFilterElement = (FilterElement) iterator.next();
 
                 Element filterElementElement =
                         document.createElement(SessionElement.FILTER_ELEMENT);
                 filterElementElement.setAttribute(SessionAttribute.ITEM,
-                        trackFilterElement.getSelectedItem());
+                        trackFilterElement.getAttributeKey());
                 filterElementElement.setAttribute(
                         SessionAttribute.OPERATOR,
                         trackFilterElement.getComparisonOperator().getValue());
                 filterElementElement.setAttribute(SessionAttribute.VALUE,
                         trackFilterElement.getValue());
-                filterElementElement.setAttribute(
-                        SessionAttribute.BOOLEAN_OPERATOR,
-                        trackFilterElement.getBooleanOperator().getValue());
+
                 filter.appendChild(filterElementElement);
             }
         }

src/main/java/org/broad/igv/track/AbstractTrack.java

@@ -175,7 +175,6 @@ public String getId() {
 
     public void setName(String name) {
         this.name = name;
-        this.setAttributeValue(Globals.TRACK_NAME_ATTRIBUTE, name);
     }
 
     public String getName() {

src/main/java/org/broad/igv/track/AttributeManager.java

@@ -45,7 +45,6 @@
 import org.broad.igv.ui.color.ColorTable;
 import org.broad.igv.ui.color.ColorUtilities;
 import org.broad.igv.ui.color.PaletteColorTable;
-import org.broad.igv.util.FileUtils;
 import org.broad.igv.util.ParsingUtils;
 import org.broad.igv.util.ResourceLocator;
 import org.broad.igv.util.Utilities;
@@ -54,19 +53,16 @@
 import java.beans.PropertyChangeEvent;
 import java.beans.PropertyChangeListener;
 import java.beans.PropertyChangeSupport;
-import java.io.BufferedReader;
 import java.io.IOException;
 import java.util.List;
 import java.util.*;
 
 /**
  * @author jrobinso
  */
-public class AttributeManager {
+public class AttributeManager implements AttributeSupplier {
 
     public static final String GROUP_AUTOSCALE = "AUTOSCALE GROUP";
-    public static List<String> defaultTrackAttributes = Arrays.asList(Globals.TRACK_NAME_ATTRIBUTE,
-            Globals.TRACK_DATA_FILE_ATTRIBUTE, Globals.TRACK_DATA_TYPE_ATTRIBUTE);
     private static Logger log = LogManager.getLogger(AttributeManager.class);
 
     private static AttributeManager singleton;
@@ -126,11 +122,6 @@ public class AttributeManager {
 
     private AttributeManager() {
         propertyChangeSupport = new PropertyChangeSupport(this);
-
-        // The default attributes
-        addAttributeName("NAME");
-        addAttributeName("DATA TYPE");
-        addAttributeName("DATA FILE");
     }
 
     static synchronized public AttributeManager getInstance() {
@@ -152,6 +143,7 @@ public void removePropertyChangeListener(PropertyChangeListener listener) {
     /**
      * Return the attribute value for the given track (trackName) and key.
      */
+    @Override
     public String getAttribute(String trackName, String attributeName) {
         Map<String, String> attributes = attributeMap.get(trackName);
         String key = attributeName.toUpperCase();
@@ -208,12 +200,6 @@ public List<String> getVisibleAttributes() {
     public void clearAllAttributes() {
         attributeMap.clear();
         attributeNames.clear();
-
-        // The default attributes
-        addAttributeName("NAME");
-        addAttributeName("DATA TYPE");
-        addAttributeName("DATA FILE");
-
         uniqueAttributeValues.clear();
         //hiddenAttributes.clear();
         loadedResources = new HashSet();
@@ -232,13 +218,6 @@ public void addAttribute(String rowId, String attributeName, String attributeVal
             return;
         }
 
-        // Add the 3 "special" attributes to ensure they are the first columns
-        if (attributeNames.isEmpty()) {
-            addAttributeName("NAME");
-            addAttributeName("DATA TYPE");
-            addAttributeName("DATA FILE");
-        }
-
         addAttributeName(attributeName);
 
         String key = attributeName.toUpperCase();

src/main/java/org/broad/igv/track/AttributeSupplier.java

@@ -0,0 +1,5 @@
+package org.broad.igv.track;
+
+public interface AttributeSupplier {
+    String getAttribute(String trackName, String attributeName);
+}