Encode hubs

src/main/java/org/igv/bedpe/HicSource.java

@@ -34,7 +34,7 @@ public HicSource(String path, Genome genome) throws IOException {
     @Override
     public List<BedPE> getFeatures(String chr, int start, int end, double bpPerPixel, String normalization, int maxFeatureCount) throws IOException {
 
-        final int binSize = getBinSize(bpPerPixel);
+        final int binSize = getBinSize(chr, bpPerPixel);
 
         List<ContactRecord> records = getRecords(chr, start, end, binSize);
 
@@ -159,7 +159,13 @@ public List<BedPE> getFeatures(String chr, int start, int end, double bpPerPixel
         return features;
     }
 
-    private int getBinSize(double bpPerPixel) {
+    private int getBinSize(String chr, double bpPerPixel) {
+
+        if("all".equalsIgnoreCase(chr)) {
+            // Special case, the whole-genome psuedo-chromosome all has a single resolution
+            return hicFile.getWGResolution();
+        }
+
         // choose resolution
         List<Integer> resolutions = hicFile.getBpResolutions();
         int index = 0;
@@ -180,7 +186,7 @@ public List<String> getNormalizationTypes() {
 
     @Override
     public boolean hasNormalizationVector(String type, String chr, double bpPerPixel) {
-        return hicFile.hasNormalizationVector(type, chr, "BP", getBinSize(bpPerPixel));
+        return hicFile.hasNormalizationVector(type, chr, "BP", getBinSize(chr, bpPerPixel));
     }
 
     /**

src/main/java/org/igv/encode/EncodeTrackChooserFactory.java

@@ -4,6 +4,17 @@
 
 package org.igv.encode;
 
+import org.igv.Globals;
+import org.igv.logging.LogManager;
+import org.igv.logging.Logger;
+import org.igv.prefs.Constants;
+import org.igv.prefs.PreferencesManager;
+import org.igv.ui.IGV;
+import org.igv.ui.action.BrowseEncodeAction;
+import org.igv.util.Pair;
+import org.igv.util.ParsingUtils;
+
+import javax.swing.text.NumberFormatter;
 import java.awt.*;
 import java.io.BufferedReader;
 import java.io.IOException;
@@ -12,17 +23,6 @@
 import java.util.*;
 import java.util.List;
 import java.util.stream.Collectors;
-import javax.swing.*;
-import javax.swing.text.NumberFormatter;
-
-import org.igv.logging.*;
-import org.igv.Globals;
-import org.igv.prefs.Constants;
-import org.igv.prefs.PreferencesManager;
-import org.igv.ui.IGV;
-import org.igv.ui.action.BrowseEncodeAction;
-import org.igv.util.Pair;
-import org.igv.util.ParsingUtils;
 
 /**
  * @author Jim Robinson
@@ -35,7 +35,9 @@ public class EncodeTrackChooserFactory {
     private static NumberFormatter numberFormatter = new NumberFormatter();
 
     private static String ENCODE_HOST = "https://www.encodeproject.org";
-    private static Set<String> filteredColumns = new HashSet(Arrays.asList("ID", "Assembly", "HREF", "path"));
+    private static Set<String> filteredColumns = new HashSet<>(Arrays.asList(
+            "ID", "Assembly", "HREF", "path",
+            "url", "Project", "name", "color", "altColor"));
 
     private static List<String> filteredExtensions = Arrays.asList("tsv", "tsv.gz");
 
@@ -53,6 +55,8 @@ public class EncodeTrackChooserFactory {
     static HashSet<String> ucscSupportedGenomes = new HashSet<>(Arrays.asList("hg19", "mm9"));
     static HashSet<String> supportedGenomes = new HashSet<>(
             Arrays.asList("ce10", "ce11", "dm3", "dm6", "GRCh38", "hg19", "mm10", "mm9"));
+    static HashSet<String> hicGenomes = new HashSet<>(
+            Arrays.asList("GRCh38", "hg19", "mm10", "mm9"));
 
     /**
      * Return a new or cached instance of a track chooser for the given genome and type.
@@ -79,14 +83,15 @@ public synchronized static TrackChooser getInstance(String genomeId, BrowseEncod
             instance = new TrackChooser(parent, headings, rows, title);
             instanceMap.put(key, instance);
         }
-
         return instance;
     }
 
     private static String getDialogTitle(String genomeId, BrowseEncodeAction.Type type) {
 
         if (type == BrowseEncodeAction.Type.UCSC) {
             return "ENCODE data hosted at UCSC (2012)";
+        } else if (type == BrowseEncodeAction.Type.FOUR_DN) {
+            return "4DN";
         } else {
             switch (type) {
                 case SIGNALS_CHIP:
@@ -103,6 +108,10 @@ public static boolean genomeSupportedUCSC(String genomeId) {
         return genomeId != null && ucscSupportedGenomes.contains(getEncodeGenomeID(genomeId));
     }
 
+    public static boolean hicSupportedUCSC(String genomeId) {
+        return genomeId != null && hicGenomes.contains(getEncodeGenomeID(genomeId));
+    }
+
     public static boolean genomeSupported(String genomeId) {
         return genomeId != null && supportedGenomes.contains(getEncodeGenomeID(genomeId));
     }
@@ -128,26 +137,16 @@ private static Pair<List<String>, List<FileRecord>> getEncodeFileRecords(String
             if (is == null) {
                 return null;
             }
-            Pair<List<String>, List<FileRecord>> headingRecordPair = parseRecords(is, type, genomeId);
-
-            if (IGV.hasInstance()) {
-                Set<String> loadedPaths = IGV.getInstance().getDataResourceLocators().stream()
-                        .map(rl -> rl.getPath())
-                        .collect(Collectors.toSet());
-
-                for (FileRecord fileRecord : headingRecordPair.getSecond()) {
-                    if (loadedPaths.contains(fileRecord.getPath())) {
-                        fileRecord.setSelected(true);
-                    }
-                }
-            }
-            return headingRecordPair;
+            return parseRecords(is, type, genomeId);
         }
     }
 
     private static InputStream getStreamFor(String genomeId, BrowseEncodeAction.Type type) throws IOException {
         if (type == BrowseEncodeAction.Type.UCSC) {
             return EncodeTrackChooserFactory.class.getResourceAsStream("encode." + genomeId + ".txt");
+        } else if (type == BrowseEncodeAction.Type.FOUR_DN) {
+            String url = PreferencesManager.getPreferences().get(Constants.FOUR_DN_FILELIST_URL) + "4dn_" + genomeId + "_tracks.txt";
+            return ParsingUtils.openInputStream(url);
         } else {
             String root = PreferencesManager.getPreferences().get(Constants.ENCODE_FILELIST_URL) + genomeId + ".";
             String url = null;
@@ -158,6 +157,9 @@ private static InputStream getStreamFor(String genomeId, BrowseEncodeAction.Type
                 case SIGNALS_OTHER:
                     url = root + "signals.other.txt.gz";
                     break;
+                case HIC:
+                    url = root + "hic.txt.gz";
+                    break;
                 case OTHER:
                     url = root + "other.txt.gz";
                     break;
@@ -175,21 +177,27 @@ private static Pair parseRecords(InputStream is, BrowseEncodeAction.Type type, S
 
         String[] headers = Globals.tabPattern.split(reader.readLine());
 
-        int pathColumn = type == BrowseEncodeAction.Type.UCSC ? 0 : Arrays.asList(headers).indexOf("HREF");
+        int pathColumn = switch (type) {
+            case UCSC, FOUR_DN -> 0;
+            default -> Arrays.asList(headers).indexOf("HREF");
+        };
 
         List<FileRecord> records = new ArrayList<>(20000);
         String nextLine;
         while ((nextLine = reader.readLine()) != null) {
             if (!nextLine.startsWith("#")) {
 
                 String[] tokens = Globals.tabPattern.split(nextLine, -1);
-                String path = type == BrowseEncodeAction.Type.UCSC ? tokens[pathColumn] : ENCODE_HOST + tokens[pathColumn];
+                String path = switch (type) {
+                    case UCSC, FOUR_DN -> tokens[pathColumn];
+                    default -> ENCODE_HOST + tokens[pathColumn];
+                };
 
                 if (filteredExtensions.stream().anyMatch(e -> path.endsWith(e))) {
                     continue;
                 }
 
-                Map<String, String> attributes = new LinkedHashMap<>();
+                Map<String, String> attributes = new HashMap<>();
                 for (int i = 0; i < headers.length; i++) {
                     String value = i < tokens.length ? tokens[i] : "";
                     if (value.length() > 0) {
@@ -198,7 +206,6 @@ private static Pair parseRecords(InputStream is, BrowseEncodeAction.Type type, S
                 }
                 final FileRecord record = new FileRecord(path, attributes);
                 records.add(record);
-
             }
         }
 

src/main/java/org/igv/encode/FileRecord.java

@@ -42,10 +42,6 @@ public String getAttributeValue(String name) {
         return value;
     }
 
-    public Collection<String> getAttributeNames() {
-        return attributes.keySet();
-    }
-
     public Map<String, String> getAttributes() {
         return attributes;
     }

src/main/java/org/igv/encode/TrackChooser.java

@@ -8,6 +8,7 @@
 import org.igv.Globals;
 import org.igv.logging.LogManager;
 import org.igv.logging.Logger;
+import org.igv.ui.IGV;
 import org.igv.util.Pair;
 
 import javax.swing.*;
@@ -24,6 +25,7 @@
 import java.text.ParseException;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Set;
 import java.util.regex.Matcher;
 import java.util.regex.Pattern;
 import java.util.stream.Collectors;
@@ -109,6 +111,18 @@ public List<FileRecord> getAllRecords() {
         return model.getRecords();
     }
 
+    public void updateRecordSelectionState() {
+
+        Set<String> loadedPaths = IGV.getInstance().getDataResourceLocators().stream()
+                .map(rl -> rl.getPath())
+                .collect(Collectors.toSet());
+
+        for (FileRecord fileRecord : model.getRecords()) {
+            if (loadedPaths.contains(fileRecord.getPath())) {
+                fileRecord.setSelected(true);
+            }
+        }
+    }
 
     private class RegexFilter extends RowFilter {
 

src/main/java/org/igv/encode/TrackChooserModel.java

@@ -108,10 +108,9 @@ public void updateSelections() {
 
         for (int row = 0; row < records.size(); row++) {
             FileRecord record = records.get(row);
-            if (loadedPaths.contains(record.getPath())) {
-                record.setSelected(true);
-            }
+            record.setSelected(loadedPaths.contains(record.getPath()));
         }
+        fireTableDataChanged();
     }
 
     public List<FileRecord> getRecords() {

src/main/java/org/igv/hic/HicFile.java

@@ -6,6 +6,7 @@
 import org.igv.logging.LogManager;
 import org.igv.logging.Logger;
 import org.igv.util.CompressionUtils;
+import org.igv.util.collections.CaseInsensitiveMap;
 import org.igv.util.collections.LRUCache;
 import org.igv.util.stream.IGVSeekableStreamFactory;
 
@@ -56,7 +57,8 @@ public int getByteSize() {
     private Map<String, Long> expectedValueVectors;
     private Map<String, Object> attributes;
     private List<Chromosome> chromosomes = new ArrayList<>();
-    private Map<String, Integer> chromosomeIndexMap = new HashMap<>();
+    private Map<String, Integer> chromosomeIndexMap = new CaseInsensitiveMap<Integer>();
+    private Integer wgResolution = null;
     private List<Integer> bpResolutions = new ArrayList<>();
     private List<Integer> fragResolutions = new ArrayList<>();
     private Map<String, String> chrAliasTable = new HashMap<>();
@@ -90,7 +92,7 @@ public int getVersion() {
     }
 
     public String getNVIString() {
-        if(this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
+        if (this.normVectorIndexPosition > 0 && this.normVectorIndexSize > 0) {
             return this.normVectorIndexPosition + "," + this.normVectorIndexSize;
         } else {
             return null;
@@ -158,17 +160,19 @@ private void readHeaderAndFooter() throws IOException {
 
         // chromosomes
         this.chromosomes = new ArrayList<>();
-        this.chromosomeIndexMap = new HashMap<>();
+        this.chromosomeIndexMap = new CaseInsensitiveMap<>();
         int nChrs = bodyParser.getInt();
         for (int i = 0; i < nChrs; i++) {
             String name = getString(bodyParser);
             long size = this.version < 9 ? bodyParser.getInt() : bodyParser.getLong();
             Chromosome chr = new Chromosome(i, name, (int) size);
-            if ("all".equalsIgnoreCase(name)) {
-                // whole genome handling omitted other fields
-            }
             this.chromosomes.add(chr);
+
+            String canonicalName = genome == null ? name : genome.getCanonicalChrName(name);
+            chrAliasTable.put(canonicalName, name);
+
             this.chromosomeIndexMap.put(name, i);
+
         }
 
         // bp resolutions
@@ -185,12 +189,6 @@ private void readHeaderAndFooter() throws IOException {
                 this.fragResolutions.add(bodyParser.getInt());
             }
         }
-
-        // build alias table
-        for (String chrName : chromosomeIndexMap.keySet()) {
-            String canonicalName = genome == null ? chrName : genome.getCanonicalChrName(chrName);
-            chrAliasTable.put(canonicalName, chrName);
-        }
     }
 
     private void readFooter() throws IOException {
@@ -280,7 +278,7 @@ public List<ContactRecord> getContactRecords(Region region1,
             if (block == null) continue;
 
             for (ContactRecord rec : block.records) {
-                if (allRecords || (rec.bin1() >= x1 && rec.bin1() < x2 && rec.bin2() >= y1 && rec.bin2() < y2)  && rec.counts() > 1) {
+                if (allRecords || (rec.bin1() >= x1 && rec.bin1() < x2 && rec.bin2() >= y1 && rec.bin2() < y2) && rec.counts() > 1) {
                     contactRecords.add(rec);
                 }
             }
@@ -289,6 +287,24 @@ public List<ContactRecord> getContactRecords(Region region1,
         return contactRecords;
     }
 
+    public int getWGResolution() {
+        if (wgResolution == null) {
+            try {
+                Integer idx = chromosomeIndexMap.get("all");
+                if (idx == null) return -1;
+                Matrix matrix = getMatrix(idx, idx);
+                if (matrix == null) return -1;
+                List<MatrixZoomData> zdArray = matrix.getBpZoomData();
+                if (zdArray.isEmpty()) return -1;
+                wgResolution = zdArray.get(0).getZoom().binSize();
+            } catch (IOException e) {
+                log.error(e.getMessage());
+                wgResolution = -1;
+            }
+        }
+        return wgResolution;
+    }
+
     private List<Block> getBlocks(Region region1, Region region2, String unit, int binSize) throws IOException {
         init();
         String chr1 = getFileChrName(region1.chr());

src/main/java/org/igv/prefs/Constants.java

@@ -320,6 +320,7 @@ private Constants() {
 
     // Misc URLS
     public static final String ENCODE_FILELIST_URL = "ENCODE_FILELIST_URL";
+    public static final String FOUR_DN_FILELIST_URL = "FOUR_DN_FILELIST_URL";
 
 
     /**