More track hub support

* Rewrite of BB is complete * Chromosome aliasing rewrite complete * Removed old MethylTrack and associated files
igvteam · Nov 22, 2023 · 6cce11c · 6cce11c
1 parent 4ac4227
commit 6cce11c
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Showing 67 changed files with 5,600 additions and 1,690 deletions.
diff --git a/src/main/java/org/broad/igv/bbfile/codecs/BBBedCodec.java b/src/main/java/org/broad/igv/bbfile/codecs/BBBedCodec.java
@@ -1,10 +1,9 @@
 package org.broad.igv.bbfile.codecs;
 
 import org.broad.igv.Globals;
-import org.broad.igv.bbfile.BBUtils;
+import org.broad.igv.ucsc.bb.BBUtils;
 import org.broad.igv.bbfile.BedData;
 import org.broad.igv.feature.*;
-import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.feature.tribble.IGVBEDCodec;
 
 import java.util.LinkedHashMap;

diff --git a/src/main/java/org/broad/igv/bbfile/codecs/BBCodecFactory.java b/src/main/java/org/broad/igv/bbfile/codecs/BBCodecFactory.java
@@ -1,9 +1,6 @@
 package org.broad.igv.bbfile.codecs;
 
-import org.broad.igv.bbfile.BBUtils;
-
-import java.util.Collections;
-import java.util.List;
+import org.broad.igv.ucsc.bb.BBUtils;
 
 public class BBCodecFactory {
 

diff --git a/src/main/java/org/broad/igv/bbfile/codecs/BBRmskCodec.java b/src/main/java/org/broad/igv/bbfile/codecs/BBRmskCodec.java
@@ -1,7 +1,7 @@
 package org.broad.igv.bbfile.codecs;
 
 import org.broad.igv.Globals;
-import org.broad.igv.bbfile.BBUtils;
+import org.broad.igv.ucsc.bb.BBUtils;
 import org.broad.igv.bbfile.BedData;
 import org.broad.igv.feature.BasicFeature;
 import org.broad.igv.feature.Exon;

diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAlias.java b/src/main/java/org/broad/igv/feature/genome/ChromAlias.java
@@ -0,0 +1,39 @@
+package org.broad.igv.feature.genome;
+
+import java.util.Collection;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ChromAlias {
+
+    private String chr;
+    private Map<String, String> aliases;
+
+    public ChromAlias(String chr) {
+        this.chr = chr;
+        this.aliases = new HashMap<>();
+        this.aliases.put("chr", chr);
+    }
+
+    public String getChr() {
+        return chr;
+    }
+
+    public void put(String nameSet, String alias) {
+        aliases.put(nameSet, alias);
+    }
+    public String get(String nameSet) {
+        return aliases.get(nameSet);
+    }
+
+    public boolean containsKey(String nameSet) {
+        return aliases.containsKey(nameSet);
+    }
+
+    public Collection<String> values() {
+        return aliases.values();
+    }
+
+
+
+}
diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasBB.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasBB.java
@@ -0,0 +1,76 @@
+package org.broad.igv.feature.genome;
+
+import org.broad.igv.feature.BasicFeature;
+import org.broad.igv.ucsc.bb.BBFile;
+import java.io.IOException;
+
+public class ChromAliasBB extends ChromAliasSource {
+
+
+    BBFile reader;
+
+    public ChromAliasBB(String path, Genome genome) throws IOException {
+        this.reader =  new BBFile(path, genome);
+    }
+
+
+    /**
+     * Return the canonical chromosome name for the alias.  If none found return the alias
+     *
+     * @param alias
+     * @returns {*}
+     */
+    public String getChromosomeName(String alias) {
+        if(aliasCache.containsKey(alias)) {
+            return aliasCache.get(alias).get("chr");
+        } else {
+            try {
+                ChromAlias aliasRecord = search(alias);
+                if(aliasRecord == null) {
+                    aliasRecord.put(alias, null);   // Prevents future attempts
+                } else {
+                    return aliasRecord.get("chr");
+                }
+            } catch (IOException e) {
+                // TODO -- log
+            }
+        }
+       return null;
+    }
+
+    /**
+     * Return an alternate chromosome name (alias).
+     *
+     * @param chr
+     * @param nameSet -- The name set, e.g. "ucsc"
+     * @returns {*|undefined}
+     */
+    public String getChromosomeAlias(String chr, String nameSet) {
+        ChromAlias aliasRecord = this.aliasCache.get(chr);
+        return aliasRecord != null && aliasRecord.containsKey(nameSet) ? aliasRecord.get(nameSet) : chr;
+    }
+
+    /**
+     * Search for chromosome alias bed record.  If found, cache results in the alias -> chr map
+     *
+     * @param alias
+     * @returns {Promise<any>}
+     */
+    public ChromAlias search(String alias) throws IOException {
+        if (!this.aliasCache.containsKey(alias)) {
+            BasicFeature f =  this.reader.search(alias);
+            if (f != null) {
+                String chr = f.getChr();
+                ChromAlias aliasRecord = new ChromAlias(chr);
+                this.aliasCache.put(chr, aliasRecord);
+                for (String key : f.getAttributeKeys()){
+                    final String a = f.getAttribute(key);
+                    aliasRecord.put(key, a);
+                    this.aliasCache.put(a, aliasRecord);      // One entry for each alias
+                }
+            }
+        }
+        return this.aliasCache.get(alias);
+    }
+
+}
diff --git a/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java b/src/main/java/org/broad/igv/feature/genome/ChromAliasDefaults.java
@@ -0,0 +1,156 @@
+package org.broad.igv.feature.genome;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+public class ChromAliasDefaults extends ChromAliasSource {
+
+    public ChromAliasDefaults(String id, List<String> chromosomeNames) {
+
+        this.init(id, chromosomeNames);
+    }
+
+    private void init(String id, List<String> chromosomeNames) {
+
+        List<ChromAlias> aliasRecords = new ArrayList<>();
+        for (String name : chromosomeNames) {
+
+            boolean skipRest = false;
+            ChromAlias record = new ChromAlias(name);
+            aliasRecords.add(record);
+
+            if (name.startsWith("gi|")) {
+                // NCBI
+                String alias = ChromAliasDefaults.getNCBIName(name);
+                record.put("ncbi-gi-versioned", alias);
+
+                // Also strip version number out, if present
+                int dotIndex = alias.lastIndexOf('.');
+                if (dotIndex > 0) {
+                    alias = alias.substring(0, dotIndex);
+                    record.put("ncbi-gi", alias);
+                }
+            } else {
+                // Special cases for human and mouse
+                if (id.startsWith("hg") || id.equals("1kg_ref") || id.equals("b37")) {
+                    switch (name) {
+                        case "chrX":
+                            record.put("ncbi", "23");
+                            skipRest = true;
+                            break;
+                        case "chrY":
+                            record.put("ncbi", "24");
+                            skipRest = true;
+                            break;
+                    }
+                } else if (id.startsWith("GRCh")) {
+                    switch (name) {
+                        case "23":
+                            record.put("ucsc", "chrX");
+                            skipRest = true;
+                            break;
+                        case "24":
+                            record.put("ucsc", "chrY");
+                            skipRest = true;
+                            break;
+                    }
+                } else if (id.startsWith("mm") || id.startsWith("rheMac")) {
+                    switch (name) {
+                        case "chrX":
+                            record.put("ncbi", "21");
+                            skipRest = true;
+                            break;
+                        case "chrY":
+                            record.put("ncbi", "22");
+                            skipRest = true;
+                            break;
+                    }
+                } else if (id.startsWith("GRCm")) {
+                    switch (name) {
+                        case "21":
+                            record.put("ucsc", "chrX");
+                            skipRest = true;
+                            break;
+                        case "22":
+                            record.put("ucsc", "chrY");
+                            skipRest = true;
+                            break;
+                    }
+                }
+                if (skipRest) continue;
+
+                //
+                if (name.equals("chrM")) {
+                    record.put("ncbi", "MT");
+                } else if (name.equals("MT")) {
+                    record.put("ucsc", "chrM");
+                } else if (name.toLowerCase().startsWith("chr")) {
+                    record.put("ncbi", name.substring(3));
+                } else if (isSmallPositiveInteger(name)) {
+                    record.put("ucsc", "chr" + name);
+                }
+            }
+        }
+
+        for (ChromAlias rec : aliasRecords) {
+            for (String a : rec.values()) {
+                this.aliasCache.put(a, rec);
+            }
+        }
+    }
+
+    /**
+     * Return the canonical chromosome name for the alias.  If none found return the alias
+     *
+     * @param alias
+     * @returns {*}
+     */
+    @Override
+    public String getChromosomeName(String alias) {
+        return this.aliasCache.containsKey(alias) ? this.aliasCache.get(alias).get("chr") : alias;
+    }
+
+    /**
+     * Return an alternate chromosome name (alias).
+     *
+     * @param chr
+     * @param nameSet -- The name set, e.g. "ucsc"
+     * @returns {*|undefined}
+     */
+    @Override
+    public String getChromosomeAlias(String chr, String nameSet) {
+        ChromAlias aliasRecord = this.aliasCache.get(chr);
+        return aliasRecord != null && aliasRecord.containsKey(nameSet) ? aliasRecord.get(nameSet) : chr;
+    }
+
+    @Override
+    public ChromAlias search(String alias) {
+        return this.aliasCache.get(alias);
+    }
+
+    /**
+     * Extract the user friendly name from an NCBI accession
+     * example: gi|125745044|ref|NC_002229.3|  =>  NC_002229.3
+     */
+
+    public static String getNCBIName(String name) {
+
+        String[] tokens = name.split("\\|");
+        return tokens[tokens.length - 1];
+    }
+
+
+    public static boolean isSmallPositiveInteger(String str) {
+        int length = str.length();
+        if (length > 100) return false;
+        for (int i = 0; i < length; i++) {
+            char c = str.charAt(i);
+            if (c < '0' || c > '9') {
+                return false;
+            }
+        }
+        return true;
+    }
+}