Add support for searching by bb extra indexes, including trix

igvteam · Nov 28, 2023 · 7df59de · 7df59de
1 parent 564b683
commit 7df59de
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Showing 13 changed files with 179 additions and 94 deletions.
diff --git a/src/main/java/org/broad/igv/feature/genome/Genome.java b/src/main/java/org/broad/igv/feature/genome/Genome.java
@@ -257,7 +257,7 @@ private void addTracks(GenomeConfig config) {
                     res.setVisibilityWindow(vw);
                 }
 
-                if(trackConfig.searchTrix != null) {
+                if (trackConfig.searchTrix != null) {
                     res.setTrixURL(trackConfig.searchTrix);
                 }
 
@@ -355,7 +355,7 @@ public Genome(String id, List<Chromosome> chromosomes) {
      * Return the canonical chromosome name for the (possibly) alias
      *
      * @param str chromosome or alias name
-     * @return the canonical chromsoome name -- i.e. chromosome name as defined by the reference sequence
+     * @return the canonical chromsoome name -if the chromosome exists.
      */
     public String getCanonicalChrName(String str) {
         if (str == null) {
@@ -365,9 +365,7 @@ public String getCanonicalChrName(String str) {
         } else if (chromAliasSource != null) {
             try {
                 ChromAlias aliasRecord = chromAliasSource.search(str);
-                if (aliasRecord == null) {
-                    return str;
-                } else {
+                if (aliasRecord != null) {
                     String chr = aliasRecord.getChr();
                     chrAliasCache.put(str, chr);
                     return chr;
@@ -491,9 +489,9 @@ public Chromosome getChromosome(String name) {
         if (chromosomeMap.containsKey(chrName)) {
             return chromosomeMap.get(chrName);
         } else {
-            int idx = this.chromosomeMap.size();
             int length = this.sequence.getChromosomeLength(chrName);
             if (length > 0) {
+                int idx = this.chromosomeMap.size();
                 Chromosome chromosome = new Chromosome(idx, chrName, length);
                 chromosomeMap.put(chrName, chromosome);
                 return chromosome;

diff --git a/src/main/java/org/broad/igv/feature/genome/Sequence.java b/src/main/java/org/broad/igv/feature/genome/Sequence.java
@@ -38,13 +38,26 @@
  */
 public interface Sequence {
 
-    byte[] getSequence(String chr, int start, int end);
+    /**
+     * Return the sequence for the given range.  If sequence named "seq" does not exist returns null.
+     * @param chr
+     * @param start
+     * @param end
+     * @return  The sequence in bytes, or null if no sequence exists
+     */
+    byte[] getSequence(String seq, int start, int end) ;
 
-    byte getBase(String chr, int position);
+    byte getBase(String seq, int position);
 
     List<String> getChromosomeNames();
 
-    int getChromosomeLength(String chrname);
+    /**
+     * Return the given sequence length.  If no sequence exists with name "seq" return -1.
+     *
+     * @param seq
+     * @return
+     */
+    int getChromosomeLength(String seq);
 
     List<Chromosome> getChromosomes();
 

diff --git a/src/main/java/org/broad/igv/feature/genome/SequenceNotFoundException.java b/src/main/java/org/broad/igv/feature/genome/SequenceNotFoundException.java
@@ -0,0 +1,7 @@
+package org.broad.igv.feature.genome;
+
+public class SequenceNotFoundException extends RuntimeException {
+    public SequenceNotFoundException(String message) {
+        super(message);
+    }
+}
diff --git a/src/main/java/org/broad/igv/feature/genome/fasta/FastaIndexedSequence.java b/src/main/java/org/broad/igv/feature/genome/fasta/FastaIndexedSequence.java
@@ -191,7 +191,7 @@ public List<String> getChromosomeNames() {
 
     @Override
     public int getChromosomeLength(String chrname) {
-        return index.getSequenceSize(chrname);
+        return  index.getSequenceSize(chrname);
     }
 
     @Override

diff --git a/src/main/java/org/broad/igv/session/History.java b/src/main/java/org/broad/igv/session/History.java
@@ -31,6 +31,7 @@
 import org.broad.igv.ui.IGV;
 import org.broad.igv.ui.action.SearchCommand;
 import org.broad.igv.ui.panel.FrameManager;
+import org.broad.igv.util.LongRunningTask;
 
 import java.util.ArrayList;
 import java.util.LinkedList;
@@ -121,7 +122,7 @@ public void processItem(Entry entry) {
                 if (FrameManager.isGeneListMode()) {
                     IGV.getInstance().setGeneList(null, false);
                 }
-                (new SearchCommand(FrameManager.getDefaultFrame(), locus, false)).execute();
+                LongRunningTask.submit(new SearchCommand(FrameManager.getDefaultFrame(), locus, false));
                 //Zoom should be implicit in the locus
                 //FrameManager.getDefaultFrame().setZoom(entry.getZoom());
             }

diff --git a/src/main/java/org/broad/igv/track/FeatureSource.java b/src/main/java/org/broad/igv/track/FeatureSource.java
@@ -26,6 +26,7 @@
 package org.broad.igv.track;
 
 import htsjdk.tribble.Feature;
+import htsjdk.tribble.NamedFeature;
 import org.broad.igv.feature.LocusScore;
 import org.broad.igv.ui.panel.ReferenceFrame;
 
@@ -92,4 +93,17 @@ default void close() {
     default Object getHeader() {
         return null;
     }
+
+    /**
+     * Return true if the source can be searched for a feature by name
+     *
+     * @return
+     */
+    default boolean isSearchable() {
+        return false;
+    }
+
+    default NamedFeature search(String name) {
+        return null;
+    }
 }
diff --git a/src/main/java/org/broad/igv/track/FeatureTrack.java b/src/main/java/org/broad/igv/track/FeatureTrack.java
@@ -26,6 +26,7 @@
 package org.broad.igv.track;
 
 import htsjdk.tribble.Feature;
+import htsjdk.tribble.NamedFeature;
 import htsjdk.tribble.TribbleException;
 import org.broad.igv.event.IGVEvent;
 import org.broad.igv.logging.*;
@@ -1056,6 +1057,16 @@ public void marshalXML(Document document, Element element) {
 
     }
 
+    @Override
+    public boolean isSearchable() {
+        return source.isSearchable();
+    }
+
+    @Override
+    public NamedFeature search(String token) {
+        return source.search(token);
+    }
+
     @Override
     public void unmarshalXML(Element element, Integer version) {
 

diff --git a/src/main/java/org/broad/igv/track/Track.java b/src/main/java/org/broad/igv/track/Track.java
@@ -31,6 +31,7 @@
 
 
 import htsjdk.tribble.Feature;
+import htsjdk.tribble.NamedFeature;
 import org.broad.igv.renderer.ContinuousColorScale;
 import org.broad.igv.renderer.DataRange;
 import org.broad.igv.renderer.Renderer;
@@ -272,9 +273,12 @@ default Color getExplicitAltColor() {
 
     void setAutoScale(boolean autoScale);
 
-    default boolean isShowFeatureNames() {return true;}
+    default boolean isShowFeatureNames() {
+        return true;
+    }
 
-    default void setShowFeatureNames(boolean b) {}
+    default void setShowFeatureNames(boolean b) {
+    }
 
     /**
      * Return the java property or attribute for the feature display name.  Default is "null", in which case the
@@ -286,6 +290,19 @@ default String getLabelField() {
         return null;
     }
 
+    /**
+     * Return true if the track can be searched for a feature by name.
+     *
+     * @return
+     */
+    default boolean isSearchable() {
+        return false;
+    }
+
+    default NamedFeature search(String token) {
+        return null;
+    }
+
     default void repaint() {
         IGV.getInstance().repaint(this);
     }

diff --git a/src/main/java/org/broad/igv/ucsc/bb/BBFeatureSource.java b/src/main/java/org/broad/igv/ucsc/bb/BBFeatureSource.java
@@ -25,14 +25,14 @@
 
 package org.broad.igv.ucsc.bb;
 
+import htsjdk.tribble.NamedFeature;
 import org.broad.igv.feature.BasicFeature;
 import org.broad.igv.feature.LocusScore;
 import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.logging.LogManager;
 import org.broad.igv.logging.Logger;
 import org.broad.igv.track.FeatureSource;
 import org.broad.igv.track.WindowFunction;
-import org.broad.igv.ucsc.Trix;
 
 import java.io.IOException;
 import java.util.*;
@@ -111,7 +111,8 @@ public boolean isSearchable() {
         return reader.isSearchable();
     }
 
-    BasicFeature search(String term) {
+    @Override
+    public NamedFeature search(String term) {
         try {
             return reader.search(term);
         } catch (IOException e) {

diff --git a/src/main/java/org/broad/igv/ucsc/bb/BBFile.java b/src/main/java/org/broad/igv/ucsc/bb/BBFile.java
@@ -1,6 +1,7 @@
 package org.broad.igv.ucsc.bb;
 
 import htsjdk.samtools.seekablestream.SeekableStream;
+import htsjdk.tribble.NamedFeature;
 import org.broad.igv.data.BasicScore;
 import org.broad.igv.feature.BasicFeature;
 import org.broad.igv.feature.LocusScore;
@@ -400,6 +401,7 @@ public boolean isSearchable() {
      * @param term
      * @returns {Promise<void>}
      */
+
     public BasicFeature search(String term) throws IOException {
 
         if (this.header == null) {

diff --git a/src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java b/src/main/java/org/broad/igv/ucsc/twobit/TwoBitSequence.java
@@ -2,6 +2,9 @@
 
 import org.broad.igv.feature.Chromosome;
 import org.broad.igv.feature.genome.Sequence;
+import org.broad.igv.feature.genome.SequenceNotFoundException;
+import org.broad.igv.logging.LogManager;
+import org.broad.igv.logging.Logger;
 import org.broad.igv.ucsc.BPIndex;
 import org.broad.igv.ucsc.BPTree;
 
@@ -22,6 +25,8 @@
 
 public class TwoBitSequence implements Sequence {
 
+    private static Logger log = LogManager.getLogger(TwoBitSequence.class);
+
     // the number 0x1A412743 in the architecture of the machine that created the file
     static int SIGNATURE = 0x1a412743;
     String path;
@@ -85,12 +90,15 @@ public List<String> getChromosomeNames() {
     }
 
     @Override
-    public int getChromosomeLength(String chrname) {
+    public int getChromosomeLength(String seq) {
         try {
-            SequenceRecord sequenceRecord = getSequenceRecord(chrname);
+            SequenceRecord sequenceRecord = getSequenceRecord(seq);
             return sequenceRecord.getDnaSize();
-        } catch (Exception e) {
-            throw new RuntimeException(e);
+        } catch (SequenceNotFoundException e) {
+            return -1;
+        } catch (IOException e) {
+            log.error("Error reading sequence " + seq, e);
+            return -1;
         }
     }
 
@@ -183,7 +191,7 @@ public SequenceRecord getSequenceRecord(String seqName) throws IOException {
         if (record == null) {
             long[] offset_length = this.index.search(seqName);
             if (offset_length == null) {
-                throw new RuntimeException("Unknown sequence: " + seqName);
+                throw new SequenceNotFoundException("Unknown sequence: " + seqName);
             }
             long offset = offset_length[0];