Restore cluster menu option for 3rd gen alignments, renamed to "Clust…

…er alignments". Fixes #1509

src/main/java/org/broad/igv/sam/Alignment.java

@@ -175,13 +175,13 @@ default ClippingCounts getClippingCounts(){
         return ClippingCounts.fromCigar(getCigar());
     }
 
-    default void setHaplotypeName(String hap) {}
+    default void setClusterName(String hap) {}
 
-    default String getHaplotypeName() {return null;}
+    default String getClusterName() {return null;}
 
     default void setHapDistance(int dist) {};
 
-    default int getHapDistance() {return 0;}
+    default int getClusterDistance() {return 0;}
 
     default Map<Integer, BaseModificationUtils> getBaseModificationMap() { return null;}
 

src/main/java/org/broad/igv/sam/AlignmentPacker.java

@@ -439,8 +439,8 @@ private Object getGroupValue(Alignment al, AlignmentTrack.RenderOptions renderOp
         String readNameParts[], movieName, zmw;
 
         switch (groupBy) {
-            case HAPLOTYPE:
-                return al.getHaplotypeName();
+            case CLUSTER:
+                return al.getClusterName();
             case STRAND:
                 return al.isNegativeStrand() ? "-" : "+";
             case SAMPLE:

src/main/java/org/broad/igv/sam/AlignmentTrack.java

@@ -164,7 +164,7 @@ public enum GroupOption {
         INSERTION_AT_POS("insertion at position", true),
         MOVIE("movie"),
         ZMW("ZMW"),
-        HAPLOTYPE("haplotype"),
+        CLUSTER("cluster"),
         READ_ORDER("read order"),
         LINKED("linked"),
         PHASE("phase"),
@@ -1711,7 +1711,11 @@ public void unmarshalXML(Element element, Integer version) {
                 sortOption = SortOption.valueOf((element.getAttribute("sortOption")));
             }
             if (element.hasAttribute("groupByOption")) {
-                groupByOption = GroupOption.valueOf(element.getAttribute("groupByOption"));
+                String value = element.getAttribute("groupByOption");
+                if(value.equals("HAPLOTYPE")) {
+                    value = "CLUSTER";  // Backward compatibility
+                }
+                groupByOption = GroupOption.valueOf(value);
             }
             if (element.hasAttribute("shadeAlignmentsByOption")) {
                 shadeAlignmentsOption = ShadeAlignmentsOption.valueOf(element.getAttribute("shadeAlignmentsByOption"));

src/main/java/org/broad/igv/sam/AlignmentTrackMenu.java

@@ -2,7 +2,6 @@
 
 import htsjdk.samtools.SAMTag;
 import org.broad.igv.Globals;
-import org.broad.igv.feature.Locus;
 import org.broad.igv.feature.Range;
 import org.broad.igv.feature.Strand;
 import org.broad.igv.jbrowse.CircularViewUtilities;
@@ -95,10 +94,6 @@ class AlignmentTrackMenu extends IGVPopupMenu {
         // Experiment type  (RNA, THIRD GEN, OTHER)
         addSeparator();
         addExperimentTypeMenuItem();
-//        if (alignmentTrack.getExperimentType() == AlignmentTrack.ExperimentType.THIRD_GEN) {
-//            addHaplotype(e);
-//        }
-
 
         // Group, sort, color, shade, and pack
         addSeparator();
@@ -186,6 +181,12 @@ class AlignmentTrackMenu extends IGVPopupMenu {
             add(sashimi);
         }
 
+        // Experimental items
+        if (alignmentTrack.getExperimentType() == AlignmentTrack.ExperimentType.THIRD_GEN) {
+            addSeparator();
+            addClusterItem(e);
+        }
+
         // Show alignments, coverage, splice junctions
         addSeparator();
         addShowItems();
@@ -233,9 +234,9 @@ private void addShowDiagram(final TrackClickEvent e, final Alignment clickedAlig
     }
 
 
-    private void addHaplotype(TrackClickEvent e) {
+    private void addClusterItem(TrackClickEvent e) {
 
-        JMenuItem item = new JMenuItem("Cluster (phase) alignments");
+        JMenuItem item = new JMenuItem("Cluster alignments  *EXPERIMENTAL*");
 
         final ReferenceFrame frame;
         if (e.getFrame() == null && FrameManager.getFrames().size() == 1) {
@@ -269,17 +270,14 @@ private void addHaplotype(TrackClickEvent e) {
             final int end = (int) frame.getEnd();
 
             AlignmentInterval interval = dataManager.getLoadedInterval(frame);
-            HaplotypeUtils haplotypeUtils = new HaplotypeUtils(interval);
-            boolean success = haplotypeUtils.clusterAlignments(frame.getChrName(), start, end, nClusters);
+            ClusterUtils clusterUtils = new ClusterUtils(interval);
+            boolean success = clusterUtils.clusterAlignments(frame.getChrName(), start, end, nClusters);
 
             if (success) {
-                groupAlignments(AlignmentTrack.GroupOption.HAPLOTYPE, null, null);
+                groupAlignments(AlignmentTrack.GroupOption.CLUSTER, null, null);
                 alignmentTrack.repaint();
             }
 
-            //dataManager.sortRows(SortOption.HAPLOTYPE, frame, (end + start) / 2, null);
-            //AlignmentTrack.repaint();
-
         });
 
 

src/main/java/org/broad/igv/sam/HaplotypeUtils.java → src/main/java/org/broad/igv/sam/ClusterUtils.java

@@ -3,7 +3,6 @@
 
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.logging.*;
-import org.broad.igv.feature.genome.Genome;
 import org.broad.igv.ui.util.MessageUtils;
 
 import java.util.*;
@@ -15,14 +14,14 @@
  * @author Jim Robinson
  */
 
-public class HaplotypeUtils {
+public class ClusterUtils {
 
-    private static Logger log = LogManager.getLogger(HaplotypeUtils.class);
+    private static Logger log = LogManager.getLogger(ClusterUtils.class);
 
     private final AlignmentInterval alignmentInterval;
 
 
-    public HaplotypeUtils(AlignmentInterval alignmentInterval) {
+    public ClusterUtils(AlignmentInterval alignmentInterval) {
         this.alignmentInterval = alignmentInterval;
     }
 
@@ -54,7 +53,7 @@ public boolean clusterAlignments(String chr, int start, int end, int nClasses) {
 
             // Clear any existing names
             for(Alignment a : this.alignmentInterval.getAlignments()) {
-                a.setHaplotypeName("NONE");
+                a.setClusterName("?");
             }
 
             // Label alignments
@@ -126,7 +125,7 @@ public boolean clusterAlignments(String chr, int start, int end, int nClasses) {
 
                     List<Alignment> alignments = labelAlignmentMap.get(l);
                     for (Alignment a : alignments) {
-                        a.setHaplotypeName(label);
+                        a.setClusterName(label);
                     }
                 }
             }

src/main/java/org/broad/igv/sam/SAMAlignment.java

@@ -685,9 +685,9 @@ public String getAlignmentValueString(double position, int mouseX, AlignmentTrac
         int basePosition = (int) position;
         StringBuffer buf = new StringBuffer();
 
-        if (getHaplotypeName() != null) {
-            buf.append("Hap name: " + getHaplotypeName() + "<br>");
-            buf.append("Dist: " + getHapDistance() + "<br>");
+        if (getClusterName() != null) {
+            buf.append("Cluster name: " + getClusterName() + "<br>");
+            buf.append("Dist: " + getClusterDistance() + "<br>");
         }
 
         boolean atInsertion = false;
@@ -1215,12 +1215,12 @@ private static boolean operatorIsMatch(boolean showSoftClipped, char operator) {
     String haplotypeName;
 
     @Override
-    public void setHaplotypeName(String hap) {
+    public void setClusterName(String hap) {
         haplotypeName = hap;
     }
 
     @Override
-    public String getHaplotypeName() {
+    public String getClusterName() {
         return haplotypeName;
     }
 
@@ -1232,7 +1232,7 @@ public void setHapDistance(int dist) {
     }
 
     @Override
-    public int getHapDistance() {
+    public int getClusterDistance() {
         return hapDistance;
     }
 

src/main/java/org/broad/igv/sam/SortOption.java

@@ -1,13 +1,10 @@
 package org.broad.igv.sam;
 
-import htsjdk.samtools.SAMTag;
 import htsjdk.samtools.util.Locatable;
 import org.broad.igv.feature.genome.ChromosomeNameComparator;
 
 import java.util.Comparator;
-import java.util.List;
 import java.util.Objects;
-import java.util.Set;
 import java.util.function.Function;
 import java.util.function.ToIntFunction;
 
@@ -134,7 +131,7 @@ Comparator<Alignment> getAlignmentComparator(final int center, final String tag,
     }, HAPLOTYPE {
         @Override
         Comparator<Alignment> getAlignmentComparator(final int center, final String tag, final byte referenceBase) {
-            return Comparator.comparingInt(Alignment::getHapDistance);
+            return Comparator.comparingInt(Alignment::getClusterDistance);
         }
     }, READ_ORDER {
         @Override