Fix broken paired end alignment popup text. Fixes igvteam#1003

Author: jrobinso

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

@@ -133,7 +133,7 @@ default void setHaplotypeName(String hap) {}
 
     default Map<Integer, BaseModification> getBaseModificationMap() { return null;}
 
-    default String getValueString(double position, int mouseX, AlignmentTrack.RenderOptions renderOptions) {
+    default String getAlignmentValueString(double position, int mouseX, AlignmentTrack.RenderOptions renderOptions) {
         return getValueString(position, mouseX, (WindowFunction) null);
     }
 }

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

@@ -812,6 +812,8 @@ private void copyToClipboard(final TrackClickEvent e, Alignment alignment, doubl
         if (alignment != null) {
             StringBuilder buf = new StringBuilder();
             buf.append(alignment.getClipboardString(location, mouseX)
+                    .replace("<b>", "")
+                    .replace("</b>", "")
                     .replace("<br>", "\n")
                     .replace("<br/>", "\n")
                     .replace("<hr>", "\n------------------\n")
@@ -964,7 +966,7 @@ public String getValueStringAt(String chr, double position, int mouseX, int mous
             } else {
                 Alignment feature = getAlignmentAt(position, mouseY, frame);
                 if (feature != null) {
-                    return feature.getValueString(position, mouseX, renderOptions);
+                    return feature.getAlignmentValueString(position, mouseX, renderOptions);
                 }
             }
 

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

@@ -27,7 +27,6 @@
 
 import org.broad.igv.feature.LocusScore;
 import org.broad.igv.feature.Strand;
-import org.broad.igv.track.WindowFunction;
 
 import java.awt.*;
 import java.util.List;
@@ -178,20 +177,20 @@ public byte getPhred(double position) {
      * does not "know" from what window function it was derived
      *
      * @param mouseX
-     * @param windowFunction
+     * @param renderOptions
      * @return
      */
-    public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
+    public String getAlignmentValueString(double position, int mouseX, AlignmentTrack.RenderOptions renderOptions) {
         StringBuffer buf = new StringBuffer();
         if (secondAlignment != null) {
             buf.append("<table><tr><td valign=\"top\">");
         }
         buf.append("<b>Left alignment</b><br/>");
-        buf.append(firstAlignment.getValueString(position, mouseX, windowFunction));
+        buf.append(firstAlignment.getAlignmentValueString(position, mouseX, renderOptions));
         if (secondAlignment != null) {
             buf.append("</td><td valign=\"top\">");
             buf.append("<b>Right alignment</b><br/>");
-            buf.append(secondAlignment.getValueString(position, mouseX, windowFunction));
+            buf.append(secondAlignment.getAlignmentValueString(position, mouseX, renderOptions));
             buf.append("</td></tr></table>");
         }
         return buf.toString();

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

@@ -39,7 +39,6 @@
 import org.broad.igv.feature.genome.GenomeManager;
 import org.broad.igv.prefs.Constants;
 import org.broad.igv.prefs.PreferencesManager;
-import org.broad.igv.track.WindowFunction;
 import org.broad.igv.ui.color.ColorUtilities;
 
 import java.awt.*;
@@ -573,11 +572,11 @@ private static List<CigarOperator> buildOperators(String cigarString) {
 
 
     public String getClipboardString(double location, int mouseX) {
-        return getValueString(location, mouseX, (AlignmentTrack.RenderOptions) null);
+        return getAlignmentValueString(location, mouseX, (AlignmentTrack.RenderOptions) null);
     }
 
 
-    public String getValueString(double position, int mouseX, AlignmentTrack.RenderOptions renderOptions) {
+    public String getAlignmentValueString(double position, int mouseX, AlignmentTrack.RenderOptions renderOptions) {
 
         boolean truncate = renderOptions != null;
         int basePosition = (int) position;