Refactor "copy read details" code, and minor reformatting of output.

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

@@ -139,7 +139,9 @@ default int getLeadingHardClipLength() {
 
     default String getLibrary(){ return null;}
 
-    String getClipboardString(double location, int mouseX);
+    default String getClipboardString(double location, int mouseX) {
+        return getValueString(location, mouseX, null);
+    }
 
     default void finish(){};
 

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

@@ -211,8 +211,8 @@ private void addDuplicatesMenuItem() {
             mi.setSelected(previous == option);
             mi.addActionListener(aEvt -> {
                 renderOptions.setDuplicatesOption(option);
-                if(previous != option) {
-                    if (previous.filtered != option.filtered){
+                if (previous != option) {
+                    if (previous.filtered != option.filtered) {
                         // duplicates are filtered out when loading the read data so a reload has to be performed in this case
                         IGVEventBus.getInstance().post(new AlignmentTrackEvent(AlignmentTrackEvent.Type.RELOAD));
                     } else {
@@ -1220,19 +1220,14 @@ void addThirdGenItems(Alignment clickedAlignment, final TrackClickEvent tce) {
     private void copyToClipboard(final TrackClickEvent e, Alignment alignment, double location, int mouseX) {
 
         if (alignment != null) {
-            StringBuilder buf = new StringBuilder();
-            buf.append(alignment.getClipboardString(location, mouseX)
+            final String clipboardString = alignment.getClipboardString(location, mouseX)
                     .replace("<b>", "")
                     .replace("</b>", "")
                     .replace("<br>", "\n")
                     .replace("<br/>", "\n")
                     .replace("<hr>", "\n------------------\n")
-                    .replace("<hr/>", "\n------------------\n"));
-            buf.append("\n");
-            buf.append("Alignment start position = ").append(alignment.getChr()).append(":").append(alignment.getAlignmentStart() + 1);
-            buf.append("\n");
-            buf.append(alignment.getReadSequence());
-            StringSelection stringSelection = new StringSelection(buf.toString());
+                    .replace("<hr/>", "\n------------------\n");
+            StringSelection stringSelection = new StringSelection(clipboardString);
             Clipboard clipboard = Toolkit.getDefaultToolkit().getSystemClipboard();
             clipboard.setContents(stringSelection, null);
         }

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

@@ -151,10 +151,6 @@ public LocusScore copy() {
         return this;
     }
 
-    public String getClipboardString(double location, int mouseX) {
-        return getValueString(location, mouseX, (WindowFunction) null);
-    }
-
     public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
         return readName + "<br>Read length = " + (getEnd() - getStart());
     }

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

@@ -143,10 +143,6 @@ public LocusScore copy() {
         return this;
     }
 
-    public String getClipboardString(double location, int mouseX) {
-        return getValueString(location, mouseX, (WindowFunction) null);
-    }
-
     public String getValueString(double position, int mouseX, WindowFunction windowFunction) {
         return readName + "<br>Read length = " + (getEnd() - getStart());
     }

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

@@ -9,7 +9,7 @@
 import java.util.*;
 
 /**
- * Class for experimenting with 10X linked reads.
+ * Represents a collection of alignments linked by a tag or read name
  */
 
 public class LinkedAlignment implements Alignment {
@@ -363,11 +363,6 @@ public String getSample() {
         return sample;
     }
 
-    @Override
-    public String getClipboardString(double location, int mouseX) {
-        return null;
-    }
-
     @Override
     public void finish() {
         alignments.sort(ALIGNMENT_START_COMPARATOR);

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

@@ -195,19 +195,6 @@ public String getAlignmentValueString(double position, int mouseX, AlignmentTrac
         return buf.toString();
     }
 
-
-    public String getClipboardString(double position, int mouseX) {
-        StringBuffer buf = new StringBuffer();
-        buf.append("<b>Left alignment</b><br/>");
-        buf.append(firstAlignment.getClipboardString(position, mouseX));
-        if (secondAlignment != null) {
-            buf.append("<br/><b>Right alignment</b><br/>");
-            buf.append(secondAlignment.getClipboardString(position, mouseX));
-        }
-        return buf.toString();
-    }
-    ////////////////////////////////////////////////////////////
-
     public boolean contains(double location) {
         return location >= start && location <= end;
     }

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

@@ -206,10 +206,6 @@ public LocusScore copy() {
         return this;
     }
 
-    public String getClipboardString(double location, int mouseX) {
-        return getValueString(location, mouseX, (WindowFunction) null);
-    }
-
     public String getValueString(double position, int mouseX, WindowFunction ignored) {
 
         StringBuffer buf = new StringBuffer();

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

@@ -34,6 +34,7 @@
 import htsjdk.samtools.SAMReadGroupRecord;
 import htsjdk.samtools.SAMRecord;
 import htsjdk.samtools.SAMTag;
+import htsjdk.samtools.util.SequenceUtil;
 import org.broad.igv.logging.*;
 import org.broad.igv.Globals;
 import org.broad.igv.feature.Strand;
@@ -658,7 +659,6 @@ private static List<CigarOperator> buildOperators(String cigarString) {
                     prevOp = new CigarOperator(nBases, op);
                     operators.add(prevOp);
                 }
-
             }
         }
         return operators;
@@ -668,7 +668,22 @@ private static List<CigarOperator> buildOperators(String cigarString) {
 
     @Override
     public String getClipboardString(double location, int mouseX) {
-        return getAlignmentValueString(location, mouseX, null);
+
+        StringBuilder buf = new StringBuilder();
+
+        String popupTextString = getAlignmentValueString(location, mouseX, null);
+        buf.append(popupTextString);
+
+        buf.append("----------------------");
+        final String readSequence = getReadSequence();
+        final String origSequence = isNegativeStrand() ? SequenceUtil.reverseComplement(readSequence) : readSequence;
+        buf.append("\n\nRead sequence = ");
+        buf.append(readSequence);
+        buf.append("\n\nOrig sequence = ");
+        buf.append(origSequence);
+        buf.append("\n");
+
+        return buf.toString();
     }
 
     private Integer positionToReadIndex(double position) {
@@ -697,6 +712,7 @@ public String getAlignmentValueString(double position, int mouseX, AlignmentTrac
 
         boolean atInsertion = false;
         boolean atBaseMod = false;
+
         // First check insertions.  Position is zero based, block coords 1 based
         if (this.insertions != null) {
             for (AlignmentBlock block : this.insertions) {

src/test/java/org/broad/igv/sam/BisulfiteBaseInfoTest.java

@@ -315,9 +315,5 @@ public String getLibrary() {
             return library;
         }
 
-        @Override
-        public String getClipboardString(double location, int mouseX) {
-            return null;
-        }
     }
 }