Fix the children order in line graph and various refactorings

src/main/java/org/variantsync/diffdetective/diff/git/GitDiffer.java

@@ -111,14 +111,12 @@ public static CommitDiffResult createCommitDiff(
         final CanonicalTreeParser currentTreeParser = new CanonicalTreeParser();
         final CanonicalTreeParser prevTreeParser = new CanonicalTreeParser();
         try (ObjectReader reader = repository.getGitRepo().getRepository().newObjectReader()) {
-            try {
-                currentTreeParser.reset(reader, childCommit.getTree());
-                if (parentCommit != null) {
-                    prevTreeParser.reset(reader, parentCommit.getTree());
-                }
-            } catch (IOException e) {
-                return CommitDiffResult.Failure(DiffError.JGIT_ERROR, e.toString());
+            currentTreeParser.reset(reader, childCommit.getTree());
+            if (parentCommit != null) {
+                prevTreeParser.reset(reader, parentCommit.getTree());
             }
+        } catch (IOException e) {
+            return CommitDiffResult.Failure(DiffError.JGIT_ERROR, e.toString());
         }
 
         final AbstractTreeIterator parentTreeIterator;

src/main/java/org/variantsync/diffdetective/gumtree/VariationDiffAdapter.java

@@ -22,6 +22,7 @@ public VariationDiffAdapter(Projection<L> node) {
         super(node);
     }
 
+    @Override
     protected VariationTreeAdapter<L> newInstance(VariationNode<?, L> node) {
         return new VariationDiffAdapter<>(Cast.unchecked(node));
     }

src/main/java/org/variantsync/diffdetective/gumtree/VariationTreeAdapter.java

@@ -2,8 +2,10 @@
 
 import java.util.ArrayList;
 import java.util.Iterator;
+import java.util.LinkedHashMap;
 import java.util.Map.Entry;
 import java.util.stream.Collectors;
+import java.util.stream.Stream;
 
 import org.variantsync.diffdetective.variation.Label;
 import org.variantsync.diffdetective.variation.tree.VariationNode;
@@ -24,15 +26,17 @@
 public class VariationTreeAdapter<L extends Label> extends AbstractTree {
     private String cachedLabel;
     private VariationNode<?, L> backingNode;
+    private LinkedHashMap<String, Object> metadata;
 
     public VariationTreeAdapter(VariationNode<?, L> node) {
         this.backingNode = node;
+        this.metadata = new LinkedHashMap<>();
 
-        if (backingNode.isConditionalAnnotation()) {
-            cachedLabel = backingNode.getFormula().toString();
-        } else {
-            cachedLabel = backingNode.getLabel().getLines().stream().collect(Collectors.joining("\n"));
-        }
+        cachedLabel =
+            Stream.concat(
+                backingNode.getLabel().getLines().stream(),
+                backingNode.getLabel().getTrailingLines().stream()
+            ).collect(Collectors.joining("\n"));
 
         var children = new ArrayList<Tree>(node.getChildren().size());
         for (var child : node.getChildren()) {
@@ -41,7 +45,7 @@ public VariationTreeAdapter(VariationNode<?, L> node) {
         setChildren(children);
     }
 
-    protected VariationTreeAdapter newInstance(VariationNode<?, L> node) {
+    protected VariationTreeAdapter<L> newInstance(VariationNode<?, L> node) {
         return new VariationTreeAdapter<>(node);
     }
 
@@ -65,12 +69,12 @@ public int getLength() {
 
     @Override
     public Iterator<Entry<String, Object>> getMetadata() {
-        throw new UnsupportedOperationException();
+        return metadata.entrySet().iterator();
     }
 
     @Override
-    public Object getMetadata(String arg0) {
-        throw new UnsupportedOperationException();
+    public Object getMetadata(String key) {
+        return metadata.get(key);
     }
 
     /**
@@ -97,8 +101,8 @@ public void setLength(int length) {
     }
 
     @Override
-    public Object setMetadata(String name, Object value) {
-        throw new UnsupportedOperationException();
+    public Object setMetadata(String key, Object value) {
+        return metadata.put(key, value);
     }
 
     @Override

src/main/java/org/variantsync/diffdetective/util/Assert.java

@@ -86,7 +86,7 @@ public static void assertFalse(boolean condition, String errorMessage) {
     }
 
     /** Throws {@link AssertionError} with {@code errorMessage} as error message. */
-    public static void fail(String errorMessage) {
+    public static <T> T fail(String errorMessage) {
         throw new AssertionError(errorMessage);
     }
 
@@ -105,12 +105,18 @@ public static void assertNull(Object o) {
     }
 
     public static <T> void assertEquals(T expected, T actual) {
+        assertEquals(expected, actual, null);
+    }
+
+    public static <T> void assertEquals(T expected, T actual, String message) {
+        String prefix = message == null ? "" : message + ": ";
+
         if (expected == null) {
             if (actual != null) {
-                fail("expected is null but actual is not!");
+                fail(prefix + "expected is null but actually it is " + actual);
             }
         } else {
-            assertTrue(expected.equals(actual), expected + " != " + actual);
+            assertTrue(expected.equals(actual), prefix + expected + " != " + actual);
         }
     }
 }

src/main/java/org/variantsync/diffdetective/variation/DiffLinesLabel.java

@@ -2,12 +2,14 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Iterator;
 import java.util.List;
 import java.util.stream.Collectors;
 
 import org.variantsync.diffdetective.diff.text.DiffLineNumber;
 import org.variantsync.diffdetective.util.Assert;
 import org.variantsync.diffdetective.util.StringUtils;
+import org.variantsync.diffdetective.variation.diff.Time;
 import org.variantsync.diffdetective.variation.diff.VariationDiff; // For Javadoc
 
 /**
@@ -82,6 +84,66 @@ public List<String> getTrailingLines() {
         return getDiffTrailingLines().stream().map(Line::content).toList();
     }
 
+    /**
+     * Returns a deep copy where the line numbers at {@code time} are set to
+     * {@link DiffLineNumber#InvalidLineNumber}.
+     */
+    @Override
+    public DiffLinesLabel withoutTimeDependentState(Time time) {
+        return new DiffLinesLabel(
+            mapWithoutTimeDependentState(getDiffLines(), time),
+            mapWithoutTimeDependentState(getDiffTrailingLines(), time)
+        );
+    }
+
+    private List<Line> mapWithoutTimeDependentState(List<Line> lines, Time time) {
+        return lines
+            .stream()
+            .map(line -> new Line(
+                line.content(),
+                line.lineNumber().withLineNumberAtTime(DiffLineNumber.InvalidLineNumber, time)
+            ))
+            .toList();
+    }
+
+    /**
+     * Returns a deep copy where the line numbers at {@code time} are copied from
+     * {@code otherLabel}. The number of lines and their content must be identical in {@code this}
+     * and {@code otherLabel}.
+     *
+     * @see withoutTimeDependentState
+     */
+    @Override
+    public DiffLinesLabel withTimeDependentStateFrom(Label otherLabel, Time time) {
+        DiffLinesLabel other = (DiffLinesLabel) otherLabel;
+
+        return new DiffLinesLabel(
+            zipWithTimeDependentStateFrom(this.getDiffLines(), other.getDiffLines(), time),
+            zipWithTimeDependentStateFrom(this.getDiffTrailingLines(), other.getDiffTrailingLines(), time)
+        );
+    }
+
+    private static List<Line> zipWithTimeDependentStateFrom(List<Line> linesA, List<Line> linesB, Time time) {
+        List<Line> result = new ArrayList<>(linesA.size());
+
+        Iterator<Line> itA = linesA.iterator();
+        Iterator<Line> itB = linesA.iterator();
+        while (itA.hasNext() && itB.hasNext()) {
+            Line lineA = itA.next();
+            Line lineB = itB.next();
+
+            Assert.assertEquals(lineA.content(), lineB.content(), "Mismatching line contents in a call to `withTimeDependentStateFrom` detected");
+            result.add(new Line(
+                lineA.content(),
+                lineB.lineNumber().withLineNumberAtTime(lineB.lineNumber().atTime(time), time)
+            ));
+        }
+
+        Assert.assertFalse(itA.hasNext() || itB.hasNext(), "Mismatching line counts in a call to `withTimeDependentStateFrom` detected");
+
+        return result;
+    }
+
     @Override
     public String toString() {
         return lines

src/main/java/org/variantsync/diffdetective/variation/Label.java

@@ -2,6 +2,8 @@
 
 import java.util.List;
 
+import org.variantsync.diffdetective.util.Assert;
+import org.variantsync.diffdetective.variation.diff.Time;
 import org.variantsync.diffdetective.variation.diff.VariationDiff; // For Javadoc
 import org.variantsync.diffdetective.variation.tree.VariationTree; // For Javadoc
 
@@ -19,6 +21,29 @@ public interface Label {
      * For example, {@code #endif}s are stored as trailing lines.
      */
     List<String> getTrailingLines();
+
+    /**
+     * Returns a deep copy where the state that is only valid at {@code time} is set to its default
+     * value. Note that not all implementations need to have time dependent state.
+     *
+     * @see withTimeDependentStateFrom
+     */
+    default Label withoutTimeDependentState(Time time) {
+        return this.clone();
+    }
+
+    /**
+     * Returns a deep copy where the state that is only valid at {@code time} is copied from
+     * {@code other}. All time independent state must be equal in {@code this} and {@code other}.
+     * Note that not all implementations need to have time dependent state.
+     *
+     * @see withoutTimeDependentState
+     */
+    default Label withTimeDependentStateFrom(Label other, Time time) {
+        Assert.assertEquals(this, other);
+        return this.clone();
+    }
+
     /**
      * Creates a deep copy of this label.
      */