remove deprecated code

Author: pmbittner

src/main/java/org/variantsync/vevos/simulation/io/TextIO.java

@@ -69,60 +69,6 @@ public static Result<List<String>, IOException> readLines(final Path p) {
         }
     }
 
-    /**
-     * Extract all lines in [lineFrom, lineTo] = i from sourceFile and put them into targetFile for each interval i in linesToTake.
-     *
-     * @param sourceFile  File from which to read lines. Won't be altered.
-     * @param targetFile  File to write the desired lines to.
-     * @param linesToTake Intervals of lines to copy.
-     * @throws IOException May occur upon writing or creating files.
-     */
-    public static void copyTextLines(final Path sourceFile, final Path targetFile, final List<Integer> linesToTake) throws IOException {
-        /// Do not use Files.readAllLines(sourceFile) as it assumes the files to be in UTF-8 and crashes otherwise.
-        //  Do also not use try (final Stream<String> linesStream = new BufferedReader(new FileReader(sourceFile.toFile())).lines()) {
-        // Apparently, Java is stupid and the BufferedReader is not closed by the try-with-resources if it is anonymous.
-        try (final BufferedReader br = new BufferedReader(new FileReader(sourceFile.toFile()));
-             final Stream<String> linesStream = br.lines()) {
-            final List<String> read_lines = linesStream.toList();
-            final StringBuilder linesToWrite = new StringBuilder();
-
-            for (final Integer lineNo : linesToTake) {
-                final int lineIndex = lineNo - 1;
-                // skip lines that exceed the content
-                if (lineIndex >= read_lines.size()) {
-                    final String logMessage = "Skipped copying line "
-                            + lineNo
-                            + " from \""
-                            + sourceFile
-                            + "\" to \""
-                            + targetFile
-                            + "\" as it is out of bounds [1, "
-                            + read_lines.size()
-                            + "]!";
-
-                    if (lineIndex > read_lines.size()) {
-                        // This was logged frequently and is caused by https://bugs.openjdk.java.net/browse/JDK-8199413
-                        // Skipping the line really is the best solution, as the empty line is created by appending a line separator
-                        // to the previous line. I added the additional if-statement, to only catch cases in which more than one line 
-                        // is out of bounds, which indicates a serious problem. 
-                        Logger.error(logMessage);
-                    }
-                } else {
-                    // The list read_lines is 0-based.
-                    // Given lines are 1-based because line numbers are typically given 1-based.
-                    // Thus, we have to -1 here because line numbers are 1-indexed
-                    // but we want to look them up in read_lines, which is 0-based.
-                    linesToWrite.append(read_lines.get(lineIndex)).append(System.lineSeparator());
-                }
-            }
-
-            Files.write(
-                    targetFile,
-                    linesToWrite.toString().getBytes(),
-                    StandardOpenOption.APPEND);
-        }
-    }
-
     /**
      * Writes the given text to the given file.
      * Creates a new file and assumes there exists no file yet at the given path.

src/main/java/org/variantsync/vevos/simulation/variability/pc/LineBasedAnnotation.java

@@ -54,13 +54,7 @@ public LineBasedAnnotation(final LineBasedAnnotation other) {
         this.style = other.style;
     }
 
-    private static void addRange(final List<Integer> list, final int fromInclusive, final int toInclusive) {
-        for (int i = fromInclusive; i <= toInclusive; ++i) {
-            list.add(i);
-        }
-    }
-
-    private static void addRange2(final List<VariantLineChunk> list, final int fromInclusive, final int toInclusive) {
+    private static void addRange(final List<VariantLineChunk> list, final int fromInclusive, final int toInclusive) {
         for (int i = fromInclusive; i <= toInclusive; ++i) {
             list.add(new VariantLine(i));
         }
@@ -154,37 +148,6 @@ private Optional<LineBasedAnnotation> deriveForVariant(final Variant variant, in
         }
     }
 
-    /**
-     * Computes all lines that should be included in the given variant when evaluating the annotations in this artefact.
-     *
-     * @param isIncluded A predicate to select subtrees. A subtree will be considered if isIncluded returns true for it.
-     * @return All line numbers that should be copied from the SPL file to the variant file. 1-based.
-     */
-    public List<Integer> getAllLinesFor(final Predicate<LineBasedAnnotation> isIncluded) {
-        final List<Integer> chunksToWrite = new ArrayList<>();
-        final int firstCodeLine = getLineFrom() + style.offset; // ignore #if
-        final int lastCodeLine = getLineTo() - style.offset; // ignore #endif
-
-        int currentLine = firstCodeLine;
-        for (final LineBasedAnnotation subtree : subtrees) {
-            if (currentLine < subtree.getLineFrom()) {
-                addRange(chunksToWrite, currentLine, subtree.getLineFrom() - 1);
-            }
-
-            if (isIncluded.test(subtree)) {
-                chunksToWrite.addAll(subtree.getAllLinesFor(isIncluded));
-            }
-
-            currentLine = subtree.getLineTo() + 1;
-        }
-
-        if (currentLine <= lastCodeLine) {
-            addRange(chunksToWrite, currentLine, lastCodeLine);
-        }
-
-        return chunksToWrite;
-    }
-
     /**
      * Computes all lines that should be included in the given variant when evaluating the annotations in this artefact.
      *
@@ -200,7 +163,7 @@ public VariantAnnotation getLinesToCopy(final Predicate<LineBasedAnnotation> isI
         int currentLine = firstCodeLine;
         for (final LineBasedAnnotation subtree : subtrees) {
             if (currentLine < subtree.getLineFrom()) {
-                addRange2(chunksToWrite, currentLine, subtree.getLineFrom() - 1);
+                addRange(chunksToWrite, currentLine, subtree.getLineFrom() - 1);
             }
 
             if (isIncluded.test(subtree)) {
@@ -211,7 +174,7 @@ public VariantAnnotation getLinesToCopy(final Predicate<LineBasedAnnotation> isI
         }
 
         if (currentLine <= lastCodeLine) {
-            addRange2(chunksToWrite, currentLine, lastCodeLine);
+            addRange(chunksToWrite, currentLine, lastCodeLine);
         }
 
         return new VariantAnnotation(