Use a flag to mark the issues that are part of modified code.

doc/dependency-graph.puml

@@ -6,7 +6,7 @@ skinparam rectangle {
   BackgroundColor<<runtime>> lightBlue
   BackgroundColor<<provided>> lightGray
 }
-rectangle "analysis-model\n\n11.16.0" as edu_hm_hafner_analysis_model_jar
+rectangle "analysis-model\n\n11.18.0-SNAPSHOT" as edu_hm_hafner_analysis_model_jar
 rectangle "jsoup\n\n1.17.2" as org_jsoup_jsoup_jar
 rectangle "commons-io\n\n2.15.1" as commons_io_commons_io_jar
 rectangle "commons-digester3\n\n3.2" as org_apache_commons_commons_digester3_jar

src/main/java/edu/hm/hafner/analysis/Issue.java

@@ -187,6 +187,7 @@ public static Predicate<Issue> byType(final String type) {
     private String description;   // fixed
 
     private String fingerprint;     // mutable, not part of equals
+    private boolean partOfModifiedCode;     // mutable
 
     /**
      * Creates a new instance of {@link Issue} using the properties of the other issue instance. The new issue has the
@@ -734,7 +735,7 @@ public String getModuleName() {
     }
 
     /**
-     * Sets the the name of the module or project (or similar concept) that contains this issue.
+     * Sets the name of the module or project (or similar concept) that contains this issue.
      *
      * @param moduleName
      *         the module name to set
@@ -781,7 +782,7 @@ public String getOriginName() {
      * @param origin
      *         the origin
      */
-    public void setOrigin(final String origin) {
+    void setOrigin(final String origin) {
         Ensure.that(origin).isNotBlank("Issue origin ID '%s' must be not blank (%s)", id, toString());
 
         this.origin = origin.intern();
@@ -795,7 +796,7 @@ public void setOrigin(final String origin) {
      * @param name
      *         the name of the origin
      */
-    public void setOrigin(final String originId, final String name) {
+    void setOrigin(final String originId, final String name) {
         setOrigin(originId);
 
         Ensure.that(name).isNotBlank("Issue origin name '%s' must be not blank (%s)", name, toString());
@@ -820,13 +821,13 @@ public String getReference() {
      * @param reference
      *         the reference
      */
-    public void setReference(@CheckForNull final String reference) {
+    void setReference(@CheckForNull final String reference) {
         this.reference = stripToEmpty(reference);
     }
 
     /**
      * Returns the fingerprint for this issue. Used to decide if two issues are equal even if the equals method returns
-     * {@code false} since some of the properties differ due to code refactorings. The fingerprint is created by
+     * {@code false} since some properties differ due to code refactorings. The fingerprint is created by
      * analyzing the content of the affected file.
      * <p>
      * Note: the fingerprint is not part of the equals method since the fingerprint might change due to an unrelated
@@ -860,6 +861,23 @@ public boolean hasFingerprint() {
         return !UNDEFINED.equals(fingerprint);
     }
 
+    /**
+     * Returns whether this issue affects a code line that has been modified recently.
+     *
+     * @return {@code true} if this issue affects a code line that has been modified recently.
+     * @see IssuesInModifiedCodeMarker
+     */
+    public boolean isPartOfModifiedCode() {
+        return partOfModifiedCode;
+    }
+
+    /**
+     * Marks the issue as part of a source control diff.
+     */
+    void markAsPartOfModifiedCode() {
+        partOfModifiedCode = true;
+    }
+
     /**
      * Returns additional properties for this issue. A static analysis tool may store additional properties in this
      * untyped object. This object will be serialized and is used in {@code equals} and {@code hashCode}.
@@ -883,6 +901,9 @@ public boolean equals(@CheckForNull final Object o) {
 
         Issue issue = (Issue) o;
 
+        if (partOfModifiedCode != issue.partOfModifiedCode) {
+            return false;
+        }
         if (lineStart != issue.lineStart) {
             return false;
         }
@@ -950,11 +971,12 @@ public int hashCode() {
         result = 31 * result + moduleName.hashCode();
         result = 31 * result + packageName.hashCode();
         result = 31 * result + fileName.hashCode();
+        result = 31 * result + (partOfModifiedCode ? 1 : 0);
         return result;
     }
 
     @Override
     public String toString() {
-        return String.format("%s(%d,%d): %s: %s: %s", getBaseName(), lineStart, columnStart, type, category, message);
+        return String.format("%s%s(%d,%d): %s: %s: %s", isPartOfModifiedCode() ? "*" : StringUtils.EMPTY, getBaseName(), lineStart, columnStart, type, category, message);
     }
 }

src/main/java/edu/hm/hafner/analysis/IssueDifference.java

@@ -187,20 +187,6 @@ public Report getNewIssues() {
         return newIssues;
     }
 
-    /**
-     * Returns the new issues that are part of the changed code lines. I.e., all issues that are part of the current
-     * report but that have not been shown up in the previous report. If the difference is computed for a specific
-     * set of changed files, then this set contains only the new issues that are part of the changes. Otherwise, this
-     * set will be empty.
-     *
-     * @return the new issues
-     * @see IssueDifference#getNewIssues()
-     */
-    @SuppressFBWarnings("EI")
-    public Report getNewIssuesInChangedCode() {
-        return newIssuesInChangedCode;
-    }
-
     /**
      * Returns the fixed issues. I.e., all issues that are part of the previous report but that are not present in the
      * current report anymore.

src/main/java/edu/hm/hafner/analysis/IssuesInModifiedCodeMarker.java

@@ -0,0 +1,43 @@
+package edu.hm.hafner.analysis;
+
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+
+import edu.hm.hafner.util.PathUtil;
+
+/**
+ * Computes old, new, and fixed issues based on the reports of two consecutive static analysis runs for the same
+ * software artifact.
+ *
+ * @author Ullrich Hafner
+ */
+@SuppressWarnings("PMD.DataClass")
+public class IssuesInModifiedCodeMarker {
+    private static final PathUtil PATH_UTIL = new PathUtil();
+
+    /**
+     * Finds and marks all issues that are part the changes in a source control diff.
+     *
+     * @param report
+     *         the report with the issues to scan
+     * @param modifiedLinesInFilesMapping
+     *         a mapping modified lines within files
+     */
+    public void markIssuesInModifiedCode(final Report report, final Map<String, Set<Integer>> modifiedLinesInFilesMapping) {
+        for (Entry<String, Set<Integer>> include : modifiedLinesInFilesMapping.entrySet()) {
+            report.filter(issue -> affectsChangedLineInFile(issue, include.getKey(), include.getValue()))
+                    .stream()
+                    .forEach(Issue::markAsPartOfModifiedCode);
+        }
+    }
+
+    private boolean affectsChangedLineInFile(final Issue issue, final String fileName, final Set<Integer> lines) {
+        var normalizedPath = PATH_UTIL.getRelativePath(fileName);
+
+        if (!issue.getFileName().endsWith(normalizedPath)) { // check only the suffix
+            return false;
+        }
+        return lines.stream().anyMatch(issue::affectsLine);
+    }
+}

src/main/java/edu/hm/hafner/analysis/LineRange.java

@@ -1,6 +1,8 @@
 package edu.hm.hafner.analysis;
 
 import java.io.Serializable;
+import java.util.NavigableSet;
+import java.util.TreeSet;
 
 import edu.umd.cs.findbugs.annotations.CheckForNull;
 
@@ -66,6 +68,19 @@ public int getEnd() {
         return end;
     }
 
+    /**
+     * Returns the lines of this line lange in a sorted set.
+     *
+     * @return the containing lines, one by one
+     */
+    public NavigableSet<Integer> getLines() {
+        var lines = new TreeSet<Integer>();
+        for (int line = getStart(); line <= getEnd(); line++) {
+            lines.add(line);
+        }
+        return lines;
+    }
+
     /**
      * Returns whether the specified line is contained in this range.
      *
@@ -76,6 +91,15 @@ public boolean contains(final int line) {
         return line >= start && line <= end;
     }
 
+    /**
+     * Returns whether this range is just a single line.
+     *
+     * @return {@code true} if this range is just a single line, {@code false} otherwise
+     */
+    public boolean isSingleLine() {
+        return start == end;
+    }
+
     @Override
     public boolean equals(@CheckForNull final Object obj) {
         if (this == obj) {

src/test/java/edu/hm/hafner/analysis/IssueDifferenceTest.java

@@ -1,7 +1,6 @@
 package edu.hm.hafner.analysis;
 
 import java.nio.charset.StandardCharsets;
-import java.util.Map;
 
 import org.junit.jupiter.api.Test;
 
@@ -20,97 +19,6 @@ class IssueDifferenceTest extends ResourceTest {
     private static final String REFERENCE_BUILD = "100";
     private static final String CURRENT_BUILD = "2";
 
-    @Test
-    void shouldFilterByPath() {
-        Report referenceIssues = new Report().addAll(
-                createIssue("OUTSTANDING 1", "OUT 1"),
-                createIssue("OUTSTANDING 2", "OUT 2"),
-                createIssue("OUTSTANDING 3", "OUT 3"),
-                createIssue("TO FIX 1", "FIX 1"),
-                createIssue("TO FIX 2", "FIX 2"));
-
-        Report currentIssues = new Report().addAll(
-                createIssue("UPD OUTSTANDING 1", "OUT 1"),
-                createIssue("OUTSTANDING 2", "UPD OUT 2"),
-                createIssue("OUTSTANDING 3", "OUT 3"),
-                createIssue("NEW 1", "NEW 1", "/include/me"),
-                createIssue("NEW 2", "NEW 2", "/remove/me"),
-                createIssue("NEW 3", "NEW 3", "/include/me"));
-
-        IssueDifference everything = new IssueDifference(currentIssues, CURRENT_BUILD, referenceIssues);
-        assertThatReportContainsExactly(everything.getFixedIssues(), "TO FIX 1", "TO FIX 2");
-        assertThatReferenceIsSet(everything.getFixedIssues(), REFERENCE_BUILD);
-        assertThatReportContainsExactly(everything.getNewIssues(), "NEW 1", "NEW 2", "NEW 3");
-        assertThatReferenceIsSet(everything.getNewIssues(), CURRENT_BUILD);
-        assertThatReportContainsExactly(everything.getNewIssuesInChangedCode());
-        assertThatReportContainsExactly(everything.getOutstandingIssues(),
-                "OUTSTANDING 2", "OUTSTANDING 3", "UPD OUTSTANDING 1");
-        assertThatReferenceIsSet(everything.getOutstandingIssues(), REFERENCE_BUILD);
-
-        IssueDifference included = new IssueDifference(currentIssues, CURRENT_BUILD, referenceIssues,
-                Map.of("/include/me", 0));
-        assertThatReportContainsExactly(included.getFixedIssues(), "TO FIX 1", "TO FIX 2");
-        assertThatReferenceIsSet(included.getFixedIssues(), REFERENCE_BUILD);
-        assertThatReportContainsExactly(included.getNewIssuesInChangedCode(), "NEW 1", "NEW 3");
-        assertThatReferenceIsSet(included.getNewIssuesInChangedCode(), CURRENT_BUILD);
-        assertThatReportContainsExactly(included.getNewIssues(), "NEW 2");
-        assertThatReferenceIsSet(included.getNewIssues(), CURRENT_BUILD);
-        assertThatReportContainsExactly(included.getOutstandingIssues(),
-                "OUTSTANDING 2", "OUTSTANDING 3", "UPD OUTSTANDING 1");
-        assertThatReferenceIsSet(included.getOutstandingIssues(), REFERENCE_BUILD);
-
-        IssueDifference sameSuffixForAll = new IssueDifference(currentIssues, CURRENT_BUILD, referenceIssues,
-                Map.of("me", 0));
-        assertThatReportContainsExactly(sameSuffixForAll.getFixedIssues(), "TO FIX 1", "TO FIX 2");
-        assertThatReferenceIsSet(sameSuffixForAll.getFixedIssues(), REFERENCE_BUILD);
-        assertThatReportContainsExactly(sameSuffixForAll.getNewIssuesInChangedCode(),
-                "NEW 1", "NEW 2", "NEW 3");
-        assertThatReferenceIsSet(sameSuffixForAll.getNewIssuesInChangedCode(), CURRENT_BUILD);
-        assertThatReportContainsExactly(sameSuffixForAll.getNewIssues());
-        assertThatReportContainsExactly(sameSuffixForAll.getOutstandingIssues(),
-                "OUTSTANDING 2", "OUTSTANDING 3", "UPD OUTSTANDING 1");
-        assertThatReferenceIsSet(sameSuffixForAll.getOutstandingIssues(), REFERENCE_BUILD);
-
-        IssueDifference allFiles = new IssueDifference(currentIssues, CURRENT_BUILD, referenceIssues,
-                Map.of("/include/me", 0, "/remove/me", 0));
-        assertThatReportContainsExactly(allFiles.getFixedIssues(), "TO FIX 1", "TO FIX 2");
-        assertThatReferenceIsSet(allFiles.getFixedIssues(), REFERENCE_BUILD);
-        assertThatReportContainsExactly(allFiles.getNewIssuesInChangedCode(),
-                "NEW 1", "NEW 2", "NEW 3");
-        assertThatReferenceIsSet(allFiles.getNewIssuesInChangedCode(), CURRENT_BUILD);
-        assertThatReportContainsExactly(allFiles.getNewIssues());
-        assertThatReportContainsExactly(allFiles.getOutstandingIssues(),
-                "OUTSTANDING 2", "OUTSTANDING 3", "UPD OUTSTANDING 1");
-        assertThatReferenceIsSet(allFiles.getOutstandingIssues(), REFERENCE_BUILD);
-
-        IssueDifference nothingNew = new IssueDifference(currentIssues, CURRENT_BUILD, referenceIssues,
-                Map.of("other", 0));
-        assertThatReportContainsExactly(nothingNew.getFixedIssues(),
-                "TO FIX 1", "TO FIX 2");
-        assertThatReferenceIsSet(nothingNew.getFixedIssues(), REFERENCE_BUILD);
-        assertThatReportContainsExactly(nothingNew.getNewIssuesInChangedCode());
-        assertThatReportContainsExactly(nothingNew.getNewIssues(), "NEW 1", "NEW 2", "NEW 3");
-        assertThatReferenceIsSet(nothingNew.getNewIssues(), CURRENT_BUILD);
-        assertThatReportContainsExactly(nothingNew.getOutstandingIssues(),
-                "OUTSTANDING 2", "OUTSTANDING 3", "UPD OUTSTANDING 1");
-        assertThatReferenceIsSet(nothingNew.getOutstandingIssues(), REFERENCE_BUILD);
-    }
-
-    private void assertThatReferenceIsSet(final Report report, final String referenceBuild) {
-        assertThat(report.get()).extracting(Issue::getReference).containsOnly(referenceBuild);
-    }
-
-    private void assertThatReportContainsExactly(final Report report, final String... messages) {
-        if (messages.length == 0) {
-            assertThat(report).isEmpty();
-        }
-        else {
-            assertThat(report.get())
-                    .extracting(Issue::getMessage)
-                    .containsExactlyInAnyOrder(messages);
-        }
-    }
-
     @Test
     void shouldCreateIssueDifferenceBasedOnPropertiesAndThenOnFingerprint() {
         Report referenceIssues = new Report().addAll(