Fixed bugs in IdentifyIntervalsFromMemberlist

src/main/java/de/cebitec/common/sequencetools/intervals/IdentifyIntervalsFromMemberlist.java

@@ -155,8 +155,9 @@ public class IdentifyIntervalsFromMemberlist {
      * Calculates all subintervals from the given members that are located in the given global interval coordinates.
      *
      * @param <T>
-     * @param members
-     * @param interval
+     * @param members A list of member. Must not be null.
+     * @param interval An interval in the global coordinate system. If the interval is empty it is not only checked
+     * whether the interval is overlapping with an existing interval, but if it is adjacent.
      * @return
      */
     public static <T> List<MemberResult<T>> identifySubintervals(List<? extends Member<? extends T>> members, Interval<Integer> interval) {
@@ -166,7 +167,7 @@ public class IdentifyIntervalsFromMemberlist {
         for (Member<? extends T> member : members) {
             final Interval<Integer> global = member.getGlobalInterval();
             Interval<Integer> local = null;
-            if (interval.isEmpty() && operations.contains(global, interval)) {
+            if (interval.isEmpty() && (operations.contains(global, interval) || operations.adjacent(global, interval))) {
                 local = operations.shift(interval, -global.getStart());
                 MemberResult<T> result = new MemberResult<>(member.getId(), local);
                 list.add(result);

src/test/java/de/cebitec/common/sequencetools/intervals/IdentifyIntervalsFromMemberlistTest.java

@@ -71,6 +71,20 @@ public class IdentifyIntervalsFromMemberlistTest {
                    hasItems(new MemberResult<>("s3", createInterval(0, 0))));
     }
 
+    @Test
+    public void testIdentifySubintervalsEmtpyIntervalAtEnd() {
+        assertThat(identifySubintervals(list, createInterval(9, 9)),
+                   hasItems(new MemberResult<>("s4", createInterval(3, 3))));
+    }
+
+    @Test
+    public void testIdentifySubintervalsEmtpyIntervalAtBeginning() {
+        List<MemberResult<String>> identifySubintervals = identifySubintervals(list, createInterval(0, 0));
+        MemberResult<String> expected = new MemberResult<>("s1", createInterval(0, 0));
+        assertThat(identifySubintervals,
+                   hasItems(expected));
+    }
+
     @Test
     public void testIdentifySubintervalsMultipleInternalIntervals() {
         assertThat(identifySubintervals(list, createInterval(5, 8)),

src/test/java/de/cebitec/common/sequencetools/intervals/SerializableIntervalTest.java

+/*
+ * Copyright (C) 2014 Lukas Jelonek <ljelonek at cebitec.uni-bielefeld.de>
+ *
+ * This program is free software: you can redistribute it and/or modify
+ * it under the terms of the GNU General Public License as published by
+ * the Free Software Foundation, either version 3 of the License, or
+ * (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package de.cebitec.common.sequencetools.intervals;
+
+import org.junit.Test;
+import static org.junit.Assert.*;
+import static org.hamcrest.Matchers.*;
+import static de.cebitec.common.sequencetools.intervals.Intervals.*;
+
+/**
+ *
+ * @author Lukas Jelonek <ljelonek at cebitec.uni-bielefeld.de>
+ */
+public class SerializableIntervalTest {
+
+    @Test
+    public void testEqualsEmptyIntervals() {
+        assertThat(createInterval(0, 0), equalTo(createInterval(0, 0)));
+    }
+    
+    @Test
+    public void testEqualsEmptyIntervals2() {
+        assertThat(createInterval(1, 1), equalTo(createInterval(1, 1)));
+    }
+
+}