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<h3>
Andreas Tille pushed to branch master
at <a href="https://salsa.debian.org/med-team/hyphy">Debian Med / hyphy</a>
</h3>
<h4>
Commits:
</h4>
<ul>
<li>
<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/3554ad3ecf5d935d3fd64a81dd9fbb60d29f3d09">3554ad3e</a></strong>
<div>
<span>by Andreas Tille</span>
<i>at 2019-12-06T12:42:44Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Refresh patches
</pre>
</li>
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<strong><a href="https://salsa.debian.org/med-team/hyphy/commit/6176567316bb409c1d39967a98343e6d9b7c611d">61765673</a></strong>
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<span>by Andreas Tille</span>
<i>at 2019-12-06T13:49:53Z</i>
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<pre class="commit-message" style="white-space: pre-wrap; margin: 0;">Some patches for gcc9 - not finished yet
</pre>
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<h4>4 changed files:</h4>
<ul>
<li class="file-stats">
<a href="#aa75673e5b6a9322e7a7fece23b2386c1bd7c1c9">
debian/patches/drop_profiling_option.patch
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<li class="file-stats">
<a href="#20775640da663809ffd0da43d13b36cabd23eb7a">
<span class="new-file">
+
debian/patches/gcc9.patch
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<li class="file-stats">
<a href="#bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
debian/patches/series
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<li class="file-stats">
<a href="#d185b62d54557160e7ddc743405a9cec66dcaa96">
debian/patches/use_debian_sqlite.patch
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<h4>Changes:</h4>
<li id="aa75673e5b6a9322e7a7fece23b2386c1bd7c1c9">
<a href="https://salsa.debian.org/med-team/hyphy/compare/df335440535562f7c62290cfdf726ced74abcdd8...6176567316bb409c1d39967a98343e6d9b7c611d#aa75673e5b6a9322e7a7fece23b2386c1bd7c1c9"><strong>debian/patches/drop_profiling_option.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -5,7 +5,7 @@ Bug-Debian: http://bugs.debian.org/793345</td>
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<pre style="margin: 0;"> <span id="LC5" class="line" lang="diff"></span>
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<td class="diff-line-num new_line" data-linenumber="6" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC6" class="line" lang="diff">--- a/CMakeLists.txt</span>
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<td class="diff-line-num new_line" data-linenumber="7" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC7" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/CMakeLists.txt</span></span>
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<pre style="margin: 0;">-<span id="LC8" class="line" lang="diff"><span class="p">@@ -54<span class="idiff left right">3,11 +543</span>,11 @@</span> set_target_properties(</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"><span class="p">@@ -54<span class="idiff left right">4,11 +544</span>,11 @@</span> set_target_properties(</span>
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<td class="diff-line-num new_line" data-linenumber="9" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC9" class="line" lang="diff"> HYPHYGTEST</span>
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<pre style="margin: 0;"> <span id="LC10" class="line" lang="diff"> PROPERTIES</span>
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<td class="diff-line-num old_line" data-linenumber="11" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #f0f0f0; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#fafafa">
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<pre style="margin: 0;"> <span id="LC11" class="line" lang="diff"> if(${OPENMP_FOUND})</span>
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<li id="20775640da663809ffd0da43d13b36cabd23eb7a">
<a href="https://salsa.debian.org/med-team/hyphy/compare/df335440535562f7c62290cfdf726ced74abcdd8...6176567316bb409c1d39967a98343e6d9b7c611d#20775640da663809ffd0da43d13b36cabd23eb7a"><strong>debian/patches/gcc9.patch</strong></a>
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<pre style="margin: 0;">+<span id="LC1" class="line" lang="diff"><span class="p">Author: Andreas Tille <tille@debian.org></span></span>
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<pre style="margin: 0;">+<span id="LC2" class="line" lang="diff"><span class="p">Last-Update: Fri, 06 Dec 2019 13:30:30 +0100</span></span>
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<pre style="margin: 0;">+<span id="LC3" class="line" lang="diff"><span class="p">Description: Fix Build issue with gcc9</span></span>
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<pre style="margin: 0;">+<span id="LC4" class="line" lang="diff"></span>
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="diff">--- a/tests/gtests/ut_avllists.cpp</span>
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<pre style="margin: 0;">+<span id="LC6" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/gtests/ut_avllists.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC7" class="line" lang="diff"><span class="p">@@ -367,7 +367,7 @@</span> TEST_F(AVLListTest,toStrTest){</span>
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<pre style="margin: 0;">+<span id="LC8" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC9" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC10" class="line" lang="diff"> _String* return_str = (_String*)al.toStr();</span>
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<pre style="margin: 0;">+<span id="LC11" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10)", return_str->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC12" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("(0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10)", return_str->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC13" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC14" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC15" class="line" lang="diff"> TEST_F(AVLListTest,RetrieveTest) {</span>
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<pre style="margin: 0;">+<span id="LC16" class="line" lang="diff"><span class="p">@@ -562,7 +562,7 @@</span> TEST_F(AVLListXTest,PopulateFromListTest</span>
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17
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<pre style="margin: 0;">+<span id="LC17" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC18" class="line" lang="diff"> alx.PopulateFromList(result_list);</span>
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19
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<pre style="margin: 0;">+<span id="LC19" class="line" lang="diff"> _String* return_str = (_String*)alx.dataList->list_data[2];</span>
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<pre style="margin: 0;">+<span id="LC20" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("hyphy", return_str->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC21" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("hyphy", return_str->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC22" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC24" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC25" class="line" lang="diff"><span class="p">@@ -602,7 +602,7 @@</span> TEST_F(AVLListXLTest,SetAndGetXtraTest){</span>
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<pre style="margin: 0;">+<span id="LC26" class="line" lang="diff"> alxl.SetXtra(0,(BaseRef)xtra_str, false);</span>
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<pre style="margin: 0;">+<span id="LC27" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC28" class="line" lang="diff"> _String* x = (_String*)alxl.GetXtra((long)0);</span>
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<pre style="margin: 0;">+<span id="LC29" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("xtra",x->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC30" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("xtra",x->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC31" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC32" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC33" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC34" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">--- a/tests/gtests/ut_list.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC35" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+++ b/tests/gtests/ut_list.cpp</span></span>
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<pre style="margin: 0;">+<span id="LC36" class="line" lang="diff"><span class="p">@@ -134,7 +134,7 @@</span> TEST_F(ListTest,_StackCopyConstructorLis</span>
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<pre style="margin: 0;">+<span id="LC37" class="line" lang="diff"> _List list = _List(str_list, 0, 4); </span>
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<pre style="margin: 0;">+<span id="LC38" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC39" class="line" lang="diff"> _String* return_str = (_String*)list[4];</span>
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<pre style="margin: 0;">+<span id="LC40" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("four", return_str->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC41" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("four", return_str->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC42" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC43" class="line" lang="diff"> }</span>
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44
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<pre style="margin: 0;">+<span id="LC44" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC45" class="line" lang="diff"><span class="p">@@ -143,7 +143,7 @@</span> TEST_F(ListTest,_SubStrConstructorListTe</span>
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46
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<pre style="margin: 0;">+<span id="LC46" class="line" lang="diff"> _String* str = new _String(",one,two,three");</span>
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47
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<pre style="margin: 0;">+<span id="LC47" class="line" lang="diff"> _List list = _List((BaseRef)str, ','); </span>
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48
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<pre style="margin: 0;">+<span id="LC48" class="line" lang="diff"> _String* return_string = (_String*)list[1];</span>
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49
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<pre style="margin: 0;">+<span id="LC49" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", return_string->getStr());</span></span>
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50
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<pre style="margin: 0;">+<span id="LC50" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", return_string->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC51" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC52" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC53" class="line" lang="diff"> TEST_F(ListTest,_DataConstructorListTest){</span>
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<pre style="margin: 0;">+<span id="LC54" class="line" lang="diff"><span class="p">@@ -152,7 +152,7 @@</span> TEST_F(ListTest,_DataConstructorListTest</span>
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<pre style="margin: 0;">+<span id="LC55" class="line" lang="diff"> _List list = _List((BaseRef)string);</span>
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<pre style="margin: 0;">+<span id="LC56" class="line" lang="diff"> _String* return_string = (_String*)list[0];</span>
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<pre style="margin: 0;">+<span id="LC57" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC58" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", return_string->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC59" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", return_string->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC61" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC63" class="line" lang="diff"><span class="p">@@ -161,7 +161,7 @@</span> TEST_F(ListTest,paranthesisTest){</span>
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64
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<pre style="margin: 0;">+<span id="LC64" class="line" lang="diff"> _List str_list = createStrList();</span>
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65
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<pre style="margin: 0;">+<span id="LC65" class="line" lang="diff"> _String* return_string = (_String*)str_list(4);</span>
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66
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<pre style="margin: 0;">+<span id="LC66" class="line" lang="diff"> </span>
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67
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<pre style="margin: 0;">+<span id="LC67" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("four", return_string->getStr());</span></span>
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68
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<pre style="margin: 0;">+<span id="LC68" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("four", return_string->get_str());</span></span>
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69
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<pre style="margin: 0;">+<span id="LC69" class="line" lang="diff"> }</span>
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70
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<pre style="margin: 0;">+<span id="LC70" class="line" lang="diff"> </span>
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71
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<pre style="margin: 0;">+<span id="LC71" class="line" lang="diff"> TEST_F(ListTest,EqualOpTest){</span>
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72
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -169,7 +169,7 @@</span> TEST_F(ListTest,EqualOpTest){</span>
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73
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<pre style="margin: 0;">+<span id="LC73" class="line" lang="diff"> _List str_list = createStrList();</span>
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74
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<pre style="margin: 0;">+<span id="LC74" class="line" lang="diff"> _List list = str_list;</span>
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75
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<pre style="margin: 0;">+<span id="LC75" class="line" lang="diff"> _String* return_string = (_String*)list[4];</span>
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76
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<pre style="margin: 0;">+<span id="LC76" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("four", return_string->getStr());</span></span>
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77
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<pre style="margin: 0;">+<span id="LC77" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("four", return_string->get_str());</span></span>
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78
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<pre style="margin: 0;">+<span id="LC78" class="line" lang="diff"> </span>
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79
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<pre style="margin: 0;">+<span id="LC79" class="line" lang="diff"> }</span>
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80
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<pre style="margin: 0;">+<span id="LC80" class="line" lang="diff"> </span>
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81
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<pre style="margin: 0;">+<span id="LC81" class="line" lang="diff"><span class="p">@@ -202,7 +202,7 @@</span> TEST_F(ListTest,AmpersandOpTest){</span>
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82
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<pre style="margin: 0;">+<span id="LC82" class="line" lang="diff"> _List result_list = list & append_list;</span>
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83
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<pre style="margin: 0;">+<span id="LC83" class="line" lang="diff"> </span>
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84
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<pre style="margin: 0;">+<span id="LC84" class="line" lang="diff"> _String* result_string = (_String*)result_list[0];</span>
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85
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<pre style="margin: 0;">+<span id="LC85" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", result_string->getStr());</span></span>
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86
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<pre style="margin: 0;">+<span id="LC86" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", result_string->get_str());</span></span>
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87
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<pre style="margin: 0;">+<span id="LC87" class="line" lang="diff"> </span>
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88
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<pre style="margin: 0;">+<span id="LC88" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC89" class="line" lang="diff"> _List* l2 = new _List(); </span>
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90
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<pre style="margin: 0;">+<span id="LC90" class="line" lang="diff"><span class="p">@@ -220,7 +220,7 @@</span> TEST_F(ListTest,Ampersand2OpTest){</span>
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91
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<pre style="margin: 0;">+<span id="LC91" class="line" lang="diff"> </span>
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92
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<pre style="margin: 0;">+<span id="LC92" class="line" lang="diff"> _String* result_string = (_String*)result_list[result_list.lLength-1];</span>
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93
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<pre style="margin: 0;">+<span id="LC93" class="line" lang="diff"> </span>
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94
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<pre style="margin: 0;">+<span id="LC94" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one",result_string->getStr());</span></span>
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95
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<pre style="margin: 0;">+<span id="LC95" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one",result_string->get_str());</span></span>
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96
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<pre style="margin: 0;">+<span id="LC96" class="line" lang="diff"> }</span>
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97
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<pre style="margin: 0;">+<span id="LC97" class="line" lang="diff"> </span>
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98
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<pre style="margin: 0;">+<span id="LC98" class="line" lang="diff"> TEST_F(ListTest,DoubleAmpersandOpTest){</span>
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99
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<pre style="margin: 0;">+<span id="LC99" class="line" lang="diff"><span class="p">@@ -232,7 +232,7 @@</span> TEST_F(ListTest,DoubleAmpersandOpTest){</span>
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100
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<pre style="margin: 0;">+<span id="LC100" class="line" lang="diff"> </span>
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101
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<pre style="margin: 0;">+<span id="LC101" class="line" lang="diff"> _String* result_string = (_String*)str_list[str_list.lLength-1];</span>
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102
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<pre style="margin: 0;">+<span id="LC102" class="line" lang="diff"> </span>
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103
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<pre style="margin: 0;">+<span id="LC103" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one",result_string->getStr());</span></span>
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104
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<pre style="margin: 0;">+<span id="LC104" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one",result_string->get_str());</span></span>
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105
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<pre style="margin: 0;">+<span id="LC105" class="line" lang="diff"> </span>
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106
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<pre style="margin: 0;">+<span id="LC106" class="line" lang="diff"> }</span>
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107
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<pre style="margin: 0;">+<span id="LC107" class="line" lang="diff"> </span>
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108
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<pre style="margin: 0;">+<span id="LC108" class="line" lang="diff"><span class="p">@@ -240,7 +240,7 @@</span> TEST_F(ListTest,DoubleAmpersand2OpTest){</span>
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109
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<pre style="margin: 0;">+<span id="LC109" class="line" lang="diff"> _List str_list = createStrList();</span>
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110
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<pre style="margin: 0;">+<span id="LC110" class="line" lang="diff"> str_list && "one"; </span>
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111
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<pre style="margin: 0;">+<span id="LC111" class="line" lang="diff"> _String* result_string = (_String*)str_list[str_list.lLength-1];</span>
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112
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<pre style="margin: 0;">+<span id="LC112" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one",result_string->getStr());</span></span>
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113
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<pre style="margin: 0;">+<span id="LC113" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one",result_string->get_str());</span></span>
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114
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<pre style="margin: 0;">+<span id="LC114" class="line" lang="diff"> }</span>
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115
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<pre style="margin: 0;">+<span id="LC115" class="line" lang="diff"> </span>
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116
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<pre style="margin: 0;">+<span id="LC116" class="line" lang="diff"> TEST_F(ListTest,DoubleLessOpTest){</span>
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117
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<pre style="margin: 0;">+<span id="LC117" class="line" lang="diff"><span class="p">@@ -251,7 +251,7 @@</span> TEST_F(ListTest,DoubleLessOpTest){</span>
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118
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<pre style="margin: 0;">+<span id="LC118" class="line" lang="diff"> str_list << str;</span>
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119
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<pre style="margin: 0;">+<span id="LC119" class="line" lang="diff"> </span>
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120
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<pre style="margin: 0;">+<span id="LC120" class="line" lang="diff"> _String* result_string = (_String*)str_list[str_list.lLength-1];</span>
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121
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<pre style="margin: 0;">+<span id="LC121" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", result_string->getStr());</span></span>
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122
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<pre style="margin: 0;">+<span id="LC122" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", result_string->get_str());</span></span>
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123
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<pre style="margin: 0;">+<span id="LC123" class="line" lang="diff"> }</span>
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124
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<pre style="margin: 0;">+<span id="LC124" class="line" lang="diff"> </span>
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125
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<pre style="margin: 0;">+<span id="LC125" class="line" lang="diff"> TEST_F(ListTest,DoubleLess2OpTest){</span>
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126
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<pre style="margin: 0;">+<span id="LC126" class="line" lang="diff"><span class="p">@@ -272,7 +272,7 @@</span> TEST_F(ListTest,DoubleLess2OpTest){</span>
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127
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<pre style="margin: 0;">+<span id="LC127" class="line" lang="diff"> _List result_list = list;</span>
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128
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<pre style="margin: 0;">+<span id="LC128" class="line" lang="diff"> </span>
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129
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<pre style="margin: 0;">+<span id="LC129" class="line" lang="diff"> _String* result_string = (_String*)result_list[5];</span>
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130
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<pre style="margin: 0;">+<span id="LC130" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ(expected_string->getStr(), result_string->getStr());</span></span>
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131
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<pre style="margin: 0;">+<span id="LC131" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ(expected_string->get_str(), result_string->get_str());</span></span>
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132
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<pre style="margin: 0;">+<span id="LC132" class="line" lang="diff"> </span>
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133
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<pre style="margin: 0;">+<span id="LC133" class="line" lang="diff"> }</span>
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134
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<pre style="margin: 0;">+<span id="LC134" class="line" lang="diff"> </span>
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135
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<pre style="margin: 0;">+<span id="LC135" class="line" lang="diff"><span class="p">@@ -283,7 +283,7 @@</span> TEST_F(ListTest,AppendNewInstanceTest){</span>
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136
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<pre style="margin: 0;">+<span id="LC136" class="line" lang="diff"> str_list.AppendNewInstance(new _String("one"));</span>
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137
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<pre style="margin: 0;">+<span id="LC137" class="line" lang="diff"> _String* result_string = (_String*)str_list[7];</span>
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138
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<pre style="margin: 0;">+<span id="LC138" class="line" lang="diff"> </span>
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139
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<pre style="margin: 0;">+<span id="LC139" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", result_string->getStr());</span></span>
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140
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<pre style="margin: 0;">+<span id="LC140" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", result_string->get_str());</span></span>
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141
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<pre style="margin: 0;">+<span id="LC141" class="line" lang="diff"> }</span>
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142
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<pre style="margin: 0;">+<span id="LC142" class="line" lang="diff"> </span>
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143
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<pre style="margin: 0;">+<span id="LC143" class="line" lang="diff"> TEST_F(ListTest,PlaceTest){</span>
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144
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<pre style="margin: 0;">+<span id="LC144" class="line" lang="diff"><span class="p">@@ -294,7 +294,7 @@</span> TEST_F(ListTest,PlaceTest){</span>
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145
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<pre style="margin: 0;">+<span id="LC145" class="line" lang="diff"> str_list.Place(new _String("one"));</span>
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146
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<pre style="margin: 0;">+<span id="LC146" class="line" lang="diff"> </span>
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147
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<pre style="margin: 0;">+<span id="LC147" class="line" lang="diff"> _String* result_string = (_String*)str_list[7];</span>
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148
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<pre style="margin: 0;">+<span id="LC148" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", result_string->getStr());</span></span>
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149
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<pre style="margin: 0;">+<span id="LC149" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", result_string->get_str());</span></span>
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150
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<pre style="margin: 0;">+<span id="LC150" class="line" lang="diff"> }</span>
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151
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<pre style="margin: 0;">+<span id="LC151" class="line" lang="diff"> </span>
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152
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<pre style="margin: 0;">+<span id="LC152" class="line" lang="diff"> TEST_F(ListTest,InsertElementTest){</span>
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153
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<pre style="margin: 0;">+<span id="LC153" class="line" lang="diff"><span class="p">@@ -302,7 +302,7 @@</span> TEST_F(ListTest,InsertElementTest){</span>
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154
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<pre style="margin: 0;">+<span id="LC154" class="line" lang="diff"> _List str_list = createStrList();</span>
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155
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<pre style="margin: 0;">+<span id="LC155" class="line" lang="diff"> str_list.InsertElement(new _String("one"),3,true);</span>
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156
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<pre style="margin: 0;">+<span id="LC156" class="line" lang="diff"> _String* result_string = (_String*)str_list[3];</span>
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157
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<pre style="margin: 0;">+<span id="LC157" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one", result_string->getStr());</span></span>
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158
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<pre style="margin: 0;">+<span id="LC158" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one", result_string->get_str());</span></span>
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159
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<pre style="margin: 0;">+<span id="LC159" class="line" lang="diff"> }</span>
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160
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<pre style="margin: 0;">+<span id="LC160" class="line" lang="diff"> </span>
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161
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<pre style="margin: 0;">+<span id="LC161" class="line" lang="diff"> TEST_F(ListTest,getStrTest){</span>
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162
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<pre style="margin: 0;">+<span id="LC162" class="line" lang="diff"><span class="p">@@ -312,7 +312,7 @@</span> TEST_F(ListTest,getStrTest){</span>
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163
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<pre style="margin: 0;">+<span id="LC163" class="line" lang="diff"> _String* str = new _String("{zero, one, two, three, four, five, six}");</span>
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164
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<pre style="margin: 0;">+<span id="LC164" class="line" lang="diff"> _String* result_string = (_String*)str_list.toStr();</span>
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165
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<pre style="margin: 0;">+<span id="LC165" class="line" lang="diff"> </span>
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166
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<pre style="margin: 0;">+<span id="LC166" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ(str->getStr(), result_string->getStr());</span></span>
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167
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<pre style="margin: 0;">+<span id="LC167" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ(str->get_str(), result_string->get_str());</span></span>
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168
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<pre style="margin: 0;">+<span id="LC168" class="line" lang="diff"> </span>
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169
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<pre style="margin: 0;">+<span id="LC169" class="line" lang="diff"> }</span>
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170
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<pre style="margin: 0;">+<span id="LC170" class="line" lang="diff"> </span>
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171
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<pre style="margin: 0;">+<span id="LC171" class="line" lang="diff"><span class="p">@@ -333,7 +333,7 @@</span> TEST_F(ListTest,bumpNInstTest){</span>
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172
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<pre style="margin: 0;">+<span id="LC172" class="line" lang="diff"> str_list.bumpNInst();</span>
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173
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<pre style="margin: 0;">+<span id="LC173" class="line" lang="diff"> </span>
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174
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<pre style="margin: 0;">+<span id="LC174" class="line" lang="diff"> _String* result_string = (_String*)str_list[3];</span>
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175
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<pre style="margin: 0;">+<span id="LC175" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("three", result_string->getStr());</span></span>
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176
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<pre style="margin: 0;">+<span id="LC176" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("three", result_string->get_str());</span></span>
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177
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<pre style="margin: 0;">+<span id="LC177" class="line" lang="diff"> }</span>
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178
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<pre style="margin: 0;">+<span id="LC178" class="line" lang="diff"> </span>
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179
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<pre style="margin: 0;">+<span id="LC179" class="line" lang="diff"> TEST_F(ListTest,FindStringTest){</span>
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180
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<pre style="margin: 0;">+<span id="LC180" class="line" lang="diff"><span class="p">@@ -362,7 +362,7 @@</span> TEST_F(ListTest,JoinTest){</span>
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181
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<pre style="margin: 0;">+<span id="LC181" class="line" lang="diff"> _String* spacer = new _String(";");</span>
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182
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<pre style="margin: 0;">+<span id="LC182" class="line" lang="diff"> _List* list = new _List((BaseRef)str, ','); </span>
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183
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<pre style="margin: 0;">+<span id="LC183" class="line" lang="diff"> _String* return_string = (_String*)list->Join((BaseRef)spacer);</span>
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184
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<pre style="margin: 0;">+<span id="LC184" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one;two;three", return_string->getStr());</span></span>
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185
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<pre style="margin: 0;">+<span id="LC185" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one;two;three", return_string->get_str());</span></span>
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186
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<pre style="margin: 0;">+<span id="LC186" class="line" lang="diff"> }</span>
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187
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<pre style="margin: 0;">+<span id="LC187" class="line" lang="diff"> </span>
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188
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<pre style="margin: 0;">+<span id="LC188" class="line" lang="diff"> TEST_F(ListTest,BinaryFindTest){</span>
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<td class="diff-line-num new new_line" data-linenumber="189" style="width: 35px; color: rgba(0,0,0,0.3); border-right-width: 1px; border-right-color: #c7f0d2; border-right-style: solid; padding: 0 5px;" align="right" bgcolor="#ddfbe6">
189
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<pre style="margin: 0;">+<span id="LC189" class="line" lang="diff"><span class="p">@@ -385,7 +385,7 @@</span> TEST_F(ListTest,BinaryInsertTest){</span>
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190
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<pre style="margin: 0;">+<span id="LC190" class="line" lang="diff"> str_list.BinaryInsert((BaseRef)new _String("one"));</span>
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191
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<pre style="margin: 0;">+<span id="LC191" class="line" lang="diff"> </span>
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192
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<pre style="margin: 0;">+<span id="LC192" class="line" lang="diff"> _String* result_string = (_String*)str_list[3];</span>
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193
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<pre style="margin: 0;">+<span id="LC193" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("three", result_string->getStr());</span></span>
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194
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<pre style="margin: 0;">+<span id="LC194" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("three", result_string->get_str());</span></span>
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195
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<pre style="margin: 0;">+<span id="LC195" class="line" lang="diff"> }</span>
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196
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<pre style="margin: 0;">+<span id="LC196" class="line" lang="diff"> </span>
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197
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<pre style="margin: 0;">+<span id="LC197" class="line" lang="diff"> TEST_F(ListTest,CompareTest){</span>
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198
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<pre style="margin: 0;">+<span id="LC198" class="line" lang="diff"><span class="p">@@ -420,7 +420,7 @@</span> TEST_F(ListTest,DeleteTest){</span>
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199
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<pre style="margin: 0;">+<span id="LC199" class="line" lang="diff"> _List str_list = createStrList();</span>
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200
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<pre style="margin: 0;">+<span id="LC200" class="line" lang="diff"> str_list.Delete(0);</span>
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201
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<pre style="margin: 0;">+<span id="LC201" class="line" lang="diff"> _String* return_string = (_String*)str_list[1];</span>
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202
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<pre style="margin: 0;">+<span id="LC202" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("two", return_string->getStr());</span></span>
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203
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<pre style="margin: 0;">+<span id="LC203" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("two", return_string->get_str());</span></span>
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204
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<pre style="margin: 0;">+<span id="LC204" class="line" lang="diff"> } </span>
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205
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<pre style="margin: 0;">+<span id="LC205" class="line" lang="diff"> </span>
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206
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<pre style="margin: 0;">+<span id="LC206" class="line" lang="diff"> TEST_F(ListTest,DeleteListTest){</span>
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207
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<pre style="margin: 0;">+<span id="LC207" class="line" lang="diff"><span class="p">@@ -441,11 +441,11 @@</span> TEST_F(ListTest,ReplaceTest){</span>
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208
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<pre style="margin: 0;">+<span id="LC208" class="line" lang="diff"> </span>
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209
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<pre style="margin: 0;">+<span id="LC209" class="line" lang="diff"> str_list.Replace(1, new _String("help"), false);</span>
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210
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<pre style="margin: 0;">+<span id="LC210" class="line" lang="diff"> _String* return_string = (_String*)str_list[1];</span>
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211
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<pre style="margin: 0;">+<span id="LC211" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("help", return_string->getStr());</span></span>
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212
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<pre style="margin: 0;">+<span id="LC212" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("help", return_string->get_str());</span></span>
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213
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<pre style="margin: 0;">+<span id="LC213" class="line" lang="diff"> </span>
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214
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<pre style="margin: 0;">+<span id="LC214" class="line" lang="diff"> str_list.Replace(1, new _String("two"), false);</span>
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<pre style="margin: 0;">+<span id="LC215" class="line" lang="diff"> _String* return_string2 = (_String*)str_list[1];</span>
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<pre style="margin: 0;">+<span id="LC216" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("two", return_string2->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC217" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("two", return_string2->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC218" class="line" lang="diff"> } </span>
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<pre style="margin: 0;">+<span id="LC219" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC220" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC221" class="line" lang="diff"><span class="p">@@ -464,7 +464,7 @@</span> TEST_F(ListTest,IntersectTest){</span>
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<pre style="margin: 0;">+<span id="LC222" class="line" lang="diff"> l3.Intersect(l1, l2, &idx, &idx2);</span>
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<pre style="margin: 0;">+<span id="LC223" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC224" class="line" lang="diff"> _String* return_string = (_String*)str_list[1];</span>
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<pre style="margin: 0;">+<span id="LC225" class="line" lang="diff"><span class="gd" style="color: #000; background-color: #fdd;">- EXPECT_STREQ("one",return_string->getStr());</span></span>
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<pre style="margin: 0;">+<span id="LC226" class="line" lang="diff"><span class="gi" style="color: #000; background-color: #dfd;">+ EXPECT_STREQ("one",return_string->get_str());</span></span>
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<pre style="margin: 0;">+<span id="LC227" class="line" lang="diff"> </span>
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<pre style="margin: 0;">+<span id="LC228" class="line" lang="diff"> }</span>
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<pre style="margin: 0;">+<span id="LC229" class="line" lang="diff"> </span></pre>
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<li id="bc34014ab4b9a49dd7a27bdd8d352912607c3a96">
<a href="https://salsa.debian.org/med-team/hyphy/compare/df335440535562f7c62290cfdf726ced74abcdd8...6176567316bb409c1d39967a98343e6d9b7c611d#bc34014ab4b9a49dd7a27bdd8d352912607c3a96"><strong>debian/patches/series</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -2,3 +2,4 @@ use_debian_sqlite.patch</td>
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2
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<pre style="margin: 0;"> <span id="LC2" class="line" lang="plaintext">drop_profiling_option.patch</span>
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3
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3
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<pre style="margin: 0;"> <span id="LC3" class="line" lang="plaintext">remove_unneeded_test.patch</span>
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4
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4
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<pre style="margin: 0;"> <span id="LC4" class="line" lang="plaintext"># msse_option_only_if_available.patch</span>
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5
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<pre style="margin: 0;">+<span id="LC5" class="line" lang="plaintext">gcc9.patch</span></pre>
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<li id="d185b62d54557160e7ddc743405a9cec66dcaa96">
<a href="https://salsa.debian.org/med-team/hyphy/compare/df335440535562f7c62290cfdf726ced74abcdd8...6176567316bb409c1d39967a98343e6d9b7c611d#d185b62d54557160e7ddc743405a9cec66dcaa96"><strong>debian/patches/use_debian_sqlite.patch</strong></a>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -20,7 +20,7 @@ Description: Use Debian packaged sqlite3</td>
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<pre style="margin: 0;"> <span id="LC20" class="line" lang="diff"> set_source_files_properties(${SRC_CORE} ${SRC_NEW} {SRC_UTILS} PROPERTIES COMPILE_FLAGS "-Weffc++ -Wextra -Wall")</span>
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<pre style="margin: 0;"> <span id="LC21" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC22" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;">-<span id="LC23" class="line" lang="diff"><span class="p">@@ -26<span class="idiff left right">4,6 +263</span>,36 @@</span> if(${CURL_FOUND} AND NOT APPLE)</span>
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<pre style="margin: 0;">+<span id="LC23" class="line" lang="diff"><span class="p">@@ -26<span class="idiff left right">5,6 +264</span>,36 @@</span> if(${CURL_FOUND} AND NOT APPLE)</span>
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<pre style="margin: 0;"> <span id="LC24" class="line" lang="diff"> endif(${CURL_FOUND} AND NOT APPLE)</span>
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<pre style="margin: 0;"> <span id="LC25" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC26" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -57,7 +57,7 @@ Description: Use Debian packaged sqlite3</td>
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<pre style="margin: 0;"> <span id="LC57" class="line" lang="diff"> # gtest dependency</span>
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<pre style="margin: 0;"> <span id="LC58" class="line" lang="diff"> #-------------------------------------------------------------------------------</span>
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<pre style="margin: 0;"> <span id="LC59" class="line" lang="diff"> add_subdirectory(contrib/gtest-1.7.0)</span>
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<pre style="margin: 0;">-<span id="LC60" class="line" lang="diff"><span class="p">@@ -30<span class="idiff left right">5,11 +334</span>,6 @@</span> set_property(</span>
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<pre style="margin: 0;">+<span id="LC60" class="line" lang="diff"><span class="p">@@ -30<span class="idiff left right">6,11 +335</span>,6 @@</span> set_property(</span>
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<pre style="margin: 0;"> <span id="LC61" class="line" lang="diff"> )</span>
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<pre style="margin: 0;"> <span id="LC62" class="line" lang="diff"> </span>
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<pre style="margin: 0;"> <span id="LC63" class="line" lang="diff"> set_property(</span>
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<td class="line_content match " style="padding-left: 0.5em; padding-right: 0.5em; color: rgba(0,0,0,0.3);" bgcolor="#fafafa">@@ -69,7 +69,7 @@ Description: Use Debian packaged sqlite3</td>
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<pre style="margin: 0;"> <span id="LC69" class="line" lang="diff"> SOURCE src/core/calcnode2.cpp</span>
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<pre style="margin: 0;"> <span id="LC70" class="line" lang="diff"> APPEND_STRING PROPERTY COMPILE_FLAGS " -fstrict-aliasing -funroll-loops"</span>
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<pre style="margin: 0;"> <span id="LC71" class="line" lang="diff"> )</span>
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<pre style="margin: 0;">-<span id="LC72" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">29,7 +353</span>,6 @@</span> include_directories(</span>
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<pre style="margin: 0;">+<span id="LC72" class="line" lang="diff"><span class="p">@@ -3<span class="idiff left right">30,7 +354</span>,6 @@</span> include_directories(</span>
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<pre style="margin: 0;"> <span id="LC73" class="line" lang="diff"> src/core/include</span>
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<pre style="margin: 0;"> <span id="LC74" class="line" lang="diff"> src/contrib</span>
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<pre style="margin: 0;"> <span id="LC75" class="line" lang="diff"> src/lib/Link src/new/include</span>
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