From 815cb09dc2fdc35cb9c1bb5b552275ed891b8663 Mon Sep 17 00:00:00 2001
From: Mungo Carstairs <gmungoc@gmail.com>
Date: Tue, 22 Oct 2019 15:50:52 +0100
Subject: [PATCH] JAL-3423 use System.lineSeparator() in code and tests

---
 src/jalview/analysis/AlignSeq.java               |   20 +++++++---------
 test/jalview/gui/PairwiseAlignmentPanelTest.java |   28 ++++++++++++----------
 2 files changed, 25 insertions(+), 23 deletions(-)

diff --git a/src/jalview/analysis/AlignSeq.java b/src/jalview/analysis/AlignSeq.java
index 1b2578e..38adeee 100755
--- a/src/jalview/analysis/AlignSeq.java
+++ b/src/jalview/analysis/AlignSeq.java
@@ -565,8 +565,8 @@ public class AlignSeq
     }
 
     pid = pid / (aseq1.length - count) * 100;
-    output.append(new Format("Percentage ID = %3.2f\n").form(pid));
-    output.append(NEWLINE);
+    output.append(new Format("Percentage ID = %3.2f").form(pid));
+    output.append(NEWLINE).append(NEWLINE);
     try
     {
       os.print(output.toString());
@@ -862,8 +862,8 @@ public class AlignSeq
    */
   public jalview.datamodel.Mapping getMappingFromS1(boolean allowmismatch)
   {
-    ArrayList<Integer> as1 = new ArrayList<Integer>(),
-            as2 = new ArrayList<Integer>();
+    ArrayList<Integer> as1 = new ArrayList<>(),
+            as2 = new ArrayList<>();
     int pdbpos = s2.getStart() + getSeq2Start() - 2;
     int alignpos = s1.getStart() + getSeq1Start() - 2;
     int lp2 = pdbpos - 3, lp1 = alignpos - 3;
@@ -914,13 +914,11 @@ public class AlignSeq
     {
       mapseq1[i++] = ip;
     }
-    ;
     i = 0;
     for (Integer ip : as2)
     {
       mapseq2[i++] = ip;
     }
-    ;
     if (lastmatch)
     {
       mapseq1[mapseq1.length - 1] = alignpos;
@@ -951,13 +949,13 @@ public class AlignSeq
           List<SequenceI> ochains, AlignmentI al, String dnaOrProtein,
           boolean removeOldAnnots)
   {
-    List<SequenceI> orig = new ArrayList<SequenceI>(),
-            repl = new ArrayList<SequenceI>();
-    List<AlignSeq> aligs = new ArrayList<AlignSeq>();
+    List<SequenceI> orig = new ArrayList<>(),
+            repl = new ArrayList<>();
+    List<AlignSeq> aligs = new ArrayList<>();
     if (al != null && al.getHeight() > 0)
     {
-      ArrayList<SequenceI> matches = new ArrayList<SequenceI>();
-      ArrayList<AlignSeq> aligns = new ArrayList<AlignSeq>();
+      ArrayList<SequenceI> matches = new ArrayList<>();
+      ArrayList<AlignSeq> aligns = new ArrayList<>();
 
       for (SequenceI sq : ochains)
       {
diff --git a/test/jalview/gui/PairwiseAlignmentPanelTest.java b/test/jalview/gui/PairwiseAlignmentPanelTest.java
index e74849f..14ab3d6 100644
--- a/test/jalview/gui/PairwiseAlignmentPanelTest.java
+++ b/test/jalview/gui/PairwiseAlignmentPanelTest.java
@@ -15,6 +15,8 @@ import junit.extensions.PA;
 
 public class PairwiseAlignmentPanelTest
 {
+  private static final String NL = System.lineSeparator();
+
   @Test(groups = "Functional")
   public void testConstructor_withSelectionGroup()
   {
@@ -38,12 +40,13 @@ public class PairwiseAlignmentPanelTest
     PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
     String text = ((JTextArea) PA.getValue(testee, "textarea")).getText()
-            .replaceAll("\r", "");
-    String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
-            + "Sequence     FER1_PEA/29-32 (Sequence length = 7)\n"
-            + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
-            + "    FER1_PEA/29-32 TKAF\n" + "                    ||.\n"
-            + "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n";
+    ;// .replaceAll("\r", "");
+    String expected = "Score = 80.0" + NL + "Length of alignment = 4" + NL
+            + "Sequence     FER1_PEA/29-32 (Sequence length = 7)" + NL
+            + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)" + NL + NL
+            + "    FER1_PEA/29-32 TKAF" + NL + "                    ||."
+            + NL + "Q93XJ9_SOLTU/23-26 LKAI" + NL + NL
+            + "Percentage ID = 50.00" + NL + NL;
     assertEquals(text, expected);
   }
 
@@ -64,12 +67,13 @@ public class PairwiseAlignmentPanelTest
     PairwiseAlignPanel testee = new PairwiseAlignPanel(viewport);
 
     String text = ((JTextArea) PA.getValue(testee, "textarea")).getText()
-            .replaceAll("\r", "");
-    String expected = "Score = 80.0\n" + "Length of alignment = 4\n"
-            + "Sequence     FER1_PEA/29-32 (Sequence length = 7)\n"
-            + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)\n\n"
-            + "    FER1_PEA/29-32 TKAF\n" + "                    ||.\n"
-            + "Q93XJ9_SOLTU/23-26 LKAI\n\n" + "Percentage ID = 50.00\n\n";
+    ;// .replaceAll("\r", "");
+    String expected = "Score = 80.0" + NL + "Length of alignment = 4" + NL
+            + "Sequence     FER1_PEA/29-32 (Sequence length = 7)" + NL
+            + "Sequence Q93XJ9_SOLTU/23-26 (Sequence length = 7)" + NL + NL
+            + "    FER1_PEA/29-32 TKAF" + NL + "                    ||."
+            + NL + "Q93XJ9_SOLTU/23-26 LKAI" + NL + NL
+            + "Percentage ID = 50.00" + NL + NL;
     assertEquals(text, expected);
   }
 }
-- 
1.7.10.2