From bce6bc4fda3db5c17c3141c0cb1b4a08c43a3042 Mon Sep 17 00:00:00 2001
From: kiramt <k.mourao@dundee.ac.uk>
Date: Tue, 16 Jan 2018 12:15:07 +0000
Subject: [PATCH] JAL-2759 Unit test for PopupMenu hideInsertions code

---
 test/jalview/gui/PopupMenuTest.java |  115 +++++++++++++++++++++++++++++++++--
 1 file changed, 111 insertions(+), 4 deletions(-)

diff --git a/test/jalview/gui/PopupMenuTest.java b/test/jalview/gui/PopupMenuTest.java
index 335240b..7e077d0 100644
--- a/test/jalview/gui/PopupMenuTest.java
+++ b/test/jalview/gui/PopupMenuTest.java
@@ -29,9 +29,12 @@ import static org.testng.AssertJUnit.assertTrue;
 import jalview.datamodel.AlignmentAnnotation;
 import jalview.datamodel.AlignmentI;
 import jalview.datamodel.Annotation;
+import jalview.datamodel.ColumnSelection;
 import jalview.datamodel.DBRefEntry;
 import jalview.datamodel.DBRefSource;
+import jalview.datamodel.HiddenColumns;
 import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
 import jalview.io.DataSourceType;
 import jalview.io.FileFormat;
@@ -41,6 +44,7 @@ import jalview.util.MessageManager;
 import java.awt.Component;
 import java.io.IOException;
 import java.util.ArrayList;
+import java.util.Iterator;
 import java.util.List;
 
 import javax.swing.JMenu;
@@ -100,7 +104,7 @@ public class PopupMenuTest
   public void testConfigureReferenceAnnotationsMenu_noSequenceSelected()
   {
     JMenuItem menu = new JMenuItem();
-    List<SequenceI> seqs = new ArrayList<SequenceI>();
+    List<SequenceI> seqs = new ArrayList<>();
     testee.configureReferenceAnnotationsMenu(menu, seqs);
     assertFalse(menu.isEnabled());
     // now try null list
@@ -469,8 +473,8 @@ public class PopupMenuTest
     List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
 
     // create list of links and list of DBRefs
-    List<String> links = new ArrayList<String>();
-    List<DBRefEntry> refs = new ArrayList<DBRefEntry>();
+    List<String> links = new ArrayList<>();
+    List<DBRefEntry> refs = new ArrayList<>();
 
     // links as might be added into Preferences | Connections dialog
     links.add("EMBL-EBI Search | http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$"
@@ -548,7 +552,7 @@ public class PopupMenuTest
     }
 
     // if there are no valid links the Links submenu is disabled
-    List<String> nomatchlinks = new ArrayList<String>();
+    List<String> nomatchlinks = new ArrayList<>();
     nomatchlinks.add("NOMATCH | http://www.uniprot.org/uniprot/$"
             + DB_ACCESSION + "$");
 
@@ -559,4 +563,107 @@ public class PopupMenuTest
     assertFalse(linkMenu.isEnabled());
 
   }
+
+  /**
+   * Test for adding feature links
+   */
+  @Test(groups = { "Functional" })
+  public void testHideInsertions()
+  {
+    // get sequences from the alignment
+    List<SequenceI> seqs = parentPanel.getAlignment().getSequences();
+    
+    // get the Popup Menu for first sequence - no insertions
+    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(0), null);
+    testee.hideInsertions_actionPerformed(null);
+    
+    HiddenColumns hidden = parentPanel.av.getAlignment().getHiddenColumns();
+    Iterator<int[]> it = hidden.iterator();
+    assertFalse(it.hasNext());
+
+    Sequence seqGap1 = new Sequence("GappySeq",
+            "AAAA----AA-AAAAAAA---AAA-----------AAAAAAAAAA--");
+    seqGap1.createDatasetSequence();
+    seqs.add(seqGap1);
+    Sequence seqGap2 = new Sequence("LessGappySeq",
+            "AAAAAA-AAAAA---AAA--AAAAA--AAAAAAA-AAAAAA");
+    seqGap2.createDatasetSequence();
+    seqs.add(seqGap2);
+    Sequence seqGap3 = new Sequence("OneGapSeq",
+            "AAAAAA-AAAAAA--AAAAAA-AAAAAAAAAAA---AAAAAAAA");
+    seqGap3.createDatasetSequence();
+    seqs.add(seqGap3);
+
+    // get the Popup Menu for GappySeq - this time we have insertions
+    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(4), null);
+    testee.hideInsertions_actionPerformed(null);
+    hidden = parentPanel.av.getAlignment().getHiddenColumns();
+    it = hidden.iterator();
+
+    assertTrue(it.hasNext());
+    int[] region = it.next();
+    assertEquals(region[0], 4);
+    assertEquals(region[1], 7);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 10);
+    assertEquals(region[1], 10);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 18);
+    assertEquals(region[1], 20);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 24);
+    assertEquals(region[1], 34);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 45);
+    assertEquals(region[1], 46);
+
+    assertFalse(it.hasNext());
+
+    ColumnSelection sel = new ColumnSelection();
+    hidden.revealAllHiddenColumns(sel);
+
+    // make a sequence group and hide insertions within the group
+    SequenceGroup sg = new SequenceGroup();
+    sg.setStartRes(8);
+    sg.setEndRes(42);
+    sg.addSequence(seqGap2, false);
+    sg.addSequence(seqGap3, false);
+    parentPanel.av.setSelectionGroup(sg);
+
+    // hide columns outside and within selection
+    // only hidden columns outside the collection will be retained (unless also
+    // gaps in the selection)
+    hidden.hideColumns(1, 10);
+    hidden.hideColumns(31, 40);
+
+    // get the Popup Menu for LessGappySeq in the sequence group
+    testee = new PopupMenu(parentPanel, (Sequence) seqs.get(5), null);
+    testee.hideInsertions_actionPerformed(null);
+    hidden = parentPanel.av.getAlignment().getHiddenColumns();
+    it = hidden.iterator();
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 1);
+    assertEquals(region[1], 7);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 13);
+    assertEquals(region[1], 14);
+
+    assertTrue(it.hasNext());
+    region = it.next();
+    assertEquals(region[0], 34);
+    assertEquals(region[1], 34);
+  }
+
 }
-- 
1.7.10.2