X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=test%2Fjalview%2Fgui%2FAlignViewportTest.java;h=eff3fdca05e1e690cc0d7211094ea8b7b7905a5e;hb=3f12f4932226512316ec113e600695150431fd0a;hp=0b5840cd796dae7eb53a74d9cdb430d310e13a91;hpb=c4fdef7e109bac9f1da72ec3954a17a931f163df;p=jalview.git
diff --git a/test/jalview/gui/AlignViewportTest.java b/test/jalview/gui/AlignViewportTest.java
index 0b5840c..eff3fdc 100644
--- a/test/jalview/gui/AlignViewportTest.java
+++ b/test/jalview/gui/AlignViewportTest.java
@@ -1,3 +1,23 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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.
+ *
+ * Jalview 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 Jalview. If not, see .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
package jalview.gui;
import static org.testng.AssertJUnit.assertEquals;
@@ -16,9 +36,10 @@ import jalview.datamodel.SequenceI;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
import jalview.structure.StructureSelectionManager;
+import jalview.util.MapList;
-import java.util.LinkedHashSet;
-import java.util.Set;
+import java.util.ArrayList;
+import java.util.List;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
@@ -28,6 +49,7 @@ public class AlignViewportTest
{
AlignmentI al;
+
AlignViewport testee;
@BeforeClass(alwaysRun = true)
@@ -37,41 +59,38 @@ public class AlignViewportTest
"test/jalview/testProps.jvprops" });
}
- @BeforeMethod(alwaysRun = true)
+ @BeforeMethod(alwaysRun = true)
public void setUp()
{
SequenceI seq1 = new Sequence("Seq1", "ABC");
SequenceI seq2 = new Sequence("Seq2", "ABC");
SequenceI seq3 = new Sequence("Seq3", "ABC");
- SequenceI[] seqs = new SequenceI[]
- { seq1, seq2, seq3 };
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3 };
al = new Alignment(seqs);
al.setDataset(null);
testee = new AlignViewport(al);
}
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testCollateForPdb()
{
+ // JBP: What behaviour is this supposed to test ?
/*
* Set up sequence pdb ids
*/
- PDBEntry pdb1 = new PDBEntry("1ABC", "A", Type.PDB, "1ABC.pdb");
- PDBEntry pdb2 = new PDBEntry("2ABC", "A", Type.PDB, "2ABC.pdb");
- PDBEntry pdb3 = new PDBEntry("3ABC", "A", Type.PDB, "3ABC.pdb");
+ PDBEntry pdb1 = new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb");
+ PDBEntry pdb2 = new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb");
+ PDBEntry pdb3 = new PDBEntry("3ABC", "D", Type.PDB, "3ABC.pdb");
/*
- * seq1 and seq3 refer to 1ABC, seq2 to 2ABC, none to 3ABC
+ * seq1 and seq3 refer to 1abcB, seq2 to 2abcC, none to 3abcD
*/
al.getSequenceAt(0).getDatasetSequence()
- .addPDBId(
- new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+ .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
al.getSequenceAt(2).getDatasetSequence()
- .addPDBId(
- new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
+ .addPDBId(new PDBEntry("1ABC", "B", Type.PDB, "1ABC.pdb"));
al.getSequenceAt(1).getDatasetSequence()
- .addPDBId(
- new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
+ .addPDBId(new PDBEntry("2ABC", "C", Type.PDB, "2ABC.pdb"));
/*
* Add a second chain PDB xref to Seq2 - should not result in a duplicate in
* the results
@@ -87,8 +106,8 @@ public class AlignViewportTest
/*
* run method under test
*/
- SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[]
- { pdb1, pdb2, pdb3 });
+ SequenceI[][] seqs = testee.collateForPDB(new PDBEntry[] { pdb1, pdb2,
+ pdb3 });
// seq1 and seq3 refer to PDBEntry[0]
assertEquals(2, seqs[0].length);
@@ -107,7 +126,7 @@ public class AlignViewportTest
* Test that a mapping is not deregistered when a second view is closed but
* the first still holds a reference to the mapping
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeregisterMapping_onCloseView()
{
/*
@@ -115,40 +134,45 @@ public class AlignViewportTest
*/
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nCAGT\n", FormatAdapter.PASTE);
-
+
+ SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 1, 4 },
+ 1, 1));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
-
- Set mappings = new LinkedHashSet();
+ acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
+ 1, 1));
+
+ List mappings = new ArrayList();
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings);
af1.newView_actionPerformed(null);
-
+
/*
* Verify that creating the alignment for the new View has registered the
* mappings
*/
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
-
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
+
/*
* Close the second view. Verify that mappings are not removed as the first
* view still holds a reference to them.
*/
af1.closeMenuItem_actionPerformed(false);
- assertEquals(2, ssm.seqmappings.size());
- assertTrue(ssm.seqmappings.contains(acf1));
- assertTrue(ssm.seqmappings.contains(acf2));
+ assertEquals(2, ssm.getSequenceMappings().size());
+ assertTrue(ssm.getSequenceMappings().contains(acf1));
+ assertTrue(ssm.getSequenceMappings().contains(acf2));
}
/**
* Test that a mapping is deregistered if no alignment holds a reference to it
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeregisterMapping_withNoReference()
{
Desktop d = Desktop.instance;
@@ -161,25 +185,35 @@ public class AlignViewportTest
">Seq1\nRSVQ\n", FormatAdapter.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+ SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+ SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+ SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+ SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+ // need to be distinct
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
-
- Set mappings1 = new LinkedHashSet();
+ acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+ 12 }, 1, 1));
+
+ List mappings1 = new ArrayList();
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- Set mappings2 = new LinkedHashSet();
+ List mappings2 = new ArrayList();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
-
+
/*
* AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
*/
- Set ssmMappings = ssm.seqmappings;
+ List ssmMappings = ssm.getSequenceMappings();
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(1, ssmMappings.size());
@@ -201,7 +235,7 @@ public class AlignViewportTest
* Test that a mapping is not deregistered if another alignment holds a
* reference to it
*/
- @Test(groups ={ "Functional" })
+ @Test(groups = { "Functional" })
public void testDeregisterMapping_withReference()
{
Desktop d = Desktop.instance;
@@ -209,31 +243,41 @@ public class AlignViewportTest
StructureSelectionManager ssm = StructureSelectionManager
.getStructureSelectionManager(Desktop.instance);
ssm.resetAll();
-
+
AlignFrame af1 = new FileLoader().LoadFileWaitTillLoaded(
">Seq1\nRSVQ\n", FormatAdapter.PASTE);
AlignFrame af2 = new FileLoader().LoadFileWaitTillLoaded(
">Seq2\nDGEL\n", FormatAdapter.PASTE);
-
+ SequenceI cs1 = new Sequence("cseq1", "CCCGGGTTTAAA");
+ SequenceI cs2 = new Sequence("cseq2", "CTTGAGTCTAGA");
+ SequenceI s1 = af1.getViewport().getAlignment().getSequenceAt(0);
+ SequenceI s2 = af2.getViewport().getAlignment().getSequenceAt(0);
+ // need to be distinct
AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ acf1.addMap(cs1, s1, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ acf2.addMap(cs2, s2, new MapList(new int[] { 1, 4 },
+ new int[] { 1, 12 }, 1, 3));
AlignedCodonFrame acf3 = new AlignedCodonFrame();
-
- Set mappings1 = new LinkedHashSet();
+ acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+ 12 }, 1, 1));
+
+ List mappings1 = new ArrayList();
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
-
- Set mappings2 = new LinkedHashSet();
+
+ List mappings2 = new ArrayList();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
-
+
/*
* AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
*/
-
- Set ssmMappings = ssm.seqmappings;
+
+ List ssmMappings = ssm.getSequenceMappings();
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(1, ssmMappings.size());
@@ -241,7 +285,7 @@ public class AlignViewportTest
assertEquals(2, ssmMappings.size());
ssm.registerMapping(acf3);
assertEquals(3, ssmMappings.size());
-
+
/*
* Closing AlignFrame2 should remove mapping acf3 from
* StructureSelectionManager, but not acf2, since AlignFrame1 still has a