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;
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();
+ acf2.addMap(s1, s1, new MapList(new int[] { 1, 4 }, new int[] { 4, 1 },
+ 1, 1));
- Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
mappings.add(acf1);
mappings.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(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));
}
/**
">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();
+ acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+ 12 }, 1, 1));
- Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
mappings1.add(acf1);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
* AlignFrame1 has mapping acf1, AlignFrame2 has acf2 and acf3
*/
- Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+ List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(1, ssmMappings.size());
">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();
+ acf3.addMap(cs2, cs2, new MapList(new int[] { 1, 12 }, new int[] { 1,
+ 12 }, 1, 1));
- Set<AlignedCodonFrame> mappings1 = new LinkedHashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings1 = new ArrayList<AlignedCodonFrame>();
mappings1.add(acf1);
mappings1.add(acf2);
af1.getViewport().getAlignment().setCodonFrames(mappings1);
- Set<AlignedCodonFrame> mappings2 = new LinkedHashSet<AlignedCodonFrame>();
+ List<AlignedCodonFrame> mappings2 = new ArrayList<AlignedCodonFrame>();
mappings2.add(acf2);
mappings2.add(acf3);
af2.getViewport().getAlignment().setCodonFrames(mappings2);
* AlignFrame1 has mappings acf1 and acf2, AlignFrame2 has acf2 and acf3
*/
- Set<AlignedCodonFrame> ssmMappings = ssm.seqmappings;
+ List<AlignedCodonFrame> ssmMappings = ssm.getSequenceMappings();
assertEquals(0, ssmMappings.size());
ssm.registerMapping(acf1);
assertEquals(1, ssmMappings.size());