--- /dev/null
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.viewmodel;
+
+import static org.testng.Assert.assertEquals;
+
+import jalview.bin.Cache;
+import jalview.bin.Jalview;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceI;
+import jalview.gui.AlignViewport;
+import jalview.gui.JvOptionPane;
+
+import org.testng.annotations.AfterClass;
+import org.testng.annotations.BeforeClass;
+import org.testng.annotations.Test;
+
+public class OverviewDimensionsTest {
+
+ boolean showConservationSetting;
+
+ SequenceI seq1 = new Sequence(
+ "Seq1",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq2 = new Sequence(
+ "Seq2",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq3 = new Sequence(
+ "Seq3",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq4 = new Sequence(
+ "Seq4",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq5 = new Sequence(
+ "Seq5",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq6 = new Sequence(
+ "Seq6",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq7 = new Sequence(
+ "Seq7",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq8 = new Sequence(
+ "Seq8",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq9 = new Sequence(
+ "Seq9",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq10 = new Sequence(
+ "Seq10",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq11 = new Sequence(
+ "Seq11",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq12 = new Sequence(
+ "Seq12",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq13 = new Sequence(
+ "Seq13",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq14 = new Sequence(
+ "Seq14",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq15 = new Sequence(
+ "Seq15",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq16 = new Sequence(
+ "Seq16",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq17 = new Sequence(
+ "Seq17",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq18 = new Sequence(
+ "Seq18",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq19 = new Sequence(
+ "Seq19",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq20 = new Sequence(
+ "Seq20",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq21 = new Sequence(
+ "Seq21",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq22 = new Sequence(
+ "Seq22",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
+ + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
+ + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ SequenceI seq23 = new Sequence(
+ "Seq23",
+ "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+
+ @BeforeClass(alwaysRun = true)
+ public void setUp()
+ {
+ JvOptionPane.setInteractiveMode(false);
+ JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+
+ Jalview.main(new String[] { "-nonews", "-props",
+ "test/jalview/testProps.jvprops" });
+
+ // get cached setting for showConservation
+ // reset it in AfterClass!
+ showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
+ }
+
+ @AfterClass(alwaysRun = true)
+ public void tearDown()
+ {
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.toString(showConservationSetting));
+ }
+
+ /**
+ * Test that the OverviewDimensions constructor sets width and height
+ * correctly
+ */
+ @Test(groups = { "Functional" })
+ public void testConstructor()
+ {
+ SequenceI seqa = new Sequence("Seq1", "ABC");
+ SequenceI seqb = new Sequence("Seq2", "ABC");
+ SequenceI seqc = new Sequence("Seq3", "ABC");
+ SequenceI seqd = new Sequence("Seq4", "ABC");
+ SequenceI seqe = new Sequence("Seq5",
+ "ABCABCABCABCABCABCABCABCBACBACBACBAC");
+
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.toString(true));
+
+ // test for alignment with width > height
+ SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
+ Alignment al1 = new Alignment(seqs1);
+ al1.setDataset(null);
+ AlignViewport av1 = new AlignViewport(al1);
+
+ OverviewDimensions od = new OverviewDimensions(av1);
+ assertEquals(od.getGraphHeight(), 20);
+ assertEquals(od.getSequencesHeight(), 266);
+ assertEquals(od.getWidth(), 400);
+ assertEquals(od.getHeight(), 286);
+
+ // test for alignment with width < height
+ SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
+ Alignment al2 = new Alignment(seqs2);
+ al2.setDataset(null);
+ AlignViewport av2 = new AlignViewport(al2);
+
+ od = new OverviewDimensions(av2);
+ assertEquals(od.getGraphHeight(), 20);
+ assertEquals(od.getSequencesHeight(), 300);
+ assertEquals(od.getWidth(), 300);
+ assertEquals(od.getHeight(), 320);
+
+ // test for alignment with width > height and sequence height scaled below
+ // min value
+ SequenceI[] seqs3 = new SequenceI[] { seqe };
+ Alignment al3 = new Alignment(seqs3);
+ al3.setDataset(null);
+ AlignViewport av3 = new AlignViewport(al3);
+
+ od = new OverviewDimensions(av3);
+ assertEquals(od.getGraphHeight(), 20);
+ assertEquals(od.getSequencesHeight(), 40);
+ assertEquals(od.getWidth(), 400);
+ assertEquals(od.getHeight(), 60);
+
+ // test for alignment with width < height and width scaled below min value
+ SequenceI[] seqs4 = new SequenceI[] { seqa, seqb, seqc, seqd, seqa,
+ seqb, seqc, seqd, seqa, seqb, seqc, seqd, seqa, seqb, seqc, seqd };
+ Alignment al4 = new Alignment(seqs4);
+ al4.setDataset(null);
+ AlignViewport av4 = new AlignViewport(al4);
+
+ od = new OverviewDimensions(av4);
+ assertEquals(od.getGraphHeight(), 20);
+ assertEquals(od.getSequencesHeight(), 300);
+ assertEquals(od.getWidth(), 120);
+ assertEquals(od.getHeight(), 320);
+
+ // test for alignment where no conservation annotation is shown
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.toString(false));
+
+ Alignment al5 = new Alignment(seqs4);
+ al5.setDataset(null);
+ AlignViewport av5 = new AlignViewport(al5);
+
+ od = new OverviewDimensions(av5);
+ assertEquals(od.getGraphHeight(), 0);
+ assertEquals(od.getSequencesHeight(), 300);
+ assertEquals(od.getWidth(), 120);
+ assertEquals(od.getHeight(), 300);
+ }
+
+ /**
+ * Test that validation after mouse adjustments to boxX and boxY sets box
+ * dimensions and scroll values correctly, when there are no hidden rows or
+ * columns
+ */
+ @Test(groups = { "Functional" })
+ public void checkValidNoHidden()
+ {
+ seq23.setStart(386);
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
+ seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
+ seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
+ Alignment al = new Alignment(seqs);
+ al.setDataset(null);
+ AlignViewport av = new AlignViewport(al);
+
+ // Initial box sizing - default path through code
+ OverviewDimensions od = new OverviewDimensions(av);
+ od.setBoxPosition();
+ od.checkValid();
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), 399);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
+
+ // negative boxX value reset to 0
+ od.setBoxX(-5);
+ od.checkValid();
+ assertEquals(od.getBoxX(), 0);
+
+ // negative boxY value reset to 0
+ od.setBoxY(-2);
+ od.checkValid();
+ assertEquals(od.getBoxY(), 0);
+
+ // overly large boxX value reset to width-boxWidth
+ od.setBoxX(100);
+ od.checkValid();
+ assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+
+ // startRes non-zero
+ av.setStartRes(50);
+ OverviewDimensions od2 = new OverviewDimensions(av);
+ od2.setBoxPosition();
+ od2.checkValid();
+ assertEquals(od2.getBoxX(), 61);
+ assertEquals(od2.getScrollCol(), 49);
+ }
+
+ /**
+ * Test setting of the box position, when there are hidden cols at the start
+ * of the alignment
+ */
+ @Test(groups = { "Functional" })
+ public void testSetBoxPosWithHiddenColsAtStart()
+ {
+ seq23.setStart(386);
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
+ seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
+ seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
+ Alignment al = new Alignment(seqs);
+ al.setDataset(null);
+ AlignViewport av = new AlignViewport(al);
+
+ av.setStartRes(50);
+ OverviewDimensions od = new OverviewDimensions(av);
+
+ // hiding columns before current position: changes boxX but not scrollCol or
+ // boxwidth
+
+ // do a reset
+ av.showAllHiddenColumns();
+ od.setBoxPosition();
+ od.checkValid();
+ int prevWidth = od.getBoxWidth();
+
+ // hide cols at start and check updated box position is correct
+ // changes boxX but not scrollCol or boxwidth
+ int lastHiddenCol = 50;
+ av.hideColumns(0, 50);
+ od.setBoxPosition();
+ assertEquals(od.getBoxX(), 124);
+ assertEquals(od.getScrollCol(), lastHiddenCol - 1);
+ assertEquals(od.getBoxWidth(), prevWidth);
+
+ // set the box position by moving viewport & check it goes to the right
+ // place
+
+ // update the box position via mouse and check it goes to the right place
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetBoxPosWithHiddenColsAtEnd()
+ {
+
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetBoxPosWithHiddenColsMiddle()
+ {
+ seq23.setStart(386);
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
+ seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
+ seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
+ Alignment al = new Alignment(seqs);
+ al.setDataset(null);
+ AlignViewport av = new AlignViewport(al);
+
+ av.setStartRes(50);
+ OverviewDimensions od = new OverviewDimensions(av);
+
+ // hiding columns after current position: changes end position but not start
+ // so scrollCol and boxX do not change but boxWidth does
+ float scalew = od.getWidth() / al.getWidth();
+ int prevWidth = od.getBoxWidth();
+ int prevX = od.getBoxX();
+ av.hideColumns(108, 110);
+ od.setBoxPosition();
+ assertEquals(od.getBoxX(), prevX);
+ assertEquals(od.getScrollCol(), 49);
+ // assertEquals(od2.getBoxWidth(), prevWidth + ((int) 2 * av.getCharWidth()
+ // / scalew));
+ }
+
+ @Test(groups = { "Functional" })
+ public void testSetBoxPosWithHiddenRowsAtStart()
+ {
+ seq23.setStart(386);
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
+ seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
+ seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
+ Alignment al = new Alignment(seqs);
+ al.setDataset(null);
+ AlignViewport av = new AlignViewport(al);
+
+ av.setStartRes(50);
+ OverviewDimensions od = new OverviewDimensions(av);
+
+ // account for hidden rows
+ SequenceI[] hidden = { seq2, seq3, seq4, seq5, seq6, seq7 };
+ av.showAllHiddenColumns();
+ av.hideSequence(hidden);
+ od.checkValid();
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getScrollRow(), 0);
+ }
+
+ /**
+ * Test that the box position is set correctly
+ */
+ @Test(groups = { "Functional" })
+ public void setBoxPosition()
+ {
+
+ SequenceI[] seqs = new SequenceI[] { seq1, seq2, seq3, seq4, seq5,
+ seq6, seq7, seq8, seq9, seq10, seq11, seq12, seq13, seq14, seq15,
+ seq16, seq17, seq18, seq19, seq20, seq21, seq22, seq23 };
+ Alignment al = new Alignment(seqs);
+ al.setDataset(null);
+ AlignViewport av = new AlignViewport(al);
+
+ // Test box is in expected location when there are no hidden rows or columns
+
+ OverviewDimensions od = new OverviewDimensions(av);
+ od.setBoxPosition();
+
+ assertEquals(od.getBoxHeight(), 81);
+ assertEquals(od.getBoxWidth(), 400);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+
+ // Account for hidden rows
+ SequenceI[] hidden = { seq2, seq3, seq4 };
+ av.hideSequence(hidden);
+
+ OverviewDimensions od1 = new OverviewDimensions(av);
+ od1.setBoxPosition();
+
+ assertEquals(od1.getBoxHeight(), 80);
+ assertEquals(od1.getBoxWidth(), 400);
+ assertEquals(od1.getBoxX(), 0);
+ assertEquals(od1.getBoxY(), 0);
+
+ // Account for hidden columns
+ av.hideColumns(10, 15);
+ av.showAllHiddenSeqs();
+
+ OverviewDimensions od2 = new OverviewDimensions(av);
+ od2.setBoxPosition();
+
+ assertEquals(od2.getBoxHeight(), 81);
+ assertEquals(od2.getBoxWidth(), 422);
+ assertEquals(od2.getBoxX(), 0);
+ assertEquals(od2.getBoxY(), 0);
+
+ // Account for hidden rows and cols
+ av.hideSequence(hidden);
+ OverviewDimensions od3 = new OverviewDimensions(av);
+ od3.setBoxPosition();
+
+ assertEquals(od3.getBoxHeight(), 80);
+ assertEquals(od3.getBoxWidth(), 422);
+ assertEquals(od3.getBoxX(), 0);
+ assertEquals(od3.getBoxY(), 0);
+ }
+}
git://source.jalview.org / jalview.git / commitdiff