import static org.testng.Assert.assertEquals;
-import jalview.bin.Cache;
-import jalview.bin.Jalview;
+import jalview.analysis.AlignmentGenerator;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceCollectionI;
+import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
-import jalview.gui.AlignViewport;
-import jalview.gui.JvOptionPane;
+
+import java.util.Hashtable;
import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
+import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
-public class OverviewDimensionsTest {
+@Test(singleThreaded = true)
+public class OverviewDimensionsTest
+{
+ AlignmentI al;
+ OverviewDimensions od;
- boolean showConservationSetting;
+ // cached widths and heights
+ int boxWidth;
+ int boxHeight;
+ int viewHeight;
+ int viewWidth;
+ int alheight;
+ int alwidth;
- SequenceI seq1 = new Sequence(
- "Seq1",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ ViewportPositionProps posProps;
- SequenceI seq2 = new Sequence(
- "Seq2",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
- SequenceI seq3 = new Sequence(
- "Seq3",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ ColumnSelection hiddenCols = new ColumnSelection();
- SequenceI seq4 = new Sequence(
- "Seq4",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ @BeforeClass(alwaysRun = true)
+ public void setUpJvOptionPane()
+ {
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ al = gen.generate(157, 525, 123, 5, 5);
+ }
- SequenceI seq5 = new Sequence(
- "Seq5",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ @BeforeMethod(alwaysRun = true)
+ public void setUp()
+ {
+ if (!hiddenRepSequences.isEmpty())
+ {
+ al.getHiddenSequences().showAll(hiddenRepSequences);
+ }
+ hiddenCols.revealAllHiddenColumns();
+
+ posProps = new ViewportPositionProps(al);
+ posProps.setStartRes(0);
+ posProps.setEndRes(62);
+ posProps.setStartSeq(0);
+ posProps.setEndSeq(17);
+
+ viewHeight = posProps.getEndSeq() - posProps.getStartSeq() + 1;
+ viewWidth = posProps.getEndRes() - posProps.getStartRes() + 1;
+
+ ColumnSelection hiddenCols = new ColumnSelection();
+
+ od = new OverviewDimensions(posProps, true);
+ // Initial box sizing - default path through code
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
- SequenceI seq6 = new Sequence(
- "Seq6",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ mouseClick(od, 0, 0);
+ moveViewport(0, 0);
- SequenceI seq7 = new Sequence(
- "Seq7",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // calculate before hidden columns so we get absolute values
+ alheight = posProps.getAbsoluteAlignmentHeight();
+ alwidth = posProps.getAbsoluteAlignmentWidth();
- SequenceI seq8 = new Sequence(
- "Seq8",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ boxWidth = Math.round((float) (posProps.getEndRes()
+ - posProps.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round((float) (posProps.getEndSeq()
+ - posProps.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
+ }
- SequenceI seq9 = new Sequence(
- "Seq9",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ @AfterClass(alwaysRun = true)
+ public void cleanUp()
+ {
+ al = null;
+ }
- SequenceI seq10 = new Sequence(
- "Seq10",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ /**
+ * 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");
+
+ int defaultGraphHeight = 20;
+ int maxWidth = 400;
+ int minWidth = 120;
+ int maxSeqHeight = 300;
+ int minSeqHeight = 40;
+
+ // test for alignment with width > height
+ SequenceI[] seqs1 = new SequenceI[] { seqa, seqb };
+ Alignment al1 = new Alignment(seqs1);
+ ViewportPositionProps props = new ViewportPositionProps(al1);
+
+ OverviewDimensions od = new OverviewDimensions(props, true);
+ int scaledHeight = 267;
+ assertEquals(od.getGraphHeight(), defaultGraphHeight);
+ assertEquals(od.getSequencesHeight(), scaledHeight);
+ assertEquals(od.getWidth(), maxWidth);
+ assertEquals(od.getHeight(), scaledHeight + defaultGraphHeight);
+
+ // test for alignment with width < height
+ SequenceI[] seqs2 = new SequenceI[] { seqa, seqb, seqc, seqd };
+ Alignment al2 = new Alignment(seqs2);
+ props = new ViewportPositionProps(al2);
+
+ od = new OverviewDimensions(props, true);
+ int scaledWidth = 300;
+ assertEquals(od.getGraphHeight(), defaultGraphHeight);
+ assertEquals(od.getSequencesHeight(), maxSeqHeight);
+ assertEquals(od.getWidth(), scaledWidth);
+ assertEquals(od.getHeight(), scaledWidth + defaultGraphHeight);
+
+ // test for alignment with width > height and sequence height scaled below
+ // min value
+ SequenceI[] seqs3 = new SequenceI[] { seqe };
+ Alignment al3 = new Alignment(seqs3);
+ props = new ViewportPositionProps(al3);
+
+ od = new OverviewDimensions(props, true);
+ assertEquals(od.getGraphHeight(), defaultGraphHeight);
+ assertEquals(od.getSequencesHeight(), minSeqHeight);
+ assertEquals(od.getWidth(), maxWidth);
+ assertEquals(od.getHeight(), minSeqHeight + defaultGraphHeight);
+
+ // 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);
+ props = new ViewportPositionProps(al4);
+
+ od = new OverviewDimensions(props, true);
+ assertEquals(od.getGraphHeight(), defaultGraphHeight);
+ assertEquals(od.getSequencesHeight(), maxSeqHeight);
+ assertEquals(od.getWidth(), minWidth);
+ assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
+
+ Alignment al5 = new Alignment(seqs4);
+ props = new ViewportPositionProps(al5);
+
+ od = new OverviewDimensions(props, false);
+ assertEquals(od.getGraphHeight(), 0);
+ assertEquals(od.getSequencesHeight(), maxSeqHeight);
+ assertEquals(od.getWidth(), minWidth);
+ assertEquals(od.getHeight(), maxSeqHeight);
+ }
- SequenceI seq11 = new Sequence(
- "Seq11",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ /**
+ * 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 testSetBoxFromMouseClick()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq12 = new Sequence(
- "Seq12",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // negative boxX value reset to 0
+ mouseClick(od, -5, 10);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollRow(),
+ Math.round((float) 10 * alheight / od.getSequencesHeight()));
+ assertEquals(od.getScrollCol(), 0);
- SequenceI seq13 = new Sequence(
- "Seq13",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // negative boxY value reset to 0
+ mouseClick(od, 6, -2);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) 6 * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq14 = new Sequence(
- "Seq14",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // overly large boxX value reset to width-boxWidth
+ mouseClick(od, 100, 6);
+ assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+ assertEquals(od.getBoxY(), 6);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(),
+ Math.round((float) od.getBoxY() * alheight
+ / od.getSequencesHeight()));
+
+ // overly large boxY value reset to sequenceHeight - boxHeight
+ mouseClick(od, 10, 520);
+ assertEquals(od.getBoxX(), 10);
+ assertEquals(od.getBoxY(), od.getSequencesHeight() - od.getBoxHeight());
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+
+ // here (float) od.getBoxY() * alheight / od.getSequencesHeight() = 507.5
+ // and round rounds to 508; however we get 507 working with row values
+ // hence the subtraction of 1
+ assertEquals(od.getScrollRow(),
+ Math.round((float) od.getBoxY() * alheight
+ / od.getSequencesHeight()) - 1);
+
+ // click past end of alignment, as above
+ mouseClick(od, 3000, 5);
+ assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(),
+ Math.round((float) od.getBoxY() * alheight
+ / od.getSequencesHeight()));
+
+ // move viewport so startRes non-zero and then mouseclick
+ moveViewportH(50);
+
+ // click at viewport position
+ int oldboxx = od.getBoxX();
+ int oldboxy = od.getBoxY();
+ mouseClick(od, od.getBoxX() + 5, od.getBoxY() + 2);
+ assertEquals(od.getBoxX(), oldboxx + 5);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getBoxY(), oldboxy + 2);
+ assertEquals(od.getScrollRow(),
+ Math.round((float) od.getBoxY() * alheight
+ / od.getSequencesHeight()));
+
+ // click at top corner
+ mouseClick(od, 0, 0);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getScrollRow(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ }
- SequenceI seq15 = new Sequence(
- "Seq15",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ /**
+ * Test setting of the box position, when there are hidden cols at the start
+ * of the alignment
+ */
+ @Test(groups = { "Functional" })
+ public void testFromMouseWithHiddenColsAtStart()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq16 = new Sequence(
- "Seq16",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // hide cols at start and check updated box position is correct
+ // changes boxX but not boxwidth
+ int lastHiddenCol = 30;
+ hiddenCols.hideColumns(0, lastHiddenCol);
+
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ assertEquals(od.getBoxX(),
+ Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+ / alwidth));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // try to click in hidden cols, check box does not move
+ int xpos = 10;
+ mouseClick(od, xpos, 0);
+ assertEquals(
+ od.getBoxX(),
+ Math.round((float) (lastHiddenCol + 1) * od.getWidth()
+ / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollRow(), 0);
+ assertEquals(od.getScrollCol(), 0);
- SequenceI seq17 = new Sequence(
- "Seq17",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // click to right of hidden columns, box moves to click point
+ testBoxIsAtClickPoint(40, 0);
+ assertEquals(od.getScrollRow(), 0);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) 40 * alwidth / od.getWidth())
+ - (lastHiddenCol + 1));
- SequenceI seq18 = new Sequence(
- "Seq18",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // click to right of hidden columns such that box runs over right hand side
+ // of alignment
+ // box position is adjusted away from the edge
+ // overly large boxX value reset to width-boxWidth
+ xpos = 100;
+ mouseClick(od, xpos, 5);
+ assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+ assertEquals(od.getBoxY(), 5);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth())
+ - (lastHiddenCol + 1));
+ assertEquals(od.getScrollRow(),
+ Math.round((float) od.getBoxY() * alheight
+ / od.getSequencesHeight()));
+ }
+
+ /**
+ * Test setting of the box position, when there are hidden cols in the middle
+ * of the alignment
+ */
+ @Test(groups = { "Functional" })
+ public void testFromMouseWithHiddenColsInMiddle()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
+
+ // hide columns 63-73, no change to box position or dimensions
+ int firstHidden = 63;
+ int lastHidden = 73;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
- SequenceI seq19 = new Sequence(
- "Seq19",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq20 = new Sequence(
- "Seq20",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // move box so that it overlaps with hidden cols on one side
+ // box width changes, boxX and scrollCol as for unhidden case
+ int xpos = 55 - boxWidth; // 55 is position in overview approx halfway
+ // between cols 60 and 70
+ mouseClick(od, xpos, 0);
+ assertEquals(od.getBoxX(), xpos);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(
+ od.getBoxWidth(),
+ Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+ * od.getWidth() / alwidth));
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round(xpos * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq21 = new Sequence(
- "Seq21",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // move box so that it completely covers hidden cols
+ // box width changes, boxX and scrollCol as for hidden case
+ xpos = 33;
+ mouseClick(od, xpos, 0);
+ assertEquals(od.getBoxX(), xpos);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(
+ od.getBoxWidth(),
+ Math.round(boxWidth + (float) (lastHidden - firstHidden + 1)
+ * od.getWidth() / alwidth));
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) xpos * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq22 = new Sequence(
- "Seq22",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
- + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC"
- + "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // move box so boxX is in hidden cols, box overhangs at right
+ // boxX and scrollCol at left of hidden area, box width extends across
+ // hidden region
+ xpos = 50;
+ mouseClick(od, xpos, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(
+ od.getBoxWidth(),
+ boxWidth
+ + Math.round((float) (lastHidden - firstHidden + 1)
+ * od.getWidth() / alwidth));
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(), firstHidden - 1);
+ assertEquals(od.getScrollRow(), 0);
- SequenceI seq23 = new Sequence(
- "Seq23",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
+ // move box so boxX is to right of hidden cols, but does not go beyond full
+ // width of alignment
+ // box width, boxX and scrollCol all as for non-hidden case
+ xpos = 75;
+ testBoxIsAtClickPoint(xpos, 0);
+ assertEquals(od.getScrollRow(), 0);
+ assertEquals(od.getScrollCol(),
+ Math.round(xpos * alwidth / od.getWidth())
+ - (lastHidden - firstHidden + 1));
+
+ // move box so it goes beyond full width of alignment
+ // boxX, scrollCol adjusted back, box width normal
+ xpos = 3000;
+ mouseClick(od, xpos, 5);
+ assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+ assertEquals(od.getBoxY(), 5);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round(((float) od.getBoxX() * alwidth / od.getWidth())
+ - (lastHidden - firstHidden + 1)));
+ assertEquals(od.getScrollRow(),
+ Math.round((float) od.getBoxY() * alheight
+ / od.getSequencesHeight()));
+ }
- @BeforeClass(alwaysRun = true)
- public void setUp()
+ /**
+ * Test setting of the box position, when there are hidden cols at the end of
+ * the alignment
+ */
+ @Test(groups = { "Functional" })
+ public void testFromMouseWithHiddenColsAtEnd()
{
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
+
+ // hide columns 140-164, no change to box position or dimensions
+ int firstHidden = 140;
+ int lastHidden = 164;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
+
+ // click to left of hidden cols, without overlapping
+ // boxX, scrollCol and width as normal
+ int xpos = 5;
+ testBoxIsAtClickPoint(xpos, 0);
+ assertEquals(od.getScrollRow(), 0);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) xpos * alwidth / od.getWidth()));
+
+ // click to left of hidden cols, with overlap
+ // boxX and scrollCol adjusted for hidden cols, width normal
+ xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
+ mouseClick(od, xpos, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+ - boxWidth + 1);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
- Jalview.main(new String[] { "-nonews", "-props",
- "test/jalview/testProps.jvprops" });
+ // click in hidden cols
+ // boxX and scrollCol adjusted for hidden cols, width normal
+ xpos = 115;
+ assertEquals(od.getBoxX(),
+ Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+ - boxWidth + 1);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
- // get cached setting for showConservation
- // reset it in AfterClass!
- showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
+ // click off end of alignment
+ // boxX and scrollCol adjusted for hidden cols, width normal
+ xpos = 3000;
+ assertEquals(od.getBoxX(),
+ Math.round((float) (firstHidden - 1) * od.getWidth() / alwidth)
+ - boxWidth + 1);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(),
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
}
- @AfterClass(alwaysRun = true)
- public void tearDown()
+ /**
+ * Test that the box position is set correctly when set from the viewport,
+ * with no hidden rows or columns
+ */
+ @Test(groups = { "Functional" })
+ public void testSetBoxFromViewport()
{
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
- Boolean.toString(showConservationSetting));
+ // move viewport to start of alignment
+ moveViewport(0, 0);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to right
+ moveViewportH(70);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 70 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport down
+ moveViewportV(100);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 70 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(),
+ Math.round(100 * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to bottom right
+ moveViewport(98, 508);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 98 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(),
+ Math.round((float) 508 * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
}
/**
- * Test that the OverviewDimensions constructor sets width and height
- * correctly
+ * Test that the box position is set correctly when there are hidden columns
+ * at the start
*/
@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);
- }
+ public void testSetBoxFromViewportHiddenColsAtStart()
+ {
+ int firstHidden = 0;
+ int lastHidden = 20;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
+
+ // move viewport to start of alignment
+ moveViewport(0, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) (lastHidden + 1) * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to end of alignment - need to make startRes by removing
+ // hidden cols because of how viewport/overview are implemented
+ moveViewport(98 - lastHidden - 1, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 98 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ }
/**
- * 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 that the box position is set correctly when there are hidden columns
+ * in the middle
*/
@Test(groups = { "Functional" })
- public void checkValidNoHidden()
+ public void testSetBoxFromViewportHiddenColsInMiddle()
{
- 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);
+ int firstHidden = 68;
+ int lastHidden = 78;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
- // Initial box sizing - default path through code
- OverviewDimensions od = new OverviewDimensions(av);
- od.setBoxPosition();
- od.checkValid();
- assertEquals(od.getBoxX(), 0);
+ // move viewport before hidden columns
+ moveViewport(3, 0);
+
+ assertEquals(od.getBoxX(),
+ Math.round((float) 3 * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
- assertEquals(od.getBoxWidth(), 399);
- assertEquals(od.getScrollCol(), 0);
- assertEquals(od.getScrollRow(), 0);
+ System.out.println(od.getBoxWidth());
+ assertEquals(od.getBoxWidth(), boxWidth);
+ System.out.println(od.getBoxWidth());
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to left of hidden columns with overlap
+ moveViewport(10, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 10 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(
+ od.getBoxWidth(),
+ boxWidth
+ + Math.round((float) (lastHidden - firstHidden + 1)
+ * od.getWidth() / alwidth));
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to straddle hidden columns
+ moveViewport(63, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 63 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(
+ od.getBoxWidth(),
+ boxWidth
+ + Math.round((lastHidden - firstHidden + 1)
+ * od.getWidth() / alwidth));
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to right of hidden columns, no overlap
+ moveViewport(80 - (lastHidden - firstHidden + 1), 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 80 * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
- // 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();
+ /**
+ * Test that the box position is set correctly when there are hidden columns
+ * at the end
+ */
+ @Test(groups = { "Functional" })
+ public void testSetBoxFromViewportHiddenColsAtEnd()
+ {
+ int firstHidden = 152;
+ int lastHidden = 164;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
+
+ // move viewport before hidden columns
+ moveViewport(3, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) 3 * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to hidden columns
+ // viewport can't actually extend into hidden cols,
+ // so move to the far right edge of the viewport
+ moveViewport(firstHidden - viewWidth, 0);
+ assertEquals(od.getBoxX(),
+ Math.round((float) (firstHidden - viewWidth)
+ * od.getWidth() / alwidth));
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ }
- // overly large boxX value reset to width-boxWidth
- od.setBoxX(100);
- od.checkValid();
- assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
+ /**
+ * Test that the box position is set correctly when there are hidden rows at
+ * the start
+ */
+ @Test(groups = { "Functional" })
+ public void testSetBoxFromViewportHiddenRowsAtStart()
+ {
+ int firstHidden = 0;
+ int lastHidden = 20;
+ hideSequences(firstHidden, lastHidden);
- // startRes non-zero
- av.setStartRes(50);
- OverviewDimensions od2 = new OverviewDimensions(av);
- od2.setBoxPosition();
- od2.checkValid();
- assertEquals(od2.getBoxX(), 61);
- assertEquals(od2.getScrollCol(), 49);
+ // move viewport to start of alignment:
+ // box moves to below hidden rows, height remains same
+ moveViewport(0, 0);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(),
+ Math.round((float) (lastHidden + 1) * od.getSequencesHeight()
+ / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to end of alignment
+ moveViewport(0, 525 - viewHeight - lastHidden - 1);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(
+ od.getBoxY(),
+ Math.round((float) (525 - viewHeight) * od.getSequencesHeight()
+ / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
}
/**
- * Test setting of the box position, when there are hidden cols at the start
- * of the alignment
+ * Test that the box position is set correctly when there are hidden rows in
+ * the middle
*/
@Test(groups = { "Functional" })
- public void testSetBoxPosWithHiddenColsAtStart()
+ public void testSetBoxFromViewportHiddenRowsInMiddle()
{
- 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();
+ int firstHidden = 200;
+ int lastHidden = 210;
+ hideSequences(firstHidden, lastHidden);
- // 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
+ // move viewport to start of alignment:
+ // box, height etc as in non-hidden case
+ moveViewport(0, 0);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to straddle hidden rows
+ moveViewport(0, 198);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
+ / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(
+ od.getBoxHeight(),
+ Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
+ * od.getSequencesHeight() / alheight));
}
+ /**
+ * Test that the box position is set correctly when there are hidden rows at
+ * the bottom
+ */
@Test(groups = { "Functional" })
- public void testSetBoxPosWithHiddenColsAtEnd()
+ public void testSetBoxFromViewportHiddenRowsAtEnd()
{
+ int firstHidden = 500;
+ int lastHidden = 524;
+ hideSequences(firstHidden, lastHidden);
+
+ // move viewport to start of alignment:
+ // box, height etc as in non-hidden case
+ moveViewport(0, 0);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // move viewport to end of alignment
+ // viewport sits above hidden rows and does not include them
+ moveViewport(0, firstHidden - viewHeight - 1);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(
+ od.getBoxY(),
+ Math.round((float) (firstHidden - viewHeight - 1)
+ * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
}
+ /**
+ * Test setting of the box position, when there are hidden rows at the start
+ * of the alignment
+ */
@Test(groups = { "Functional" })
- public void testSetBoxPosWithHiddenColsMiddle()
+ public void testFromMouseWithHiddenRowsAtStart()
{
- 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));
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
+
+ // hide rows at start and check updated box position is correct
+ // changes boxY but not boxheight
+ int lastHiddenRow = 30;
+ hideSequences(0, lastHiddenRow);
+
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(),
+ Math.round((float) (lastHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // click in hidden rows - same result
+ mouseClick(od, 0, 0);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(
+ od.getBoxY(),
+ Math.round((float) (lastHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // click below hidden rows
+ mouseClick(od, 0, 150);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 150);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
}
+ /**
+ * Test setting of the box position, when there are hidden rows at the middle
+ * of the alignment
+ */
@Test(groups = { "Functional" })
- public void testSetBoxPosWithHiddenRowsAtStart()
+ public void testFromMouseWithHiddenRowsInMiddle()
{
- 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();
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+
+ assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(), 0);
assertEquals(od.getScrollRow(), 0);
+
+ // hide rows in middle and check updated box position is correct
+ // no changes
+ int firstHiddenRow = 50;
+ int lastHiddenRow = 54;
+ hideSequences(firstHiddenRow, lastHiddenRow);
+
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // click above hidden rows, so that box overlaps
+ int ypos = 35; // column value in residues
+ mouseClick(od, 0,
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(),
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(
+ od.getBoxHeight(),
+ boxHeight
+ + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
+
+ // click so that box straddles hidden rows
+ ypos = 44; // column value in residues
+ mouseClick(od, 0,
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(),
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(
+ od.getBoxHeight(),
+ boxHeight
+ + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
}
- /**
- * Test that the box position is set correctly
- */
+ /**
+ * Test setting of the box position, when there are hidden rows at the end of
+ * the alignment
+ */
@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);
+ public void testFromMouseWithHiddenRowsAtEnd()
+ {
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ assertEquals(od.getScrollCol(), 0);
+ assertEquals(od.getScrollRow(), 0);
+
+ // hide rows at end and check updated box position is correct
+ // no changes
+ int firstHidden = 500;
+ int lastHidden = 524;
+ hideSequences(firstHidden, lastHidden);
+
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(), 0);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // click above hidden rows
+ int ypos = 40; // row 40
+ mouseClick(od, 0,
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(od.getBoxY(),
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // click above hidden rows so box overlaps
+ // boxY moved upwards, boxHeight remains same
+ ypos = 497; // row 497
+ mouseClick(od, 0,
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(
+ od.getBoxY(),
+ Math.round((float) (firstHidden - viewHeight)
+ * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ // click within hidden rows
+ ypos = 505;
+ mouseClick(od, 0,
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
+ assertEquals(od.getBoxX(), 0);
+ assertEquals(
+ od.getBoxY(),
+ Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
+ / alheight));
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+ }
+
+ /*
+ * Move viewport horizontally: startRes + previous width gives new horizontal extent. Vertical extent stays the same.
+ */
+ private void moveViewportH(int startRes)
+ {
+ posProps.setStartRes(startRes);
+ posProps.setEndRes(startRes + viewWidth - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ }
+
+ /*
+ * Move viewport vertically: startSeq and endSeq give new vertical extent. Horizontal extent stays the same.
+ */
+ private void moveViewportV(int startSeq)
+ {
+ posProps.setStartSeq(startSeq);
+ posProps.setEndSeq(startSeq + viewHeight - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ }
+
+ /*
+ * Move viewport horizontally and vertically.
+ */
+ private void moveViewport(int startRes, int startSeq)
+ {
+ posProps.setStartRes(startRes);
+ posProps.setEndRes(startRes + viewWidth - 1);
+ posProps.setStartSeq(startSeq);
+ posProps.setEndSeq(startSeq + viewHeight - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ }
+
+ /*
+ * Mouse click as position x,y in overview window
+ */
+ private void mouseClick(OverviewDimensions od, int x, int y)
+ {
+ od.updateViewportFromMouse(x, y, al.getHiddenSequences(), hiddenCols,
+ posProps);
+
+ // updates require an OverviewPanel to exist which it doesn't here
+ // so call setBoxPosition() as it would be called by the AlignmentPanel
+ // normally
+
+ posProps.setStartRes(od.getScrollCol());
+ posProps.setEndRes(od.getScrollCol() + viewWidth - 1);
+ posProps.setStartSeq(od.getScrollRow());
+ posProps.setEndSeq(od.getScrollRow() + viewHeight - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
+ }
+
+ /*
+ * Test that the box is positioned with the top left corner at xpos, ypos
+ * and with the original width and height
+ */
+ private void testBoxIsAtClickPoint(int xpos, int ypos)
+ {
+ mouseClick(od, xpos, ypos);
+ assertEquals(od.getBoxX(), xpos);
+ assertEquals(od.getBoxY(), ypos);
+ assertEquals(od.getBoxWidth(), boxWidth);
+ assertEquals(od.getBoxHeight(), boxHeight);
+
+ }
+
+ /*
+ * Hide sequences between start and end
+ */
+ private void hideSequences(int start, int end)
+ {
+ SequenceI[] allseqs = al.getSequencesArray();
+ SequenceGroup theseSeqs = new SequenceGroup();
+
+ for (int i = start; i <= end; i++)
+ {
+ theseSeqs.addSequence(allseqs[i], false);
+ al.getHiddenSequences().hideSequence(allseqs[i]);
+ }
+
+ hiddenRepSequences.put(allseqs[start], theseSeqs);
}
}
git://source.jalview.org / jalview.git / blobdiff