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.AlignFrame;
-import jalview.gui.AlignViewport;
-import jalview.gui.Desktop;
-import jalview.gui.JvOptionPane;
-import jalview.io.DataSourceType;
-import jalview.io.FileLoader;
-import java.util.List;
+import java.util.Hashtable;
-import org.testng.annotations.AfterMethod;
+import org.testng.annotations.AfterClass;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@Test(singleThreaded = true)
-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");
-
- AlignFrame af;
- AlignViewport av;
+public class OverviewDimensionsTest
+{
+ AlignmentI al;
OverviewDimensions od;
- float scalew;
- float scaleh;
+ // cached widths and heights
int boxWidth;
int boxHeight;
-
int viewHeight;
-
int viewWidth;
-
int alheight;
-
int alwidth;
+ ViewportPositionProps posProps;
+
+ Hashtable<SequenceI, SequenceCollectionI> hiddenRepSequences = new Hashtable<SequenceI, SequenceCollectionI>();
+
+ ColumnSelection hiddenCols = new ColumnSelection();
+
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
- JvOptionPane.setInteractiveMode(false);
- JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
+ // create random alignment
+ AlignmentGenerator gen = new AlignmentGenerator(false);
+ al = gen.generate(157, 525, 123, 5, 5);
}
@BeforeMethod(alwaysRun = true)
public void setUp()
{
- Jalview.main(new String[] { "-nonews", "-props",
- "test/jalview/testProps.jvprops" });
-
- Cache.applicationProperties.setProperty("SHOW_IDENTITY",
- Boolean.TRUE.toString());
- af = new FileLoader().LoadFileWaitTillLoaded(
- "examples/testdata/bigal.fa",
- DataSourceType.FILE);
-
- /*
- * Wait for viewport to initialise
- */
- synchronized (this)
+ if (!hiddenRepSequences.isEmpty())
{
- while (af.getViewport().getEndRes() == 0)
- {
- try
- {
- wait(50);
- } catch (InterruptedException e)
- {
- }
- }
+ al.getHiddenSequences().showAll(hiddenRepSequences);
}
-
- /*
- * wait for Consensus thread to complete
- */
- synchronized (this)
- {
- while (af.getViewport().getConsensusSeq() == null)
- {
- try
- {
- wait(50);
- } catch (InterruptedException e)
- {
- }
- }
- }
-
- // get cached setting for showConservation
- // reset it in AfterClass!
- showConservationSetting = Cache.getDefault("SHOW_CONSERVATION", true);
+ hiddenCols.revealAllHiddenColumns();
- av = af.getViewport();
-
- od = new OverviewDimensions(av);
+ posProps = new ViewportPositionProps(al);
+ posProps.setStartRes(0);
+ posProps.setEndRes(62);
+ posProps.setStartSeq(0);
+ posProps.setEndSeq(17);
- while (av.isCalcInProgress())
- {
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
+ 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();
-
- init();
- }
-
- private void init()
- {
- av.showAllHiddenColumns();
- av.showAllHiddenSeqs();
- av.setSelectionGroup(null);
- // o/w hidden seqs retain selection group, causes problems later when hiding
- // sequences
-
- // wait for conservation calc to complete
- while (av.isCalcInProgress())
- {
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
-
- }
- }
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
mouseClick(od, 0, 0);
moveViewport(0, 0);
- viewHeight = av.getEndSeq() - av.getStartSeq();
- viewWidth = av.getEndRes() - av.getStartRes();
-
- // wait for gui to get set up
- while (viewHeight != 17 || viewWidth != 59)
- {
- try
- {
- Thread.sleep(50);
- viewHeight = av.getEndSeq() - av.getStartSeq();
- viewWidth = av.getEndRes() - av.getStartRes();
- } catch (InterruptedException e)
- {
-
- }
- }
-
// calculate before hidden columns so we get absolute values
- alheight = av.getAlignment().getHeight();
- alwidth = av.getAlignment().getWidth();
-
- boxWidth = Math.round((float) (av.getEndRes() - av.getStartRes() + 1)
- / alwidth * od.getWidth());
- boxHeight = Math.round((float) (av.getEndSeq() - av.getStartSeq())
- / alheight * od.getHeight());
- System.out.println(boxHeight);
-
+ alheight = posProps.getAbsoluteAlignmentHeight();
+ alwidth = posProps.getAbsoluteAlignmentWidth();
+
+ boxWidth = Math.round((float) (posProps.getEndRes()
+ - posProps.getStartRes() + 1)
+ * od.getWidth() / alwidth);
+ boxHeight = Math.round((float) (posProps.getEndSeq()
+ - posProps.getStartSeq() + 1)
+ * od.getSequencesHeight() / alheight);
}
- @AfterMethod(alwaysRun = true)
- public void tearDown()
+ @AfterClass(alwaysRun = true)
+ public void cleanUp()
{
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
- Boolean.toString(showConservationSetting));
- Desktop.instance.closeAll_actionPerformed(null);
+ al = null;
}
/**
int maxSeqHeight = 300;
int minSeqHeight = 40;
- 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);
+ ViewportPositionProps props = new ViewportPositionProps(al1);
- OverviewDimensions od = new OverviewDimensions(av1);
- int scaledHeight = 266;
+ OverviewDimensions od = new OverviewDimensions(props, true);
+ int scaledHeight = 267;
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), scaledHeight);
assertEquals(od.getWidth(), maxWidth);
// 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);
+ props = new ViewportPositionProps(al2);
- od = new OverviewDimensions(av2);
+ od = new OverviewDimensions(props, true);
int scaledWidth = 300;
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), maxSeqHeight);
// min value
SequenceI[] seqs3 = new SequenceI[] { seqe };
Alignment al3 = new Alignment(seqs3);
- al3.setDataset(null);
- AlignViewport av3 = new AlignViewport(al3);
+ props = new ViewportPositionProps(al3);
- od = new OverviewDimensions(av3);
+ od = new OverviewDimensions(props, true);
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), minSeqHeight);
assertEquals(od.getWidth(), maxWidth);
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);
+ props = new ViewportPositionProps(al4);
- od = new OverviewDimensions(av4);
+ od = new OverviewDimensions(props, true);
assertEquals(od.getGraphHeight(), defaultGraphHeight);
assertEquals(od.getSequencesHeight(), maxSeqHeight);
assertEquals(od.getWidth(), minWidth);
assertEquals(od.getHeight(), maxSeqHeight + defaultGraphHeight);
- // 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);
+ props = new ViewportPositionProps(al5);
- od = new OverviewDimensions(av5);
+ od = new OverviewDimensions(props, false);
assertEquals(od.getGraphHeight(), 0);
assertEquals(od.getSequencesHeight(), maxSeqHeight);
assertEquals(od.getWidth(), minWidth);
* 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.
- *
- * The current implementation uses multiple transformations between coordinate
- * systems which often involve casting to int, which causes values to be
- * truncated. As a result we can lose accuracy. The tests below use
- * approximate test values where appropriate.
*/
@Test(groups = { "Functional" })
public void testSetBoxFromMouseClick()
{
- od.setBoxPositionByMouse(0, 0);
+ 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(),
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()));
+ / od.getSequencesHeight()) - 1);
// click past end of alignment, as above
mouseClick(od, 3000, 5);
@Test(groups = { "Functional" })
public void testFromMouseWithHiddenColsAtStart()
{
- od.setBoxPositionByMouse(0, 0);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
// hide cols at start and check updated box position is correct
// changes boxX but not boxwidth
int lastHiddenCol = 30;
- hideColumns(0, lastHiddenCol);
+ hiddenCols.hideColumns(0, lastHiddenCol);
- od.setBoxPosition();
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
assertEquals(od.getBoxX(),
Math.round((float) (lastHiddenCol + 1) * od.getWidth()
/ alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
// try to click in hidden cols, check box does not move
- // this test currently fails as the overview box does not behave like this!
- /* int xpos = 10;
- mouseClick(od, xpos, 0);
- assertEquals(od.getBoxX(),
- Math.round ((lastHiddenCol + 1) * od.getWidth() / alwidth));
- assertEquals(od.getBoxY(), 0);
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(od.getScrollRow(), 0);
- assertEquals(od.getScrollCol(),
- Math.round (xpos * alwidth / od.getWidth()));
- */
+ 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);
+
// click to right of hidden columns, box moves to click point
testBoxIsAtClickPoint(40, 0);
assertEquals(od.getScrollRow(), 0);
// of alignment
// box position is adjusted away from the edge
// overly large boxX value reset to width-boxWidth
- int xpos = 100;
+ xpos = 100;
mouseClick(od, xpos, 5);
assertEquals(od.getBoxX(), od.getWidth() - od.getBoxWidth());
assertEquals(od.getBoxY(), 5);
@Test(groups = { "Functional" })
public void testFromMouseWithHiddenColsInMiddle()
{
- od.setBoxPositionByMouse(0, 0);
+ 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 60-68, no change to box position or dimensions
- int firstHidden = 60;
- int lastHidden = 68;
- hideColumns(firstHidden, lastHidden);
+ // hide columns 63-73, no change to box position or dimensions
+ int firstHidden = 63;
+ int lastHidden = 73;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
- od.setBoxPosition();
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
// move box so that it overlaps with hidden cols on one side
// box width changes, boxX and scrollCol as for unhidden case
- int xpos = 50 - boxWidth; // 50 is position in overview halfway between cols
- // 60 and 70
+ 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);
// move box so that it completely covers hidden cols
// box width changes, boxX and scrollCol as for hidden case
- xpos = 30;
+ xpos = 33;
mouseClick(od, xpos, 0);
assertEquals(od.getBoxX(), xpos);
assertEquals(od.getBoxY(), 0);
* od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
assertEquals(od.getScrollCol(),
- Math.round(xpos * alwidth / od.getWidth()));
+ Math.round((float) xpos * alwidth / od.getWidth()));
assertEquals(od.getScrollRow(), 0);
// move box so boxX is in hidden cols, box overhangs at right
- // box width back to normal, boxX and scrollCol move to right of hidden area
- // TODO currently this test fails in the Jalview GUI, there is a gap between
- // the rhs of the hidden area and the box
- /* xpos = 50;
- mouseClick(od, xpos, 0);
- assertEquals(od.getBoxX(),
- (lastHidden + 1) * scalew * av.getCharWidth());
- assertEquals(od.getBoxY(), 0);
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(od.getScrollCol(),
- Math.round(xpos * alwidth / od.getWidth()));
- assertEquals(od.getScrollRow(), 0);*/
+ // 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);
// 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
- // TODO currently this test fails in the Jalview GUI because boxX is
- // calculated
- // based on the current boxWidth, which includes hidden columns, thereby
- // pushing
- // the box off the end of the alignment. So boxX is adjusted backwards
- // unnecessarily.
- /* xpos = 72;
- testBoxIsAtClickPoint(xpos, 0);
- assertEquals(od.getScrollRow(), 0);
- assertEquals(od.getScrollCol(),
- Math.round(xpos * alwidth / od.getWidth())
- - lastHidden);*/
+ 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
@Test(groups = { "Functional" })
public void testFromMouseWithHiddenColsAtEnd()
{
- od.setBoxPositionByMouse(0, 0);
+ 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 140-157, no change to box position or dimensions
+ // hide columns 140-164, no change to box position or dimensions
int firstHidden = 140;
- int lastHidden = 157;
- hideColumns(firstHidden, lastHidden);
- od.setBoxPosition();
+ 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);
// click to left of hidden cols, with overlap
// boxX and scrollCol adjusted for hidden cols, width normal
- // TODO this fails because setBoxPosition screws up the hidden cols calc
- // only works in GUI because of AlignmentPanel::setScrollValues
- /*xpos = 115 - boxWidth;
+ xpos = Math.round((float) 145 * od.getWidth() / alwidth) - boxWidth;
mouseClick(od, xpos, 0);
- assertEquals(
- od.getBoxX(),
- Math.round((firstHidden - 1) * scalew * av.getCharWidth())
- - od.getBoxWidth());
+ 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(od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(od.getScrollRow(), 0);*/
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
// click in hidden cols
// boxX and scrollCol adjusted for hidden cols, width normal
- // TODO breaks as above test
- /*xpos = 115;
- assertEquals(
- od.getBoxX(),
- Math.round((firstHidden - 1) * scalew * av.getCharWidth())
- - od.getBoxWidth());
+ 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(od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(od.getScrollRow(), 0);*/
+ Math.round((float) od.getBoxX() * alwidth / od.getWidth()));
+ assertEquals(od.getScrollRow(), 0);
// click off end of alignment
// boxX and scrollCol adjusted for hidden cols, width normal
- // TODO breaks as above test
- /* xpos = 3000;
- assertEquals(
- od.getBoxX(),
- Math.round((firstHidden - 1) * scalew * av.getCharWidth())
- - od.getBoxWidth());
- assertEquals(od.getBoxY(), 0);
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight);
- assertEquals(od.getScrollCol(),
- Math.round(od.getBoxX() * alwidth / od.getWidth()));
- assertEquals(od.getScrollRow(), 0);*/
+ 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);
}
/**
{
int firstHidden = 0;
int lastHidden = 20;
- hideColumns(firstHidden, lastHidden);
+ hiddenCols.hideColumns(firstHidden, lastHidden);
// move viewport to start of alignment
moveViewport(0, 0);
@Test(groups = { "Functional" })
public void testSetBoxFromViewportHiddenColsInMiddle()
{
- int firstHidden = 65;
- int lastHidden = 75;
- hideColumns(firstHidden, lastHidden);
+ int firstHidden = 68;
+ int lastHidden = 78;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
// move viewport before hidden columns
moveViewport(3, 0);
assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to straddle hidden columns
- moveViewport(60, 0);
+ moveViewport(63, 0);
assertEquals(od.getBoxX(),
- Math.round((float) 60 * od.getWidth() / alwidth));
+ Math.round((float) 63 * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
assertEquals(
od.getBoxWidth(),
@Test(groups = { "Functional" })
public void testSetBoxFromViewportHiddenColsAtEnd()
{
- int firstHidden = 145;
- int lastHidden = 157;
- hideColumns(firstHidden, lastHidden);
+ int firstHidden = 152;
+ int lastHidden = 164;
+ hiddenCols.hideColumns(firstHidden, lastHidden);
// move viewport before hidden columns
moveViewport(3, 0);
assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to hidden columns
- // TODO boxwidth includes hidden in overview panel (why?)
- moveViewport(98, 0);
+ moveViewport(102, 0);
assertEquals(od.getBoxX(),
- Math.round((float) 98 * od.getWidth() / alwidth));
+ Math.round((float) 102 * od.getWidth() / alwidth));
assertEquals(od.getBoxY(), 0);
- assertEquals(
- od.getBoxWidth(),
- boxWidth
+ assertEquals(od.getBoxWidth(), boxWidth
+ Math.round((float) (lastHidden - firstHidden + 1)
* od.getWidth() / alwidth));
assertEquals(od.getBoxHeight(), boxHeight);
{
int firstHidden = 0;
int lastHidden = 20;
- hideSequences(firstHidden, lastHidden + 1, lastHidden + 1);
+ hideSequences(firstHidden, lastHidden);
// move viewport to start of alignment:
// box moves to below hidden rows, height remains same
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- // move viewport to end of alignment, need to account for hidden rows
- // because of how alignment panel/overview panel are implemented
-
- // AlignViewport adjusts endSeq using Alignment height which excludes hidden
- // rows if we happen to be at the bottom of the alignment
- // od.setBoxPosition adjusts endSeq to include hidden rows
- // od.checkValid adjusts scroll position to exclude hidden rows
- // TODO this test fails because of the above!
-
- /* moveViewport(0, 525 - viewHeight - lastHidden - 1);
- assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- (525 - viewHeight) * scaleh
- * av.getCharHeight());
- 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);
}
/**
{
int firstHidden = 200;
int lastHidden = 210;
- hideSequences(firstHidden, lastHidden + 1, lastHidden + 1);
+ hideSequences(firstHidden, lastHidden);
// move viewport to start of alignment:
// box, height etc as in non-hidden case
- // TODO fails with boxy=12 because that's what setBoxPosition sets it to!
- /*moveViewport(0, 0);
+ moveViewport(0, 0);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight);*/
+ assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to straddle hidden rows
- // TODO also fails with boxY out by 12
- /*moveViewport(0, 198);
+ moveViewport(0, 198);
assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(), Math.round (198 * scaleh * av.getCharHeight()),
- 1.5);
+ assertEquals(od.getBoxY(), Math.round ((float)198 * od.getSequencesHeight()
+ / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight
- + ((lastHidden - firstHidden) * scaleh * av.getCharHeight()),
- 1.5);*/
+ assertEquals(
+ od.getBoxHeight(),
+ Math.round((float) (viewHeight + lastHidden - firstHidden + 1)
+ * od.getSequencesHeight() / alheight));
}
/**
{
int firstHidden = 500;
int lastHidden = 524;
- hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);
+ hideSequences(firstHidden, lastHidden);
// move viewport to start of alignment:
// box, height etc as in non-hidden case
assertEquals(od.getBoxHeight(), boxHeight);
// move viewport to end of alignment
- // TODO fails with wrong boxHeight who knows why
- /*moveViewport(0, firstHidden - viewHeight - 1);
- assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(),
- Math.round ((firstHidden - viewHeight - 1)
- * scaleh * av.getCharHeight()));
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(
- od.getBoxHeight(),
- boxHeight
- + Math.round ((lastHidden - firstHidden + 1) * scaleh * av
- .getCharHeight()));*/
+ // 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(groups = { "Functional" })
public void testFromMouseWithHiddenRowsAtStart()
{
- od.setBoxPositionByMouse(0, 0);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxHeight(), boxHeight);
// hide rows at start and check updated box position is correct
// changes boxY but not boxheight
int lastHiddenRow = 30;
- hideSequences(0, lastHiddenRow + 1, lastHiddenRow + 1);
+ hideSequences(0, lastHiddenRow);
- od.setBoxPosition();
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(),
Math.round((float) (lastHiddenRow + 1)
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(od.getBoxHeight(), boxHeight);
- // click in hidden rows
- // TODO fails because boxHeight is 27 not 25 (possible rounding issue)
- /* mouseClick(od, 0, 0);
- assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(), 0);
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight
- + Math.round ((lastHiddenRow + 1) * scaleh * av.getCharHeight()),
- 1.5);*/
+ // 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);
@Test(groups = { "Functional" })
public void testFromMouseWithHiddenRowsInMiddle()
{
- od.setBoxPositionByMouse(0, 0);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
// hide rows in middle and check updated box position is correct
// no changes
int firstHiddenRow = 50;
- int lastHiddenRow = 60;
- hideSequences(firstHiddenRow, lastHiddenRow + 1, lastHiddenRow + 1);
+ int lastHiddenRow = 54;
+ hideSequences(firstHiddenRow, lastHiddenRow);
- od.setBoxPosition();
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxHeight(), boxHeight);
// click above hidden rows, so that box overlaps
- int ypos = 40;
- // TODO test fails because box does not change height - dealt with by scroll
- // values
- /* mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
- assertEquals(od.getBoxX(), 0);
- assertEquals(od.getBoxY(), Math.round (ypos * alheight / od.getSequencesHeight()),
- 1.5);
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(
- od.getBoxHeight(),
- boxHeight
- + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
- .getCharHeight()));
- */
+ 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 = 48;
- // TODO test fails because box does not change height - dealt with by scroll
- // values
- /*mouseClick(od, 0, Math.round (ypos * alheight / od.getSequencesHeight()));
+ 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 (ypos * alheight / od.getSequencesHeight()),
- 1.5);
+ assertEquals(od.getBoxY(),
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
assertEquals(
od.getBoxHeight(),
boxHeight
- + Math.round ((lastHiddenRow - firstHiddenRow + 1) / scaleh / av
- .getCharHeight()));*/
+ + Math.round((float) (lastHiddenRow - firstHiddenRow + 1)
+ * od.getSequencesHeight() / alheight));
}
/**
@Test(groups = { "Functional" })
public void testFromMouseWithHiddenRowsAtEnd()
{
- od.setBoxPositionByMouse(0, 0);
+ od.updateViewportFromMouse(0, 0, al.getHiddenSequences(), hiddenCols,
+ posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
// no changes
int firstHidden = 500;
int lastHidden = 524;
- hideSequences(firstHidden - 1, lastHidden, firstHidden - 1);
+ hideSequences(firstHidden, lastHidden);
- od.setBoxPosition();
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
assertEquals(od.getBoxX(), 0);
assertEquals(od.getBoxY(), 0);
assertEquals(od.getBoxWidth(), boxWidth);
// click above hidden rows so box overlaps
// boxY moved upwards, boxHeight remains same
- // TODO fails with boxY located at row 497 - correction done by
- // setScrollValues
- /* ypos = 497; // row 497
- mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
- assertEquals(od.getBoxX(), 0);
- assertEquals(
- od.getBoxY(),
- Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
- 1.5);
- assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight);*/
+ 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;
- // TODO: fails with wrong boxHeight - correction done by setScrollValues(?)
- /*mouseClick(od, 0, Math.round (ypos * scaleh * av.getCharHeight()));
+ mouseClick(od, 0,
+ Math.round((float) ypos * od.getSequencesHeight() / alheight));
assertEquals(od.getBoxX(), 0);
assertEquals(
od.getBoxY(),
- Math.round ((firstHidden - viewHeight) * scaleh * av.getCharHeight()),
- 1.5);
+ Math.round((firstHidden - viewHeight) * od.getSequencesHeight()
+ / alheight));
assertEquals(od.getBoxWidth(), boxWidth);
- assertEquals(od.getBoxHeight(), boxHeight);*/
+ assertEquals(od.getBoxHeight(), boxHeight);
}
/*
*/
private void moveViewportH(int startRes)
{
- av.setStartRes(startRes);
- av.setEndRes(startRes + viewWidth);
- od.setBoxPosition();
+ posProps.setStartRes(startRes);
+ posProps.setEndRes(startRes + viewWidth - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
}
/*
*/
private void moveViewportV(int startSeq)
{
- av.setStartSeq(startSeq);
- av.setEndSeq(startSeq + viewHeight);
- od.setBoxPosition();
+ posProps.setStartSeq(startSeq);
+ posProps.setEndSeq(startSeq + viewHeight - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
}
/*
*/
private void moveViewport(int startRes, int startSeq)
{
- av.setStartRes(startRes);
- av.setEndRes(startRes + viewWidth);
- av.setStartSeq(startSeq);
- av.setEndSeq(startSeq + viewHeight);
- od.setBoxPosition();
+ posProps.setStartRes(startRes);
+ posProps.setEndRes(startRes + viewWidth - 1);
+ posProps.setStartSeq(startSeq);
+ posProps.setEndSeq(startSeq + viewHeight - 1);
+ od.setBoxPosition(al.getHiddenSequences(), hiddenCols, posProps);
}
/*
*/
private void mouseClick(OverviewDimensions od, int x, int y)
{
- od.setBoxPositionByMouse(x, 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
- // int width = av.getEndRes() - av.getStartRes();
- // int height = av.getEndSeq() - av.getStartSeq();
- av.setStartRes(od.getScrollCol());
- av.setEndRes(od.getScrollCol() + viewWidth);
- av.setStartSeq(od.getScrollRow());
- av.setEndSeq(od.getScrollRow() + viewHeight);
- od.setBoxPosition();
+
+ 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);
}
/*
- * Hide sequences between start and end, using hideseq to do the hiding
- * (start <= hideseq <= end. Sequence hideseq is not hidden but the others are
+ * Hide sequences between start and end
*/
- private void hideSequences(int start, int end, int hideseq)
+ private void hideSequences(int start, int end)
{
- SequenceGroup sg = new SequenceGroup();
- List<SequenceI> allseqs = av.getAlignment().getSequences();
- for (int i = start; i <= end; ++i)
- {
- sg.addSequence(allseqs.get(i), false);
- }
- av.setSelectionGroup(sg);
-
- /*
- * hide group
- */
- av.hideSequences(allseqs.get(hideseq), true);
-
- while (av.isCalcInProgress())
+ SequenceI[] allseqs = al.getSequencesArray();
+ SequenceGroup theseSeqs = new SequenceGroup();
+
+ for (int i = start; i <= end; i++)
{
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
- System.out.println("Hiding seqs interruption");
- }
+ theseSeqs.addSequence(allseqs[i], false);
+ al.getHiddenSequences().hideSequence(allseqs[i]);
}
- }
- private void hideColumns(int firstHidden, int lastHidden)
- {
- av.hideColumns(firstHidden, lastHidden);
-
- while (av.isCalcInProgress())
- {
- try
- {
- Thread.sleep(50);
- } catch (InterruptedException e)
- {
- System.out.println("Hiding cols interruption");
- }
- }
+ hiddenRepSequences.put(allseqs[start], theseSeqs);
}
}
git://source.jalview.org / jalview.git / blobdiff