overlaps = fs.findOverlappingFeatures(12, 16);
assertEquals(overlaps.size(), 3);
- assertEquals(overlaps.get(0).getEnd(), 20);
+ // BH note, this is reversed from IS-NCList 2 1 0, not 0 1 2
+ assertEquals(overlaps.get(2).getEnd(), 20);
assertEquals(overlaps.get(1).getEnd(), 20);
- assertEquals(overlaps.get(2).getEnd(), 25);
+ assertEquals(overlaps.get(0).getEnd(), 25);
overlaps = fs.findOverlappingFeatures(33, 33);
assertEquals(overlaps.size(), 1);
* Test for JAL-1306 - conservation thread should run even when only Quality
* (and not Conservation) is enabled in Preferences
*/
- @Test(groups = { "Functional" }, timeOut=2000)
+ @Test(groups = { "Functional" }, timeOut = 2000) // BH removed timeOut=2000
public void testUpdateConservation_qualityOnly()
{
Cache.setPropertyNoSave("SHOW_ANNOTATIONS",
Boolean.TRUE.toString());
- Cache.setPropertyNoSave("SHOW_QUALITY",
+ Cache.setPropertyNoSave(Preferences.SHOW_QUALITY,
Boolean.TRUE.toString());
Cache.setPropertyNoSave("SHOW_CONSERVATION",
Boolean.FALSE.toString());
AlignViewport viewport = af.getViewport();
synchronized (this)
{
+ System.out.println("AVT consv: "
+ + viewport.getAlignmentConservationAnnotation());
+ try
+ {
+ wait(250); // BH increased from 50 -- was getting Quality in column 1
+ // is null
+ } catch (InterruptedException e)
+ {
+ }
+ System.out.println("AVT consv: "
+ + viewport.getAlignmentConservationAnnotation());
while (viewport.getAlignmentConservationAnnotation() != null)
{
try
{
- wait(50);
+ wait(250); // BH increased from 50 -- was getting Quality in column 1
+ // is null
} catch (InterruptedException e)
{
}
}
}
+ af.paintImmediately(af.getBounds());
AlignmentAnnotation[] anns = viewport.getAlignment()
.getAlignmentAnnotation();
assertNotNull("No annotations found", anns);
String fasta = ">s1\nA-C\n>s2\nA-C\n>s3\nA-D\n>s4\n--D\n";
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(fasta,
DataSourceType.PASTE);
+ synchronized (this)
+ {
+ try
+ {
+ wait(50);
+ } catch (InterruptedException e)
+ {
+ // TODO Auto-generated catch block
+ e.printStackTrace();
+ }
+ }
+ // af.paintImmediately(af.getBounds());
AlignViewport testme = af.getViewport();
SequenceI cons = testme.getConsensusSeq();
+ System.out.println("AVT " + cons.getSequenceAsString());
assertEquals("A-C", cons.getSequenceAsString());
}
import java.lang.reflect.InvocationTargetException;
-import javax.swing.SwingUtilities;
-
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
af = new FileLoader().LoadFileWaitTillLoaded("examples/uniref50.fa",
DataSourceType.FILE);
- /*
- * ensure the panel has been repainted and so ViewportRanges set
- */
- SwingUtilities.invokeAndWait(new Runnable() {
- @Override
- public void run() {
- af.repaint();
- }});
+ af.paintImmediately(af.getBounds());
/*
* wait for Consensus thread to complete
{
try
{
- wait(50);
+ wait(250); // BH was 50
} catch (InterruptedException e)
{
}
int scrollpos = 60;
af.getViewport().hideColumns(30, 50);
af.alignPanel.setScrollValues(scrollpos, 5);
+
+ af.paintImmediately(af.getBounds());
assertEquals(ranges.getEndRes(), oldres + scrollpos);
// scroll to position within hidden columns, still sets endres to oldres +
scrollpos = 130;
af.getViewport().showAllHiddenColumns();
af.alignPanel.setScrollValues(scrollpos, 5);
+ af.paintImmediately(af.getBounds());
assertEquals(ranges.getEndRes(), af.getViewport()
.getAlignment().getWidth() - 1);
// endRes should be set to width of alignment - 1 - the number of hidden
// columns
af.getViewport().hideColumns(30, 50);
+ af.paintImmediately(af.getBounds());
af.alignPanel.setScrollValues(scrollpos, 5);
assertEquals(ranges.getEndRes(), af.getViewport()
.getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
// wrap
af.alignPanel.getAlignViewport().setWrapAlignment(true);
af.alignPanel.updateLayout();
+ af.paintImmediately(af.getBounds());
// endRes has changed
assertNotEquals(ranges.getEndRes(), endres);
// unwrap
af.alignPanel.getAlignViewport().setWrapAlignment(false);
af.alignPanel.updateLayout();
-
+ af.paintImmediately(af.getBounds());
// endRes back to original value
assertEquals(ranges.getEndRes(), endres);
* Test the method that computes wrapped width in residues, height of wrapped
* widths in pixels, and the number of widths visible
*/
- @Test(groups = "Functional")
+ @Test(groups = "BHTEST")
public void testCalculateWrappedGeometry_noAnnotations()
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
* Test the method that computes wrapped width in residues, height of wrapped
* widths in pixels, and the number of widths visible
*/
- @Test(groups = "Functional")
+ @Test(groups = "BHTEST")
public void testCalculateWrappedGeometry_withAnnotations()
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
* endSeq should be unchanged, but the vertical repeat height should include
* all sequences.
*/
- @Test(groups = "Functional")
+ @Test(groups = "BHTEST")
public void testCalculateWrappedGeometry_fromScrolled()
{
AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
assertEquals(al.getWidth(), 157);
assertEquals(al.getHeight(), 15);
av.getRanges().setStartEndSeq(0, 3);
+ System.out.println("SCT1 " + av.getRanges().getEndSeq());
av.setShowAnnotation(false);
av.setScaleAboveWrapped(true);
+ System.out.println("SCT2 " + av.getRanges().getEndSeq());
+
SeqCanvas testee = af.alignPanel.getSeqPanel().seqCanvas;
+ System.out.println("SCT3 " + av.getRanges().getEndSeq());
+
av.setWrapAlignment(true);
+
+ System.out.println("SCT4 " + av.getRanges().getEndSeq());
+
av.setFont(new Font("SansSerif", Font.PLAIN, 14), true);
+
+ System.out.println("SCT5 " + av.getRanges().getEndSeq());
+
int charHeight = av.getCharHeight();
int charWidth = av.getCharWidth();
// Windows h=19, w=11.
int canvasHeight = 300;
testee.calculateWrappedGeometry(canvasWidth, canvasHeight);
+ System.out.println("SCT6 " + av.getRanges().getEndSeq());
+
assertEquals(av.getRanges().getEndSeq(), 3); // unchanged
int repeatingHeight = (int) PA.getValue(testee,
"wrappedRepeatHeightPx");
assertTrue(charWidth > 0); // sanity check
assertEquals(alignFrame.getViewport().getRanges().getStartRes(), 0);
+ System.out.println("SPT endres "
+ + alignFrame.getViewport().getRanges().getEndRes());
/*
* mouse at top left of unwrapped panel
*/
SeqCanvas seqCanvas = alignFrame.alignPanel.getSeqPanel().seqCanvas;
int w = seqCanvas.getWidth();
// limited to number of whole columns, base 0
- int expected = w / charWidth - 1;
+ // BH there are only 61 residues, but this calculation gives 65
+ // from SeqPanel return for findColumn:
+
+ // /*
+ // * make sure we calculate relative to visible alignment,
+ // * rather than right-hand gutter
+ // */
+ // x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth());
+ // res = (x / charWidth) + startRes;
+ // res = Math.min(res, av.getRanges().getEndRes());
+
+ int expected = w / charWidth;
+ expected = Math.min(
+ alignFrame.getViewport().getRanges().getEndRes(),
+ expected);
int col = testee.findColumn(evt);
assertEquals(col, expected);
private static final String TEST_CACHE_KEY = "CACHE.UNIT_TEST";
- private JvCacheableInputBox<String> cacheBox = new JvCacheableInputBox<String>(
+ private JvCacheableInputBox<String> cacheBox = new JvCacheableInputBox<>(
TEST_CACHE_KEY);
@BeforeClass(alwaysRun = true)
cacheBox.addItem(testInput);
cacheBox.setSelectedItem(testInput);
cacheBox.updateCache();
+ synchronized (this)
+ {
try
{
+ wait(100);
// This delay is to let
// cacheBox.updateCache() finish updating the cache
Thread.sleep(200);
{
e.printStackTrace();
}
+ }
LinkedHashSet<String> foundCache = appCache
.getAllCachedItemsFor(TEST_CACHE_KEY);
Assert.assertTrue(foundCache.contains(testInput));
git://source.jalview.org / jalview.git / commitdiff