import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertNotEquals;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.FontMetrics;
+import java.lang.reflect.InvocationTargetException;
+
+import javax.swing.SwingUtilities;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+import jalview.api.AlignViewportI;
import jalview.bin.Cache;
import jalview.bin.Jalview;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SequenceI;
import jalview.io.DataSourceType;
import jalview.io.FileLoader;
import jalview.viewmodel.ViewportRanges;
-import org.testng.annotations.BeforeMethod;
-import org.testng.annotations.Test;
-
public class AlignmentPanelTest
{
- 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");
-
- SequenceI seq23 = new Sequence(
- "Seq23",
- "ABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBACABCABCABCABCABCABCABCABCBACBACBACBAC");
-
AlignFrame af;
@BeforeMethod(alwaysRun = true)
- public void setUp()
+ public void setUp() throws InvocationTargetException, InterruptedException
{
- Jalview.main(new String[] { "-nonews", "-props",
- "test/jalview/testProps.jvprops" });
+ Jalview.main(
+ new String[]
+ { "-nonews", "-props", "test/jalview/testProps.jvprops" });
Cache.applicationProperties.setProperty("SHOW_IDENTITY",
Boolean.TRUE.toString());
DataSourceType.FILE);
/*
+ * ensure the panel has been repainted and so ViewportRanges set
+ */
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ af.repaint();
+ }
+ });
+
+ /*
* wait for Consensus thread to complete
*/
- synchronized (this)
+ do
{
- while (af.getViewport().getConsensusSeq() == null)
+ try
+ {
+ Thread.sleep(50);
+ } catch (InterruptedException x)
{
- try
- {
- wait(50);
- } catch (InterruptedException e)
- {
- }
}
- }
+ } while (af.getViewport().getCalcManager().isWorking());
}
-
/**
* Test side effect that end residue is set correctly by setScrollValues, with
* or without hidden columns
*/
@Test(groups = "Functional")
- public void TestSetScrollValues()
+ public void testSetScrollValues()
{
ViewportRanges ranges = af.getViewport().getRanges();
af.alignPanel.setScrollValues(0, 0);
scrollpos = 130;
af.getViewport().showAllHiddenColumns();
af.alignPanel.setScrollValues(scrollpos, 5);
- assertEquals(ranges.getEndRes(), af.getViewport()
- .getAlignment().getWidth() - 1);
+ assertEquals(ranges.getEndRes(),
+ af.getViewport().getAlignment().getWidth() - 1);
// now hide some columns, and scroll to position within <width>
// distance of the end of the alignment
// columns
af.getViewport().hideColumns(30, 50);
af.alignPanel.setScrollValues(scrollpos, 5);
- assertEquals(ranges.getEndRes(), af.getViewport()
- .getAlignment().getWidth() - 1 - 21); // 21 is the number of hidden
- // columns
+ assertEquals(ranges.getEndRes(),
+ af.getViewport().getAlignment().getWidth() - 1 - 21); // 21 is the
+ // number of
+ // hidden
+ // columns
}
/**
* Test that update layout reverts to original (unwrapped) values for endRes
- * and endSeq when switching from wrapped to unwrapped mode (JAL-2739)
+ * when switching from wrapped back to unwrapped mode (JAL-2739)
*/
@Test(groups = "Functional")
- public void TestUpdateLayout_endRes()
+ public void testUpdateLayout_endRes()
{
// get details of original alignment dimensions
ViewportRanges ranges = af.getViewport().getRanges();
af.alignPanel.getAlignViewport().setWrapAlignment(true);
af.alignPanel.updateLayout();
- // endRes changes
+ // endRes has changed
assertNotEquals(ranges.getEndRes(), endres);
// unwrap
af.alignPanel.getAlignViewport().setWrapAlignment(false);
af.alignPanel.updateLayout();
- // endRes and endSeq back to original values
+ // endRes back to original value
assertEquals(ranges.getEndRes(), endres);
+ }
+ /**
+ * Test the variant of calculateIdWidth that only recomputes the width if it
+ * is not already saved in the viewport (initial value is -1)
+ */
+ @Test(groups = "Functional")
+ public void testCalculateIdWidth_noArgs()
+ {
+ AlignViewportI av = af.alignPanel.getAlignViewport();
+ av.setShowJVSuffix(true);
+ av.setFont(new Font("Courier", Font.PLAIN, 15), true);
+
+ av.setIdWidth(0);
+ Dimension d = af.alignPanel.calculateIdWidth();
+ assertEquals(d.width, 0);
+ assertEquals(d.height, 0);
+
+ av.setIdWidth(99);
+ d = af.alignPanel.calculateIdWidth();
+ assertEquals(d.width, 99);
+ assertEquals(d.height, 0);
+
+ /*
+ * note 4 pixels padding are added to the longest sequence name width
+ */
+ av.setIdWidth(-1); // force recalculation
+ d = af.alignPanel.calculateIdWidth();
+ assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
+ assertEquals(d.height, 12);
+ assertEquals(d.width, av.getIdWidth());
+ }
+
+ /**
+ * Test the variant of calculateIdWidth that computes the longest of any
+ * sequence name or annotation label width
+ */
+ @Test(groups = "Functional")
+ public void testCalculateIdWidth_withMaxWidth()
+ {
+ AlignViewportI av = af.alignPanel.getAlignViewport();
+ av.setShowJVSuffix(true);
+ av.setFont(new Font("Courier", Font.PLAIN, 15), true);
+ av.setShowAnnotation(false);
+ av.setIdWidth(18);
+
+ /*
+ * note 4 pixels 'padding' are added to the longest seq name/annotation label
+ */
+ Dimension d = af.alignPanel.calculateIdWidth(2000);
+ assertEquals(d.width, 166); // 4 + pixel width of "Q93Z60_ARATH/1-118"
+ assertEquals(d.height, 12); // fixed value (not used?)
+ assertEquals(av.getIdWidth(), 18); // not changed by this method
+
+ /*
+ * make the longest sequence name longer
+ */
+ SequenceI seq = af.viewport.getAlignment()
+ .findSequenceMatch("Q93Z60_ARATH")[0];
+ seq.setName(seq.getName() + "MMMMM");
+ d = af.alignPanel.calculateIdWidth(2000);
+ assertEquals(d.width, 211); // 4 + pixel width of "Q93Z60_ARATHMMMMM/1-118"
+ assertEquals(d.height, 12);
+ assertEquals(av.getIdWidth(), 18); // unchanged
+
+ /*
+ * make the longest annotation name even longer
+ * note this is checked even if annotations are not shown
+ */
+ AlignmentAnnotation aa = av.getAlignment().getAlignmentAnnotation()[0];
+ aa.label = "THIS IS A VERY LONG LABEL INDEED";
+ FontMetrics fmfor = af.alignPanel
+ .getFontMetrics(af.alignPanel.getAlabels().getFont());
+ // Assumption ID_WIDTH_PADDING == 4
+ int expwidth = 4 + fmfor.stringWidth(aa.label);
+ d = af.alignPanel.calculateIdWidth(2000);
+ assertEquals(d.width, expwidth); // 228 == ID_WIDTH_PADDING + pixel width of
+ // "THIS IS A VERY LONG LABEL INDEED"
+ assertEquals(d.height, 12);
+
+ /*
+ * override with maxwidth
+ * note the 4 pixels padding is added to this value
+ */
+ d = af.alignPanel.calculateIdWidth(213);
+ assertEquals(d.width, 217);
+ assertEquals(d.height, 12);
+ }
+
+ @Test(groups = { "Functional", "Not-bamboo" })
+ public void testGetVisibleWidth()
+ {
+ /*
+ * width for onscreen rendering is IDPanel width
+ */
+ int w = af.alignPanel.getVisibleIdWidth(true);
+ assertEquals(w, af.alignPanel.getIdPanel().getWidth());
+ assertEquals(w, 115);
+
+ /*
+ * width for offscreen rendering is the same
+ * if no fixed id width is specified in preferences
+ */
+ Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.FALSE.toString());
+ Cache.removeProperty("FIGURE_FIXEDIDWIDTH");
+ assertEquals(w, af.alignPanel.getVisibleIdWidth(false));
+
+ /*
+ * preference for fixed id width - note 4 pixels padding is added
+ */
+ Cache.setProperty("FIGURE_FIXEDIDWIDTH", "120");
+ assertEquals(124, af.alignPanel.getVisibleIdWidth(false));
+
+ /*
+ * preference for auto id width overrides fixed width
+ */
+ Cache.setProperty("FIGURE_AUTOIDWIDTH", Boolean.TRUE.toString());
+ assertEquals(115, af.alignPanel.getVisibleIdWidth(false));
}
}
git://source.jalview.org / jalview.git / blobdiff