*/
public class AnnotationChooserTest
{
- /*
- * number of automatically computed annotation rows
- * (Conservation, Quality, Consensus, Occupancy)
- */
- private static final int AUTOCALCD = 4;
@BeforeClass(alwaysRun = true)
public void setUpJvOptionPane()
{
Cache.loadProperties("test/jalview/io/testProps.jvprops");
// pin down annotation sort order for test
- Cache.applicationProperties.setProperty(Preferences.SORT_ANNOTATIONS,
+ Cache.setPropertyNoSave(Preferences.SORT_ANNOTATIONS,
SequenceAnnotationOrder.NONE.name());
final String TRUE = Boolean.TRUE.toString();
- Cache.applicationProperties.setProperty(
+ Cache.setPropertyNoSave(
Preferences.SHOW_AUTOCALC_ABOVE, TRUE);
- Cache.applicationProperties.setProperty("SHOW_QUALITY", TRUE);
- Cache.applicationProperties.setProperty("SHOW_CONSERVATION", TRUE);
- Cache.applicationProperties.setProperty("SHOW_IDENTITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_QUALITY", TRUE);
+ Cache.setPropertyNoSave("SHOW_CONSERVATION", TRUE);
+ Cache.setPropertyNoSave("SHOW_IDENTITY", TRUE);
AlignmentI al = new FormatAdapter().readFile(TEST_DATA,
DataSourceType.PASTE, FileFormat.Fasta);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
- assertTrue(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
setSelected(getTypeCheckbox("JMol"), true);
assertTrue(anns[0].visible); // Conservation
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- assertTrue(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
setSelected(getTypeCheckbox("JMol"), true);
assertTrue(anns[0].visible); // Conservation
// select JMol - all hidden
setSelected(typeCheckbox, true);
- assertFalse(anns[AUTOCALCD + 2].visible); // JMol for seq3
- assertFalse(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+ assertFalse(anns[autocalc + 4].visible); // JMol for seq1
// deselect JMol - all unhidden
setSelected(typeCheckbox, false);
- assertTrue(anns[0].visible); // Conservation
- assertTrue(anns[1].visible); // Quality
- assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // Occupancy
- assertTrue(anns[4].visible); // IUPred for seq0
- assertTrue(anns[5].visible); // Beauty
- assertTrue(anns[6].visible); // JMol for seq3
- assertTrue(anns[7].visible); // IUPRED for seq2
- assertTrue(anns[8].visible); // JMol for seq1
+ for (AlignmentAnnotation ann : anns)
+ {
+ assertTrue(ann.visible);
+ }
+ }
+
+ /**
+ * Returns a count of autocalculated annotations in the set provided
+ *
+ * @param anns
+ * @return
+ */
+ private int countAutocalc(AlignmentAnnotation[] anns)
+ {
+ int count = 0;
+ for (AlignmentAnnotation ann : anns)
+ {
+ if (ann.autoCalculated)
+ {
+ count++;
+ }
+ }
+ return count;
}
/**
setSelected(allSequencesCheckbox, true);
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
- assertFalse(anns[AUTOCALCD + 2].visible); // JMol for seq3
- assertFalse(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertFalse(anns[autocalc + 2].visible); // JMol for seq3
+ assertFalse(anns[autocalc + 4].visible); // JMol for seq1
// ...now show them...
setSelected(showCheckbox, true);
- assertTrue(anns[0].visible); // Conservation
- assertTrue(anns[1].visible); // Quality
- assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // Occupancy
- assertTrue(anns[4].visible); // IUPred for seq0
- assertTrue(anns[5].visible); // Beauty
- assertTrue(anns[6].visible); // JMol for seq3
- assertTrue(anns[7].visible); // IUPRED for seq2
- assertTrue(anns[8].visible); // JMol for seq1
+ for (AlignmentAnnotation ann : anns)
+ {
+ assertTrue(ann.visible);
+ }
}
/**
setSelected(hideCheckbox, true);
setSelected(getTypeCheckbox("JMol"), true);
- assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
- assertFalse(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertFalse(anns[autocalc + 4].visible); // JMol for seq1
// ...now show them...
setSelected(showCheckbox, true);
- assertTrue(anns[0].visible); // Conservation
- assertTrue(anns[1].visible); // Quality
- assertTrue(anns[2].visible); // Consensus
- assertTrue(anns[3].visible); // Occupancy
- assertTrue(anns[4].visible); // IUPred for seq0
- assertTrue(anns[5].visible); // Beauty
- assertTrue(anns[6].visible); // JMol for seq3
- assertTrue(anns[7].visible); // IUPRED for seq2
- assertTrue(anns[8].visible); // JMol for seq1
+ for (AlignmentAnnotation ann : anns)
+ {
+ assertTrue(ann.visible);
+ }
}
/**
final Checkbox typeCheckbox = getTypeCheckbox("JMol");
// select JMol - all shown
setSelected(typeCheckbox, true);
- assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
- assertTrue(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
// deselect JMol - all hidden
setSelected(typeCheckbox, false);
// select JMol - should remain visible
setSelected(getTypeCheckbox("JMol"), true);
- assertTrue(anns[AUTOCALCD + 2].visible); // JMol for seq3
- assertTrue(anns[AUTOCALCD + 4].visible); // JMol for seq1
+ int autocalc = countAutocalc(anns);
+ assertTrue(anns[autocalc + 2].visible); // JMol for seq3
+ assertTrue(anns[autocalc + 4].visible); // JMol for seq1
// deselect JMol - should be hidden for selected sequences only
setSelected(getTypeCheckbox("JMol"), false);
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- assertFalse(testee.isInActionScope(anns[AUTOCALCD]));
- assertFalse(testee.isInActionScope(anns[AUTOCALCD + 1]));
- assertFalse(testee.isInActionScope(anns[AUTOCALCD + 2]));
- assertTrue(testee.isInActionScope(anns[AUTOCALCD + 3]));
- assertTrue(testee.isInActionScope(anns[AUTOCALCD + 4]));
+ int autocalc = countAutocalc(anns);
+ assertFalse(testee.isInActionScope(anns[autocalc]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 1]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 2]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 3]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 4]));
}
/**
AlignmentAnnotation[] anns = parentPanel.getAlignment()
.getAlignmentAnnotation();
- assertTrue(testee.isInActionScope(anns[AUTOCALCD]));
- assertTrue(testee.isInActionScope(anns[AUTOCALCD + 1]));
- assertTrue(testee.isInActionScope(anns[AUTOCALCD + 2]));
- assertFalse(testee.isInActionScope(anns[AUTOCALCD + 3]));
- assertFalse(testee.isInActionScope(anns[AUTOCALCD + 4]));
+ int autocalc = countAutocalc(anns);
+ assertTrue(testee.isInActionScope(anns[autocalc]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 1]));
+ assertTrue(testee.isInActionScope(anns[autocalc + 2]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 3]));
+ assertFalse(testee.isInActionScope(anns[autocalc + 4]));
}
/**