<td><em>Application</em>
<ul>
<li>3D Structure chooser opens with 'Cached structures' view if structures already loaded</li>
+ <li>Progress bar reports models as they are loaded to structure views</li>
</ul></td>
<td>
<div align="left">
+ <em>General</em>
+ <ul>
+ <li>Colour by conservation always enabled and no tick shown in menu when PID shading applied</li>
+ </ul>
<em>Application</em>
<ul>
+ <li>Jalview projects with views of local PDB structure files saved on Windows cannot be opened on OSX</li>
+ <li>Multiple structure views can be opened and superposed without timeout for structures with multiple models or multiple sequences in alignment</li>
<li>Cannot import or associated local PDB files without a PDB ID HEADER line</li>
<li>RMSD is not output in Jmol console when superposition is performed</li>
<li>Drag and drop of URL from Browser fails for Linux and OSX versions earlier than El Capitan</li>
<li>ENA client ignores invalid content from ENA server</li>
- <li>Exceptions are not raised when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
- <li>Exceptions are not raised when a new view is created on the alignment</li>
+ <li>Exceptions are not raised in console when ENA client attempts to fetch non-existent IDs via Fetch DB Refs UI option</li>
+ <li>Exceptions are not raised in console when a new view is created on the alignment</li>
</ul>
<em>New Known Issues</em>
<ul><li>Drag and drop from URL links in browsers do not work on Windows</li></ul>
boolean recalc = false;
if (cs != null)
{
- cs.setConservationApplied(recalc = getConservationSelected());
+ recalc = getConservationSelected();
if (getAbovePIDThreshold() || cs instanceof PIDColourScheme
|| cs instanceof Blosum62ColourScheme)
{
cs.setConsensus(hconsensus);
cs.setConservation(hconservation);
}
+ cs.setConservationApplied(getConservationSelected());
cs.alignmentChanged(alignment, hiddenRepSequences);
}
if (getColourAppliesToAllGroups())
import jalview.datamodel.SequenceI;
import jalview.io.FileLoader;
import jalview.io.FormatAdapter;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.PIDColourScheme;
import jalview.structure.StructureSelectionManager;
import jalview.util.MapList;
assertNotNull("Quality in column 1 is null", annotations[0]);
assertTrue("No quality value in column 1", annotations[0].value > 10f);
}
+
+ @Test(groups = { "Functional" })
+ public void testSetGlobalColourScheme()
+ {
+ /*
+ * test for JAL-2283 don't inadvertently turn on colour by conservation
+ */
+ Cache.applicationProperties.setProperty("SHOW_ANNOTATIONS",
+ Boolean.TRUE.toString());
+ Cache.applicationProperties.setProperty("SHOW_CONSERVATION",
+ Boolean.FALSE.toString());
+ Cache.applicationProperties.setProperty("DEFAULT_COLOUR_PROT", "NONE");
+ AlignFrame af = new FileLoader().LoadFileWaitTillLoaded(
+ "examples/uniref50.fa", FormatAdapter.FILE);
+ ColourSchemeI cs = new PIDColourScheme();
+ af.getViewport().setGlobalColourScheme(cs);
+ assertFalse(cs.conservationApplied());
+ }
}