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JAL-2089 fix broken help link
[jalview.git]
/
src
/
jalview
/
gui
/
Jalview2XML_V1.java
diff --git
a/src/jalview/gui/Jalview2XML_V1.java
b/src/jalview/gui/Jalview2XML_V1.java
index
61e20fa
..
f8a296f
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML_V1.java
+++ b/
src/jalview/gui/Jalview2XML_V1.java
@@
-20,6
+20,7
@@
*/
package jalview.gui;
*/
package jalview.gui;
+import jalview.analysis.Conservation;
import jalview.binding.Annotation;
import jalview.binding.AnnotationElement;
import jalview.binding.Features;
import jalview.binding.Annotation;
import jalview.binding.AnnotationElement;
import jalview.binding.Features;
@@
-37,7
+38,6
@@
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.datamodel.PDBEntry;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
-import jalview.schemes.ResidueProperties;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
@@
-359,8
+359,7
@@
public class Jalview2XML_V1
if (groups[i].getConsThreshold() != 0)
{
if (groups[i].getConsThreshold() != 0)
{
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
+ Conservation c = new Conservation("All", 3,
sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);