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JAL-1780 JAL-653 organise imports
[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
586e2fa
..
cb572cd
100755
(executable)
--- a/
src/jalview/gui/Jalview2XML_V1.java
+++ b/
src/jalview/gui/Jalview2XML_V1.java
@@
-1,6
+1,6
@@
/*
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*
* This file is part of Jalview.
*
@@
-34,6
+34,7
@@
import jalview.binding.Setting;
import jalview.binding.Tree;
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.binding.Tree;
import jalview.binding.UserColours;
import jalview.binding.Viewport;
+import jalview.datamodel.PDBEntry;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.ResidueProperties;
@@
-240,7
+241,17
@@
public class Jalview2XML_V1
{
jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
entry.setId(ids[p].getId());
{
jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
entry.setId(ids[p].getId());
- entry.setType(ids[p].getType());
+ if (ids[p].getType() != null)
+ {
+ if (ids[p].getType().equalsIgnoreCase("PDB"))
+ {
+ entry.setType(PDBEntry.Type.PDB);
+ }
+ else
+ {
+ entry.setType(PDBEntry.Type.FILE);
+ }
+ }
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
StructureSelectionManager.getStructureSelectionManager(
Desktop.instance).registerPDBEntry(entry);
@@
-371,15
+382,14
@@
public class Jalview2XML_V1
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.setFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), view.getFontSize()));
- af.alignPanel.fontChanged();
+ af.viewport.setFont(
+ new java.awt.Font(view.getFontName(), view.getFontStyle(), view
+ .getFontSize()), true);
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+ af.viewport.setShowAnnotation(view.isShowAnnotation());
af.viewport.setShowBoxes(view.getShowBoxes());
af.viewport.setShowText(view.getShowText());
af.viewport.setShowBoxes(view.getShowBoxes());
af.viewport.setShowText(view.getShowText());
@@
-405,6
+415,7
@@
public class Jalview2XML_V1
af.viewport.setGlobalColourScheme(cs);
af.viewport.setColourAppliesToAllGroups(false);
af.viewport.setGlobalColourScheme(cs);
af.viewport.setColourAppliesToAllGroups(false);
+ af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{