/*
- * 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.
*
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;
{
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);
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.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.setGlobalColourScheme(cs);
af.viewport.setColourAppliesToAllGroups(false);
+ af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{