/*
- * 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 2.9.0b2)
+ * Copyright (C) 2015 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;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
+import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.io.InputStreamReader;
import java.util.Hashtable;
import javax.swing.JOptionPane;
-import jalview.util.MessageManager;
-import jalview.util.jarInputStreamProvider;
import org.exolab.castor.xml.IDResolver;
-import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
/**
* DOCUMENT ME!
+ "\n");
JOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new String[]
- { file }), MessageManager
+ new String[] { file }), MessageManager
.getString("label.url_not_found"),
JOptionPane.WARNING_MESSAGE);
}
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
- MessageManager.formatMessage("label.error_loading_file_params", new String[]{file}), MessageManager.getString("label.error_loading_jalview_file"),
+ MessageManager.formatMessage(
+ "label.error_loading_file_params", new String[]
+ { file }), MessageManager
+ .getString("label.error_loading_jalview_file"),
JOptionPane.WARNING_MESSAGE);
}
});
{
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);
for (int s = 0; s < ids.length; s++)
{
- seqs.addElement(seqids
- .elementAt(ids[s]));
+ seqs.addElement(seqids.elementAt(ids[s]));
}
jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
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)
{
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
- featureColours.put(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ featureColours.put(setting.getType(),
+ new java.awt.Color(setting.getColour()));
renderOrder[fs] = setting.getType();
if (setting.getDisplay())
{
- featuresDisplayed.put(setting.getType(), new Integer(
- setting.getColour()));
+ featuresDisplayed.put(setting.getType(),
+ new Integer(setting.getColour()));
}
}
- FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, new Hashtable(), featureColours, 1.0f, null);
- af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().transferSettings(frs);
+ FeatureRendererSettings frs = new FeatureRendererSettings(
+ renderOrder, new Hashtable(), featureColours, 1.0f, null);
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .transferSettings(frs);
}
af.setMenusFromViewport(af.viewport);