import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
- newColours[i] = new java.awt.Color(Integer.parseInt(colours
- .getUserColourScheme().getColour(i).getRGB(), 16));
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i).getRGB(), 16));
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
- new String[] { file }), MessageManager
- .getString("label.url_not_found"),
+ new String[]
+ { file }),
+ MessageManager.getString("label.url_not_found"),
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.error_loading_file_params", new String[]
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.error_loading_file_params", new String[]
.getString("label.error_loading_jalview_file"),
JvOptionPane.WARNING_MESSAGE);
}
.getString("label.error_loading_jalview_file"),
JvOptionPane.WARNING_MESSAGE);
}
- jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- features[f].getType(), features[f].getDescription(),
- features[f].getStatus(), features[f].getBegin(),
+ SequenceFeature sf = new SequenceFeature(features[f].getType(),
+ features[f].getDescription(), features[f].getBegin(),
- StructureSelectionManager.getStructureSelectionManager(
- Desktop.instance).registerPDBEntry(entry);
+ StructureSelectionManager
+ .getStructureSelectionManager(Desktop.instance)
+ .registerPDBEntry(entry);
- af.viewport.setSequenceColour(af.viewport.getAlignment()
- .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
+ af.viewport.setSequenceColour(
+ af.viewport.getAlignment().getSequenceAt(i),
+ new java.awt.Color(JSEQ[i].getColour()));
- cs = ColourSchemeProperty.getColourScheme(al, groups[i].getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(groups[i].getPidThreshold(), true);
+ cs = ColourSchemeProperty.getColourScheme(al,
+ groups[i].getColour());
seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
- Conservation c = new Conservation("All", sg.getSequences(null),
- 0, sg.getWidth() - 1);
+ Conservation c = new Conservation("All", sg.getSequences(null), 0,
+ sg.getWidth() - 1);
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
- af.viewport.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
+ af.viewport.getRanges().setStartRes(view.getStartRes());
+ // startSeq set in af.alignPanel.updateLayout below
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
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()), true);
+ 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());
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
- }
+ // if (cs != null)
+ // {
+ // cs.setThreshold(view.getPidThreshold(), true);
+ // cs.setConsensus(af.viewport.getSequenceConsensusHash());
+ // }
- af.viewport.setGlobalColourScheme(cs);
+ af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
+ true);
+ af.viewport.getResidueShading()
+ .setConsensus(af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
Hashtable featureColours = new Hashtable();
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
Hashtable featureColours = new Hashtable();
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
- FeatureRendererSettings frs = new FeatureRendererSettings(
- renderOrder, new Hashtable(), featureColours, 1.0f, null);
+ FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
+ new Hashtable(), featureColours, 1.0f, null);
new jalview.io.NewickFile(tree.getNewick()),
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
new jalview.io.NewickFile(tree.getNewick()),
tree.getTitle(), tree.getWidth(), tree.getHeight(),
tree.getXpos(), tree.getYpos());
- tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
- .getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+ tree.getFontStyle(), tree.getFontSize()));
- tp.setTreeFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), tree.getFontSize()));
+ tp.setTreeFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(), tree.getFontSize()));