import java.net.*;\r
\r
import java.util.*;\r
+\r
import java.util.jar.*;\r
\r
import javax.swing.*;\r
AlignViewport av = af.viewport;\r
\r
JalviewModel object = new JalviewModel();\r
- object.setVamsasModel(new VamsasModel());\r
+ object.setVamsasModel(new jalview.binding.VamsasModel());\r
\r
object.setCreationDate(new java.util.Date(timeStamp));\r
object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
tree.setThreshold(tp.treeCanvas.threshold);\r
\r
tree.setFitToWindow(tp.fitToWindow.getState());\r
- tree.setFontName(tp.getFont().getName());\r
- tree.setFontSize(tp.getFont().getSize());\r
- tree.setFontStyle(tp.getFont().getStyle());\r
+ tree.setFontName(tp.getTreeFont().getName());\r
+ tree.setFontSize(tp.getTreeFont().getSize());\r
+ tree.setFontStyle(tp.getTreeFont().getStyle());\r
tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
+\r
tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
tree.setShowDistances(tp.distanceMenu.getState());\r
\r
view.setShowBoxes(av.getShowBoxes());\r
view.setShowColourText(av.getColourText());\r
view.setShowConservation(av.showConservation);\r
- view.setShowFullId(av.getShowFullId());\r
+ view.setShowFullId(av.getShowJVSuffix());\r
view.setShowIdentity(av.showIdentity);\r
view.setShowQuality(av.showQuality);\r
view.setShowSequenceFeatures(av.showSequenceFeatures);\r
af.viewport.setConservationSelected(view.getConservationSelected());\r
af.conservationMenuItem.setSelected(view.getConservationSelected());\r
\r
- af.viewport.setShowFullId(view.getShowFullId());\r
- af.fullSeqId.setSelected(view.getShowFullId());\r
+ af.viewport.setShowJVSuffix(view.getShowFullId());\r
+ af.seqLimits.setSelected(view.getShowFullId());\r
\r
af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
view.getFontStyle(), view.getFontSize()));\r
\r
if (view.getShowSequenceFeatures())\r
{\r
+ af.featureSettings.setEnabled(true);\r
af.viewport.showSequenceFeatures = true;\r
af.sequenceFeatures.setSelected(true);\r
new SequenceFeatureFetcher(al, af.alignPanel);\r
tp.fitToWindow_actionPerformed(null);\r
\r
if(tree.getFontName()!=null)\r
- tp.setFont(new java.awt.Font(tree.getFontName(),\r
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
tree.getFontStyle(),\r
tree.getFontSize()));\r
else\r
- tp.setFont(new java.awt.Font(view.getFontName(),\r
+ tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
view.getFontStyle(),\r
tree.getFontSize()));\r
\r
+ tp.showPlaceholders(tree.getMarkUnlinked());\r
+ tp.showBootstrap(tree.getShowBootstrap());\r
+ tp.showDistances(tree.getShowDistances());\r
\r
- tp.placeholdersMenu.setState(tree.getMarkUnlinked());\r
- tp.placeholdersMenu_actionPerformed(null);\r
- tp.bootstrapMenu.setState(tree.getShowBootstrap());\r
- tp.bootstrapMenu_actionPerformed(null);\r
- tp.distanceMenu.setState(tree.getShowDistances());\r
- tp.distanceMenu_actionPerformed(null);\r
tp.treeCanvas.threshold = tree.getThreshold();\r
\r
if (tree.getCurrentTree())\r