import jalview.gui.AppVarna;
import jalview.gui.ChimeraViewFrame;
import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
import jalview.gui.PCAPanel;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
view.setFollowHighlight(av.isFollowHighlight());
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+ view.setShowComplementFeatures(av.isShowComplementFeatures());
+ view.setShowComplementFeaturesOnTop(
+ av.isShowComplementFeaturesOnTop());
if (av.getFeaturesDisplayed() != null)
{
FeatureSettings fs = new FeatureSettings();
- FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+ FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
.getFeatureRenderer();
String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
- * @param origFile
+ * @param suffixModel
* null or original file - so new file can be given the same suffix
* as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix, String origFile)
+ String jarEntryName, String prefix, String suffixModel)
{
BufferedReader in = null;
PrintWriter out = null;
String suffix = ".tmp";
- if (origFile == null)
+ if (suffixModel == null)
{
- origFile = jarEntryName;
+ suffixModel = jarEntryName;
}
- int sfpos = origFile.lastIndexOf(".");
- if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ int sfpos = suffixModel.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
{
- suffix = "." + origFile.substring(sfpos + 1);
+ suffix = "." + suffixModel.substring(sfpos + 1);
}
try
{
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera", null);
+ "chimera", ".py");
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
viewport.setShowGroupConsensus(view.isShowGroupConsensus());
viewport.setShowGroupConservation(view.isShowGroupConservation());
+ viewport.setShowComplementFeatures(view.isShowComplementFeatures());
+ viewport.setShowComplementFeaturesOnTop(
+ view.isShowComplementFeaturesOnTop());
// recover feature settings
if (jm.getFeatureSettings() != null)
{
- FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
+ FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());