import jalview.io.FileLoader;
import jalview.io.HtmlSvgOutput;
import jalview.io.IdentifyFile;
+import jalview.schemes.AnnotationColourGradient;
import jalview.structure.StructureImportSettings;
import jalview.structure.StructureImportSettings.TFType;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.ws.dbsources.EBIAlfaFold;
+import mc_view.PDBChain;
public class Commands
{
}
}
}
+ String shading = ArgParser.getValue(m, Arg.TEMPFAC_SHADING);
+ if (shading != null)
+ {
+ Console.debug(
+ "Annotation colour scheme : " + shading + " (ignored value)");
+ AlignFrame af = afMap.get(id);
+ for (AlignmentAnnotation aa : af.alignPanel.getAlignment()
+ .findAnnotation(PDBChain.class.getName().toString()))
+ {
+ AnnotationColourGradient acg = new AnnotationColourGradient(aa,
+ af.alignPanel.av.getGlobalColourScheme(), 0);
+ acg.setSeqAssociated(true);
+ af.changeColour(acg);
+ Console.info("Changed colour " + acg.toString());
+ }
+
+ }
}
protected void processImages(String id)
*/
package jalview.gui;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentAnnotation;
-import jalview.datamodel.GraphLine;
-import jalview.datamodel.SequenceGroup;
-import jalview.gui.JalviewColourChooser.ColourChooserListener;
-import jalview.schemes.AnnotationColourGradient;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.JLayeredPane;
import javax.swing.JPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentAnnotation;
+import jalview.datamodel.GraphLine;
+import jalview.datamodel.SequenceGroup;
+import jalview.gui.JalviewColourChooser.ColourChooserListener;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
import net.miginfocom.swing.MigLayout;
@SuppressWarnings("serial")