/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
- * Copyright (C) 2014 The Jalview Authors
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
*/
package jalview.gui;
-import java.awt.Rectangle;
-
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.Viewer;
+import jalview.datamodel.StructureViewerModel;
import jalview.structure.StructureSelectionManager;
+import java.awt.Rectangle;
+
/**
* proxy for handling structure viewers.
*
{
StructureSelectionManager ssm;
- public enum Viewer
+ public enum ViewerType
{
JMOL, CHIMERA
};
- public Viewer getViewerType()
+ public ViewerType getViewerType()
{
- String viewType = Cache.getDefault("STRUCTURE_DISPLAY", "JMOL");
- return Viewer.valueOf(viewType);
+ String viewType = Cache.getDefault(Preferences.STRUCTURE_DISPLAY,
+ ViewerType.JMOL.name());
+ return ViewerType.valueOf(viewType);
}
- public void setViewerType(Viewer type)
+ public void setViewerType(ViewerType type)
{
- Cache.setProperty("STRUCTURE_DISPLAY", type.toString());
+ Cache.setProperty(Preferences.STRUCTURE_DISPLAY, type.name());
}
public StructureViewer(StructureSelectionManager structureSelectionManager)
public JalviewStructureDisplayI viewStructures(AlignmentPanel ap,
PDBEntry[] pr, SequenceI[][] collateForPDB)
{
+ return viewStructures(getViewerType(), ap, pr, collateForPDB);
+ }
+
+ public JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+ AlignmentPanel ap, PDBEntry[] pr, SequenceI[][] collateForPDB)
+ {
JalviewStructureDisplayI sview = null;
- switch (getViewerType())
+ if (viewerType.equals(ViewerType.JMOL))
{
- case JMOL:
-
sview = new AppJmol(ap, pr, ap.av.collateForPDB(pr));
+ }
+ else if (viewerType.equals(ViewerType.CHIMERA))
+ {
+ sview = new ChimeraViewFrame(ap, pr, ap.av.collateForPDB(pr));
+ }
+ else
+ {
+ Cache.log.error("Unknown structure viewer type "
+ + getViewerType().toString());
+ }
+ return sview;
+ }
- break;
- case CHIMERA:
- break;
- default:
+ public JalviewStructureDisplayI viewStructures(ViewerType viewerType,
+ AlignmentPanel ap, PDBEntry pr, SequenceI[] collateForPDB)
+ {
+ JalviewStructureDisplayI sview = null;
+ if (viewerType.equals(ViewerType.JMOL))
+ {
+ sview = new AppJmol(pr, collateForPDB, null, ap);
+ }
+ else if (viewerType.equals(ViewerType.CHIMERA))
+ {
+ sview = new ChimeraViewFrame(pr, collateForPDB, null, ap);
+ }
+ else
+ {
Cache.log.error("Unknown structure viewer type "
+ getViewerType().toString());
}
public JalviewStructureDisplayI viewStructures(PDBEntry pdb,
SequenceI[] sequenceIs, Object object, AlignmentPanel ap)
{
- return viewStructures(ap, new PDBEntry[]
- { pdb }, new SequenceI[][]
- { sequenceIs });
+ return viewStructures(getViewerType(), ap, pdb, sequenceIs);
}
- public JalviewStructureDisplayI createView(Viewer jmol, String[] pdbf,
- String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
- boolean useinJmolsuperpos, boolean usetoColourbyseq,
- boolean jmolColouring, String fileloc, Rectangle rect, String vid)
+ /**
+ * Create a new panel controlling a structure viewer.
+ *
+ * @param type
+ * @param pdbf
+ * @param id
+ * @param sq
+ * @param alignPanel
+ * @param viewerData
+ * @param fileloc
+ * @param rect
+ * @param vid
+ * @return
+ */
+ public JalviewStructureDisplayI createView(ViewerType type,
+ String[] pdbf, String[] id, SequenceI[][] sq,
+ AlignmentPanel alignPanel, StructureViewerModel viewerData, String fileloc,
+ Rectangle rect, String vid)
{
+ final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
+ final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
+ final boolean viewerColouring = viewerData.isColourByViewer();
+
JalviewStructureDisplayI sview = null;
- switch (getViewerType())
+ switch (type)
{
case JMOL:
-
- sview = new AppJmol(pdbf, id, sq, alignPanel, useinJmolsuperpos,
- usetoColourbyseq, jmolColouring, fileloc, rect, vid);
-
+ sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
+ useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
break;
case CHIMERA:
+ Cache.log.error("Unsupported structure viewer type "
+ + type.toString());
break;
default:
- Cache.log.error("Unknown structure viewer type "
- + getViewerType().toString());
+ Cache.log.error("Unknown structure viewer type " + type.toString());
}
return sview;
}