*/
package jalview.gui;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.datamodel.StructureViewerModel;
-import jalview.structure.StructureSelectionManager;
-
-import java.awt.Rectangle;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.Map.Entry;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.structure.StructureSelectionManager;
+
/**
* A proxy for handling structure viewers, that orchestrates adding selected
* structures, associated with sequences in Jalview, to an existing viewer, or
public enum ViewerType
{
- JMOL, CHIMERA
+ JMOL, CHIMERA, CHIMERAX, PYMOL
};
/**
sview = new ChimeraViewFrame(pdbsForFile, superposeAdded, theSeqs,
ap);
}
+ else if (viewerType.equals(ViewerType.CHIMERAX))
+ {
+ sview = new ChimeraXViewFrame(pdbsForFile, superposeAdded, theSeqs,
+ ap);
+ }
+ else if (viewerType.equals(ViewerType.PYMOL))
+ {
+ sview = new PymolViewer(pdbsForFile, superposeAdded, theSeqs, ap);
+ }
else
{
Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
sview.addToExistingViewer(pdb, seqsForPdb, null, ap, pdbId);
}
sview.updateTitleAndMenus();
+ sview.raiseViewer();
return sview;
}
ViewerType viewerType = getViewerType();
{
sview = new ChimeraViewFrame(pdb, seqsForPdb, null, ap);
}
+ else if (viewerType.equals(ViewerType.CHIMERAX))
+ {
+ sview = new ChimeraXViewFrame(pdb, seqsForPdb, null, ap);
+ }
+ else if (viewerType.equals(ViewerType.PYMOL))
+ {
+ sview = new PymolViewer(pdb, seqsForPdb, null, ap);
+ }
else
{
Cache.log.error(UNKNOWN_VIEWER_TYPE + getViewerType().toString());
}
/**
- * Create a new panel controlling a structure viewer.
+ * Creates a new panel controlling a structure viewer
*
* @param type
- * @param pdbf
- * @param id
- * @param sq
* @param alignPanel
* @param viewerData
- * @param fileloc
- * @param rect
+ * @param sessionFile
* @param vid
* @return
*/
- public JalviewStructureDisplayI createView(ViewerType type, String[] pdbf,
- String[] id, SequenceI[][] sq, AlignmentPanel alignPanel,
- StructureViewerModel viewerData, String fileloc, Rectangle rect,
- String vid)
+ public static JalviewStructureDisplayI createView(ViewerType type,
+ AlignmentPanel alignPanel, StructureViewerModel viewerData,
+ String sessionFile, String vid)
{
- final boolean useinViewerSuperpos = viewerData.isAlignWithPanel();
- final boolean usetoColourbyseq = viewerData.isColourWithAlignPanel();
- final boolean viewerColouring = viewerData.isColourByViewer();
-
+ JalviewStructureDisplayI viewer = null;
switch (type)
{
case JMOL:
- sview = new AppJmol(pdbf, id, sq, alignPanel, usetoColourbyseq,
- useinViewerSuperpos, viewerColouring, fileloc, rect, vid);
+ viewer = new AppJmol(viewerData, alignPanel, sessionFile, vid);
+ // todo or construct and then openSession(sessionFile)?
break;
case CHIMERA:
- Cache.log.error(
- "Unsupported structure viewer type " + type.toString());
+ viewer = new ChimeraViewFrame(viewerData, alignPanel, sessionFile,
+ vid);
+ break;
+ case CHIMERAX:
+ viewer = new ChimeraXViewFrame(viewerData, alignPanel, sessionFile,
+ vid);
+ break;
+ case PYMOL:
+ viewer = new PymolViewer(viewerData, alignPanel, sessionFile, vid);
break;
default:
Cache.log.error(UNKNOWN_VIEWER_TYPE + type.toString());
}
- return sview;
+ return viewer;
}
public boolean isBusy()