import java.io.File;
import java.util.ArrayList;
import java.util.List;
+import java.util.Map;
import javax.swing.JInternalFrame;
import javax.swing.JMenuItem;
import jalview.bin.Cache;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
* @param colourBySequence
* @param newViewId
*/
- public PymolViewer(String sessionFile, AlignmentPanel alignPanel,
- PDBEntry[] pdbArray, SequenceI[][] seqsArray,
- boolean colourByPymol, boolean colourBySequence, String newViewId)
+ public PymolViewer(StructureViewerModel viewerModel,
+ AlignmentPanel alignPanel, String sessionFile, String vid)
{
// TODO convert to base/factory class method
this();
- setViewId(newViewId);
+ setViewId(vid);
this.pymolSessionFile = sessionFile;
+ Map<File, StructureData> pdbData = viewerModel.getFileData();
+ PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
+ SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
+ int i = 0;
+ for (StructureData data : pdbData.values())
+ {
+ PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+ PDBEntry.Type.PDB, data.getFilePath());
+ pdbArray[i] = pdbentry;
+ List<SequenceI> sequencesForPdb = data.getSeqList();
+ seqsArray[i] = sequencesForPdb
+ .toArray(new SequenceI[sequencesForPdb.size()]);
+ i++;
+ }
+
openNewPymol(alignPanel, pdbArray, seqsArray);
- if (colourByPymol)
+ if (viewerModel.isColourByViewer())
{
binding.setColourBySequence(false);
seqColour.setSelected(false);
viewerColour.setSelected(true);
}
- else if (colourBySequence)
+ else if (viewerModel.isColourWithAlignPanel())
{
binding.setColourBySequence(true);
seqColour.setSelected(true);
boolean opened = binding.openSession(pymolSessionFile);
if (!opened)
{
- System.err.println("An error occurred opening PyMOL session file "
+ Cache.log.error(
+ "An error occurred opening PyMOL session file "
+ pymolSessionFile);
}
}