+\r
+ System.err.println("Couldn't locate Jalview XML file : " + ex\r
+ + "\n");\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + file, "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+ }\r
+ ;\r
+ } catch (Exception ex)\r
+ {\r
+ System.err.println("Exception whilst loading jalview XML file : ");\r
+ ex.printStackTrace();\r
+ if (raiseGUI)\r
+ {\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Error loading " + file, "Error loading Jalview file",\r
+ JOptionPane.WARNING_MESSAGE);\r
+ }\r
+ });\r
+ }\r
+ }\r
+\r
+ return af;\r
+ }\r
+\r
+ AlignFrame LoadFromObject(JalviewModel object, String file)\r
+ {\r
+ Vector seqids = new Vector();\r
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
+ Sequence[] vamsasSeq = vamsasSet.getSequence();\r
+\r
+ JalviewModelSequence jms = object.getJalviewModelSequence();\r
+\r
+ // ////////////////////////////////\r
+ // LOAD SEQUENCES\r
+ jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
+ for (int i = 0; i < vamsasSeq.length; i++)\r
+ {\r
+ jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
+ vamsasSeq[i].getSequence());\r
+ jseqs[i].setStart(JSEQ[i].getStart());\r
+ jseqs[i].setEnd(JSEQ[i].getEnd());\r
+ seqids.add(jseqs[i]);\r
+ }\r
+\r
+ // /SequenceFeatures are added to the DatasetSequence,\r
+ // so we must create the dataset before loading features\r
+ // ///////////////////////////////\r
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+ al.setDataset(null);\r
+ // ///////////////////////////////\r
+\r
+ for (int i = 0; i < vamsasSeq.length; i++)\r
+ {\r
+ if (JSEQ[i].getFeaturesCount() > 0)\r
+ {\r
+ Features[] features = JSEQ[i].getFeatures();\r
+ for (int f = 0; f < features.length; f++)\r
+ {\r
+ jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(\r
+ features[f].getType(), features[f].getDescription(),\r
+ features[f].getStatus(), features[f].getBegin(),\r
+ features[f].getEnd(), null);\r
+\r
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
+ }\r
+ }\r
+ if (JSEQ[i].getPdbidsCount() > 0)\r
+ {\r
+ Pdbids[] ids = JSEQ[i].getPdbids();\r
+ for (int p = 0; p < ids.length; p++)\r
+ {\r
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
+ entry.setId(ids[p].getId());\r
+ entry.setType(ids[p].getType());\r
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r