+ if (av.hasHiddenRows)\r
+ {\r
+ jseq.setHidden(jalhidden.getHiddenSequences().isHidden(\r
+ jal.getSequenceAt(i)));\r
+\r
+ if(jal.getSequenceAt(i).getHiddenSequences()!=null)\r
+ {\r
+ jalview.datamodel.SequenceI [] reps =\r
+ jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);\r
+\r
+ for(int h=0; h<reps.length; h++)\r
+ {\r
+ jseq.addHiddenSequences(\r
+ jal.findIndex(reps[h])\r
+ );\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
+ {\r
+ jalview.datamodel.SequenceFeature[] sf\r
+ = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ int index = 0;\r
+ while(index < sf.length)\r
+ {\r
+ Features features = new Features();\r
+\r
+ features.setBegin(sf[index].getBegin());\r
+ features.setEnd(sf[index].getEnd());\r
+ features.setDescription(sf[index].getDescription());\r
+ features.setType(sf[index].getType());\r
+ features.setFeatureGroup(sf[index].getFeatureGroup());\r
+ features.setScore(sf[index].getScore());\r
+ if(sf[index].links!=null)\r
+ {\r
+ for(int l=0; l<sf[index].links.size(); l++)\r
+ {\r
+ OtherData keyValue = new OtherData();\r
+ keyValue.setKey("LINK_"+l);\r
+ keyValue.setValue(sf[index].links.elementAt(l).toString());\r
+ features.addOtherData(keyValue);\r
+ }\r
+ }\r
+ if(sf[index].otherDetails!=null)\r
+ {\r
+ String key;\r
+ Enumeration keys = sf[index].otherDetails.keys();\r
+ while(keys.hasMoreElements())\r
+ {\r
+ key = keys.nextElement().toString();\r
+ OtherData keyValue = new OtherData();\r
+ keyValue.setKey( key );\r
+ keyValue.setValue(\r
+ sf[index].otherDetails.get(key).toString());\r
+ features.addOtherData(keyValue);\r
+ }\r
+ }\r
+\r
+ jseq.addFeatures(features);\r
+ index ++;\r
+ }\r
+ }\r
+\r
+ if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
+ {\r
+ Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
+ while(en.hasMoreElements())\r
+ {\r
+ Pdbids pdb = new Pdbids();\r
+ jalview.datamodel.PDBEntry entry\r
+ = (jalview.datamodel.PDBEntry)en.nextElement();\r
+\r
+ pdb.setId(entry.getId());\r
+ pdb.setType(entry.getType());\r
+\r
+ if(entry.getFile()!=null)\r
+ {\r
+ if(pdbfiles==null)\r
+ pdbfiles = new Vector();\r
+\r
+\r
+ if(!pdbfiles.contains(entry.getId()))\r
+ {\r
+ pdbfiles.addElement(entry.getId());\r
+ try\r
+ {\r
+ File file = new File(entry.getFile());\r
+ if(file.exists())\r
+ {\r
+ byte[] data = new byte[ (int) file.length()];\r
+ jout.putNextEntry(new JarEntry(entry.getId()));\r
+ DataInputStream dis = new DataInputStream(new\r
+ FileInputStream(file));\r
+ dis.readFully(data);\r
+\r
+ DataOutputStream dout = new DataOutputStream(jout);\r
+ dout.write(data, 0, data.length);\r
+ jout.closeEntry();\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+\r
+ if(entry.getProperty()!=null)\r
+ {\r
+ PdbentryItem item = new PdbentryItem();\r
+ Hashtable properties = entry.getProperty();\r
+ Enumeration en2 = properties.keys();\r
+ while(en2.hasMoreElements())\r
+ {\r
+ Property prop = new Property();\r
+ String key = en2.nextElement().toString();\r
+ prop.setName(key);\r
+ prop.setValue( properties.get(key).toString() );\r
+ item.addProperty(prop);\r
+ }\r
+ pdb.addPdbentryItem(item);\r
+ }\r
+\r
+ jseq.addPdbids(pdb);\r
+ }\r
+ }\r
+\r