new Insets(0, 4, 0, 0), 1, 0));\r
this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
, GridBagConstraints.CENTER,\r
- GridBagConstraints.HORIZONTAL,\r
- new Insets(0, 0, 0, 6), 200, 1));\r
+ GridBagConstraints.NONE,\r
+ new Insets(0, 0, 0, 6), 211, 1));\r
}\r
\r
JComboBox database = new JComboBox();\r
else if (database.getSelectedItem().equals("EMBL")\r
|| database.getSelectedItem().equals("EMBLCDS"))\r
{\r
- EBIFetchClient dbFetch = new EBIFetchClient();\r
- String[] reply = dbFetch.fetchData(\r
- database.getSelectedItem().toString().toLowerCase(\r
- ) + ":" + textfield.getText(),\r
- "fasta", "raw");\r
+ StringTokenizer st = new StringTokenizer(textfield.getText(), ";");\r
+ while(st.hasMoreTokens())\r
+ {\r
+ EBIFetchClient dbFetch = new EBIFetchClient();\r
+\r
+ String[] reply = dbFetch.fetchData(\r
+ database.getSelectedItem().toString().toLowerCase(\r
+ ) + ":" + st.nextToken(),\r
+ "fasta", "raw");\r
+//\r
+ if (reply != null)\r
+ {\r
+ for (int i = 0; i < reply.length; i++)\r
+ result.append(reply[i] + "\n");\r
+ }\r
+ }\r
\r
- if(reply!=null)\r
+ if(result!=null)\r
{\r
- for (int i = 0; i < reply.length; i++)\r
- result.append(reply[i] + "\n");\r
+ System.out.println(result.toString());\r
\r
parseResult(result.toString(), null);\r
}\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
+\r
SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
Vector entries = sff.getUniprotEntries(file);\r
\r
while (en.hasMoreElements())\r
{\r
UniprotEntry entry = (UniprotEntry) en.nextElement();\r
- StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
+\r
+ StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
Enumeration en2 = entry.getAccession().elements();\r
while (en2.hasMoreElements())\r
{\r
name.append(en2.nextElement());\r
}\r
\r
- if (entry.getProteinName() != null)\r
- name.append(" " + entry.getProteinName().elementAt(0));\r
+ if (entry.getProtein() != null)\r
+ {\r
+ name.append(" " + entry.getProtein().getName().elementAt(0));\r
+ }\r
\r
result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
"\n");\r
}\r
\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\r
-\r
+ if (entry.getFeature() != null)\r
+ {\r
+ e = entry.getFeature().elements();\r
+ while (e.hasMoreElements())\r
+ {\r
+ SequenceFeature sf = (SequenceFeature) e.nextElement();\r
+ sf.setFeatureGroup("Uniprot");\r
+ sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
+ }\r
+ }\r
}\r
}\r
}\r
\r
SequenceI[] parseResult(String result, String title)\r
{\r
- String format = IdentifyFile.Identify(result, "Paste");\r
+ String format = new IdentifyFile().Identify(result, "Paste");\r
SequenceI[] sequences = null;\r
\r
if (FormatAdapter.formats.contains(format))\r
AlignFrame.NEW_WINDOW_WIDTH,\r
AlignFrame.NEW_WINDOW_HEIGHT);\r
af.statusBar.setText("Successfully pasted alignment file");\r
+\r
try\r
{\r
af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
\r
// We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
// JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
- DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
+ DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);\r
sequences[i].getDatasetSequence().addDBRef(dbentry);\r
}\r
else\r
\r
}\r
\r
- void showErrorMessage(String error)\r
+ void showErrorMessage(final String error)\r
{\r
resetDialog();\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data",\r
+ javax.swing.SwingUtilities.invokeLater(new Runnable()\r
+ {\r
+ public void run()\r
+ {\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ error, "Error Retrieving Data",\r
JOptionPane.WARNING_MESSAGE);\r
- return;\r
+ }\r
+ });\r
}\r
}\r
\r