/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\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
+ DBRefFetcher dbref = new DBRefFetcher();\r
+ Vector entries = dbref.getUniprotEntries(file);\r
\r
if (entries != null)\r
{\r
onlyPdbEntries.addElement(pdb);\r
}\r
\r
+ Enumeration en2 = entry.getAccession().elements();\r
+ while (en2.hasMoreElements())\r
+ {\r
+ sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,\r
+ "0",\r
+ en2.nextElement().toString()));\r
+ }\r
+\r
+\r
+\r
+\r
sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
if (entry.getFeature() != null)\r
{\r
}\r
\r
EBIFetchClient ebi = new EBIFetchClient();\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
- if (reply == null)\r
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();\r
+ if (file == null)\r
return null;\r
try\r
{\r
- PDBfile pdbfile = new PDBfile(reply);\r
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);\r
for (int i = 0; i < pdbfile.chains.size(); i++)\r
{\r
if (chain == null ||\r
( (PDBChain) pdbfile.chains.elementAt(i)).id.\r
toUpperCase().equals(chain))\r
+\r
result.append("\n>PDB|" + id + "|" +\r
( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
getName() +\r
String format = new IdentifyFile().Identify(result, "Paste");\r
SequenceI[] sequences = null;\r
\r
- if (FormatAdapter.formats.contains(format))\r
+ if (FormatAdapter.isValidFormat(format))\r
{\r
sequences = null;\r
try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
{\r
if (alignFrame == null)\r
{\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences),\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT\r
+);\r
af.currentFileFormat = format;\r
if(title==null)\r
title = "Retrieved from " + database.getSelectedItem();\r
Desktop.addInternalFrame(af,\r
title,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
af.statusBar.setText("Successfully pasted alignment file");\r
- if (jalview.bin.Cache.getDefault("WRAP_ALIGNMENT", false))\r
- {\r
- af.wrapMenuItem.setSelected(true);\r
- af.wrapMenuItem_actionPerformed(null);\r
- }\r
\r
try\r
{\r