/*\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
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
- SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
- Vector entries = sff.getUniprotEntries(file);\r
+\r
+ DBRefFetcher dbref = new DBRefFetcher();\r
+ Vector entries = dbref.getUniprotEntries(file);\r
\r
if (entries != null)\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
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
- e = entry.getFeature().elements();\r
- while(e.hasMoreElements())\r
+ if (entry.getFeature() != null)\r
{\r
- sequence[i].getDatasetSequence().addSequenceFeature((SequenceFeature)e.nextElement());\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
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
\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
+ 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
+\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
git://source.jalview.org / jalview.git / blobdiff