-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\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
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import jalview.io.EBIFetchClient;\r
-import MCview.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.AlignSeq;\r
-import java.io.File;\r
-import jalview.io.*;\r
-import java.util.*;\r
-\r
-public class SequenceFetcher\r
- extends JPanel implements Runnable\r
-{\r
- JInternalFrame frame;\r
- AlignFrame alignFrame;\r
- StringBuffer result;\r
- final String noDbSelected = "-- Select Database --";\r
- public SequenceFetcher(AlignFrame af)\r
- {\r
- alignFrame = af;\r
- database.addItem(noDbSelected);\r
- database.addItem("Uniprot");\r
- database.addItem("EMBL");\r
- database.addItem("EMBLCDS");\r
- database.addItem("PDB");\r
- database.addItem("PFAM");\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
- else\r
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
- }\r
-\r
- private String getFrameTitle()\r
- {\r
- return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(gridBagLayout1);\r
-\r
- database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- database.setMinimumSize(new Dimension(160, 21));\r
- database.setPreferredSize(new Dimension(160, 21));\r
- jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
- jLabel1.setText(\r
- "Separate multiple accession ids with semi colon \";\"");\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- close.setText("Close");\r
- close.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- close_actionPerformed(e);\r
- }\r
- });\r
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- textfield.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.add(ok);\r
- jPanel1.add(close);\r
- this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(7, 4, 0, 6), 77, 6));\r
- this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.BOTH,\r
- new Insets(7, -2, 7, 12), 241, -2));\r
- this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\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.NONE,\r
- new Insets(0, 0, 0, 6), 211, 1));\r
- }\r
-\r
- JComboBox database = new JComboBox();\r
- JLabel jLabel1 = new JLabel();\r
- JButton ok = new JButton();\r
- JButton close = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- JTextField textfield = new JTextField();\r
- GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- public void close_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- database.setEnabled(false);\r
- textfield.setEnabled(false);\r
- ok.setEnabled(false);\r
- close.setEnabled(false);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
- private void resetDialog()\r
- {\r
- database.setEnabled(true);\r
- textfield.setEnabled(true);\r
- ok.setEnabled(true);\r
- close.setEnabled(true);\r
- }\r
-\r
- public void run()\r
- {\r
- String error = "";\r
- if (database.getSelectedItem().equals(noDbSelected))\r
- error += "Please select the source database\n";\r
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
- textfield.setText(empty.replaceAll(textfield.getText()));\r
- if (textfield.getText().length() == 0)\r
- error += "Please enter a (semi-colon separated list of) database id(s)";\r
- if (error.length() > 0)\r
- {\r
- showErrorMessage(error);\r
- resetDialog();\r
- return;\r
- }\r
-\r
- result = new StringBuffer();\r
- if (database.getSelectedItem().equals("Uniprot"))\r
- {\r
- getUniprotFile(textfield.getText());\r
- }\r
- else if (database.getSelectedItem().equals("EMBL")\r
- || database.getSelectedItem().equals("EMBLCDS"))\r
- {\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(result!=null)\r
- {\r
- System.out.println(result.toString());\r
-\r
- parseResult(result.toString(), null);\r
- }\r
- }\r
- else if (database.getSelectedItem().equals("PDB"))\r
- {\r
- StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");\r
- String query;\r
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
- {\r
- StringBuffer respart = getPDBFile(query.toUpperCase());\r
- if(respart!=null)\r
- result.append(respart);\r
- }\r
-\r
-\r
- if (result.length()>0)\r
- parseResult(result.toString(), null);\r
- }\r
- else if( database.getSelectedItem().equals("PFAM"))\r
- {\r
- try{\r
- result.append(new FastaFile(\r
- "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
- + textfield.getText().toUpperCase(), "URL").print()\r
- );\r
-\r
- if(result.length()>0)\r
- parseResult( result.toString(), textfield.getText().toUpperCase() );\r
-\r
- }catch(java.io.IOException ex)\r
- { result = null; }\r
- }\r
-\r
- if (result == null || result.length() == 0)\r
- showErrorMessage("Error retrieving " + textfield.getText()\r
- + " from " + database.getSelectedItem());\r
-\r
- resetDialog();\r
- return;\r
- }\r
-\r
- void getUniprotFile(String id)\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
-\r
- DBRefFetcher dbref = new DBRefFetcher();\r
- Vector entries = dbref.getUniprotEntries(file);\r
-\r
- if (entries != null)\r
- {\r
- //First, make the new sequences\r
- Enumeration en = entries.elements();\r
- while (en.hasMoreElements())\r
- {\r
- UniprotEntry entry = (UniprotEntry) en.nextElement();\r
-\r
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
- en2 = entry.getName().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
-\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
-\r
- //Then read in the features and apply them to the dataset\r
- SequenceI[] sequence = parseResult(result.toString(), null);\r
- for (int i = 0; i < entries.size(); i++)\r
- {\r
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while (e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry) e.nextElement();\r
- if (!pdb.getType().equals("PDB"))\r
- continue;\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
- 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
- StringBuffer getPDBFile(String id)\r
- {\r
- StringBuffer result = new StringBuffer();\r
- String chain = null;\r
- if (id.indexOf(":") > -1)\r
- {\r
- chain = id.substring(id.indexOf(":") + 1);\r
- id = id.substring(0, id.indexOf(":"));\r
- }\r
-\r
- EBIFetchClient ebi = new EBIFetchClient();\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(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
- "\n"\r
- +\r
- ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.\r
- getSequence());\r
- }\r
- }\r
- catch (Exception ex) // Problem parsing PDB file\r
- {\r
- jalview.bin.Cache.log.warn("Exception when retrieving " +\r
- textfield.getText() + " from " +\r
- database.getSelectedItem(), ex);\r
- return null;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- SequenceI[] parseResult(String result, String title)\r
- {\r
- String format = new IdentifyFile().Identify(result, "Paste");\r
- SequenceI[] sequences = null;\r
-\r
- if (FormatAdapter.isValidFormat(format))\r
- {\r
- sequences = null;\r
- try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
- format);}\r
- catch(Exception ex){}\r
-\r
- if (sequences != null && sequences.length > 0)\r
- {\r
- if (alignFrame == null)\r
- {\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.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
- catch (Exception ex)\r
- {}\r
- }\r
- else\r
- {\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- alignFrame.viewport.alignment.addSequence(sequences[i]);\r
-\r
- ////////////////////////////\r
- //Dataset needs extension;\r
- /////////////////////////////\r
- Sequence ds = new Sequence(sequences[i].getName(),\r
- AlignSeq.extractGaps("-. ",\r
- sequences[i].getSequence()),\r
- sequences[i].getStart(),\r
- sequences[i].getEnd());\r
- sequences[i].setDatasetSequence(ds);\r
- alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
- }\r
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
- getHeight());\r
- alignFrame.viewport.alignment.getWidth();\r
- alignFrame.viewport.firePropertyChange("alignment", null,\r
- alignFrame.viewport.\r
- getAlignment().getSequences());\r
-\r
- }\r
-\r
- if (database.getSelectedItem().equals("PDB"))\r
- {\r
- // Parse out the ids from the structured names\r
- boolean errors = false;\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(\r
- "PDB\\|([0-9A-z]{4})\\|(.)");\r
- if (idbits.search(sequences[i].getName()))\r
- {\r
- String pdbid = idbits.substring(1);\r
- String pdbccode = idbits.substring(2);\r
- // Construct the PDBEntry\r
- entry.setId(pdbid);\r
- if (entry.getProperty() == null)\r
- entry.setProperty(new Hashtable());\r
- entry.getProperty().put("chains",\r
- pdbccode\r
- + "=" + sequences[i].getStart()\r
- + "-" + sequences[i].getEnd());\r
- sequences[i].getDatasetSequence().addPDBId(entry);\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(jalview.datamodel.DBRefSource.PDB,"0",pdbid);\r
- sequences[i].getDatasetSequence().addDBRef(dbentry);\r
- }\r
- else\r
- {\r
- // don't add an entry for this chain, but this is probably a bug\r
- // that the user should know about.\r
- jalview.bin.Cache.log.warn(\r
- "No PDBEntry constructed for sequence " + i + " : " +\r
- sequences[i].getName());\r
- errors = true;\r
- }\r
- }\r
- if (errors)\r
- jalview.bin.Cache.log.warn(\r
- "Query string that resulted in PDBEntry construction failure was :\n" +\r
- textfield.getText());\r
- }\r
-\r
- }\r
- else\r
- showErrorMessage("Error retrieving " + textfield.getText()\r
- + " from " + database.getSelectedItem());\r
- }\r
-\r
- return sequences;\r
-\r
- }\r
-\r
- void showErrorMessage(final String error)\r
- {\r
- resetDialog();\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
- }\r
- });\r
- }\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.*;
+import jalview.io.EBIFetchClient;
+import MCview.*;
+import jalview.datamodel.*;
+import jalview.analysis.AlignSeq;
+import java.io.File;
+import jalview.io.*;
+import java.util.*;
+
+public class SequenceFetcher
+ extends JPanel implements Runnable
+{
+ JInternalFrame frame;
+ AlignFrame alignFrame;
+ StringBuffer result;
+ final String noDbSelected = "-- Select Database --";
+ public SequenceFetcher(AlignFrame af)
+ {
+ alignFrame = af;
+ database.addItem(noDbSelected);
+ database.addItem("Uniprot");
+ database.addItem("EMBL");
+ database.addItem("EMBLCDS");
+ database.addItem("PDB");
+ database.addItem("PFAM");
+
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (System.getProperty("os.name").startsWith("Mac"))
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);
+ else
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);
+ }
+
+ private String getFrameTitle()
+ {
+ return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ this.setLayout(gridBagLayout1);
+
+ database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ database.setMinimumSize(new Dimension(160, 21));
+ database.setPreferredSize(new Dimension(160, 21));
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setText(
+ "Separate multiple accession ids with semi colon \";\"");
+ ok.setText("OK");
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ close.setText("Close");
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed(e);
+ }
+ });
+ textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textfield.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed(e);
+ }
+ });
+ jPanel1.add(ok);
+ jPanel1.add(close);
+ this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0
+ , GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(7, 4, 0, 6), 77, 6));
+ this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0
+ , GridBagConstraints.WEST,
+ GridBagConstraints.BOTH,
+ new Insets(7, -2, 7, 12), 241, -2));
+ this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0
+ , GridBagConstraints.WEST,
+ GridBagConstraints.NONE,
+ new Insets(0, 4, 0, 0), 1, 0));
+ this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0
+ , GridBagConstraints.CENTER,
+ GridBagConstraints.NONE,
+ new Insets(0, 0, 0, 6), 211, 1));
+ }
+
+ JComboBox database = new JComboBox();
+ JLabel jLabel1 = new JLabel();
+ JButton ok = new JButton();
+ JButton close = new JButton();
+ JPanel jPanel1 = new JPanel();
+ JTextField textfield = new JTextField();
+ GridBagLayout gridBagLayout1 = new GridBagLayout();
+ public void close_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {}
+ }
+
+ public void ok_actionPerformed(ActionEvent e)
+ {
+ database.setEnabled(false);
+ textfield.setEnabled(false);
+ ok.setEnabled(false);
+ close.setEnabled(false);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ private void resetDialog()
+ {
+ database.setEnabled(true);
+ textfield.setEnabled(true);
+ ok.setEnabled(true);
+ close.setEnabled(true);
+ }
+
+ public void run()
+ {
+ String error = "";
+ if (database.getSelectedItem().equals(noDbSelected))
+ error += "Please select the source database\n";
+ com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");
+ textfield.setText(empty.replaceAll(textfield.getText()));
+ if (textfield.getText().length() == 0)
+ error += "Please enter a (semi-colon separated list of) database id(s)";
+ if (error.length() > 0)
+ {
+ showErrorMessage(error);
+ resetDialog();
+ return;
+ }
+
+ result = new StringBuffer();
+ if (database.getSelectedItem().equals("Uniprot"))
+ {
+ getUniprotFile(textfield.getText());
+ }
+ else if (database.getSelectedItem().equals("EMBL")
+ || database.getSelectedItem().equals("EMBLCDS"))
+ {
+ StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
+ while(st.hasMoreTokens())
+ {
+ EBIFetchClient dbFetch = new EBIFetchClient();
+
+ String[] reply = dbFetch.fetchData(
+ database.getSelectedItem().toString().toLowerCase(
+ ) + ":" + st.nextToken(),
+ "fasta", "raw");
+//
+ if (reply != null)
+ {
+ for (int i = 0; i < reply.length; i++)
+ result.append(reply[i] + "\n");
+ }
+ }
+
+ if(result!=null && result.length()>1) // arbitrary minimum length for a seuqence file
+ {
+ System.out.println(result.toString());
+
+ parseResult(result.toString(), null);
+ }
+ }
+ else if (database.getSelectedItem().equals("PDB"))
+ {
+ StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
+ String query;
+ while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
+ {
+ StringBuffer respart = getPDBFile(query.toUpperCase());
+ if(respart!=null)
+ result.append(respart);
+ }
+
+
+ if (result.length()>0)
+ parseResult(result.toString(), null);
+ }
+ else if( database.getSelectedItem().equals("PFAM"))
+ {
+ try{
+ result.append(new FastaFile(
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="
+ + textfield.getText().toUpperCase(), "URL").print()
+ );
+
+ if(result.length()>0)
+ parseResult( result.toString(), textfield.getText().toUpperCase() );
+
+ }catch(java.io.IOException ex)
+ { result = null; }
+ }
+
+ if (result == null || result.length() == 0)
+ showErrorMessage("Error retrieving " + textfield.getText()
+ + " from " + database.getSelectedItem());
+
+ resetDialog();
+ return;
+ }
+
+ void getUniprotFile(String id)
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);
+
+ DBRefFetcher dbref = new DBRefFetcher();
+ Vector entries = dbref.getUniprotEntries(file);
+
+ if (entries != null)
+ {
+ //First, make the new sequences
+ Enumeration en = entries.elements();
+ while (en.hasMoreElements())
+ {
+ UniprotEntry entry = (UniprotEntry) en.nextElement();
+
+ StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");
+ Enumeration en2 = entry.getAccession().elements();
+ while (en2.hasMoreElements())
+ {
+ name.append("|");
+ name.append(en2.nextElement());
+ }
+ en2 = entry.getName().elements();
+ while (en2.hasMoreElements())
+ {
+ name.append("|");
+ name.append(en2.nextElement());
+ }
+
+ if (entry.getProtein() != null)
+ {
+ name.append(" " + entry.getProtein().getName().elementAt(0));
+ }
+
+ result.append(name + "\n" + entry.getUniprotSequence().getContent() +
+ "\n");
+
+ }
+
+ //Then read in the features and apply them to the dataset
+ SequenceI[] sequence = parseResult(result.toString(), null);
+ for (int i = 0; i < entries.size(); i++)
+ {
+ UniprotEntry entry = (UniprotEntry) entries.elementAt(i);
+ Enumeration e = entry.getDbReference().elements();
+ Vector onlyPdbEntries = new Vector();
+ while (e.hasMoreElements())
+ {
+ PDBEntry pdb = (PDBEntry) e.nextElement();
+ if (!pdb.getType().equals("PDB"))
+ continue;
+
+ onlyPdbEntries.addElement(pdb);
+ }
+
+ Enumeration en2 = entry.getAccession().elements();
+ while (en2.hasMoreElements())
+ {
+ sequence[i].getDatasetSequence().addDBRef(new DBRefEntry(DBRefSource.UNIPROT,
+ "0",
+ en2.nextElement().toString()));
+ }
+
+
+
+
+ sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);
+ if (entry.getFeature() != null)
+ {
+ e = entry.getFeature().elements();
+ while (e.hasMoreElements())
+ {
+ SequenceFeature sf = (SequenceFeature) e.nextElement();
+ sf.setFeatureGroup("Uniprot");
+ sequence[i].getDatasetSequence().addSequenceFeature( sf );
+ }
+ }
+ }
+ }
+ }
+
+ StringBuffer getPDBFile(String id)
+ {
+ StringBuffer result = new StringBuffer();
+ String chain = null;
+ if (id.indexOf(":") > -1)
+ {
+ chain = id.substring(id.indexOf(":") + 1);
+ id = id.substring(0, id.indexOf(":"));
+ }
+
+ EBIFetchClient ebi = new EBIFetchClient();
+ String file = ebi.fetchDataAsFile("pdb:" + id, "pdb", "raw").getAbsolutePath();
+ if (file == null)
+ return null;
+ try
+ {
+ PDBfile pdbfile = new PDBfile(file, jalview.io.AppletFormatAdapter.FILE);
+ for (int i = 0; i < pdbfile.chains.size(); i++)
+ {
+ if (chain == null ||
+ ( (PDBChain) pdbfile.chains.elementAt(i)).id.
+ toUpperCase().equals(chain))
+
+ result.append("\n>PDB|" + id + "|" +
+ ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
+ getName() +
+ "\n"
+ +
+ ( (PDBChain) pdbfile.chains.elementAt(i)).sequence.
+ getSequence());
+ }
+ }
+ catch (Exception ex) // Problem parsing PDB file
+ {
+ jalview.bin.Cache.log.warn("Exception when retrieving " +
+ textfield.getText() + " from " +
+ database.getSelectedItem(), ex);
+ return null;
+ }
+
+ return result;
+ }
+
+ SequenceI[] parseResult(String result, String title)
+ {
+ String format = new IdentifyFile().Identify(result, "Paste");
+ SequenceI[] sequences = null;
+
+ if (FormatAdapter.isValidFormat(format))
+ {
+ sequences = null;
+ try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",
+ format);}
+ catch(Exception ex){}
+
+ if (sequences != null && sequences.length > 0)
+ {
+ if (alignFrame == null)
+ {
+ AlignFrame af = new AlignFrame(new Alignment(sequences),
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT
+);
+ af.currentFileFormat = format;
+ if(title==null)
+ title = "Retrieved from " + database.getSelectedItem();
+ Desktop.addInternalFrame(af,
+ title,
+ AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ af.statusBar.setText("Successfully pasted alignment file");
+
+ try
+ {
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));
+ }
+ catch (Exception ex)
+ {}
+ }
+ else
+ {
+ for (int i = 0; i < sequences.length; i++)
+ {
+ alignFrame.viewport.alignment.addSequence(sequences[i]);
+
+ ////////////////////////////
+ //Dataset needs extension;
+ /////////////////////////////
+ Sequence ds = new Sequence(sequences[i].getName(),
+ AlignSeq.extractGaps("-. ",
+ sequences[i].getSequence()),
+ sequences[i].getStart(),
+ sequences[i].getEnd());
+ sequences[i].setDatasetSequence(ds);
+ alignFrame.viewport.alignment.getDataset().addSequence(ds);
+ }
+ alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
+ getHeight());
+ alignFrame.viewport.alignment.getWidth();
+ alignFrame.viewport.firePropertyChange("alignment", null,
+ alignFrame.viewport.
+ getAlignment().getSequences());
+
+ }
+
+ if (database.getSelectedItem().equals("PDB"))
+ {
+ // Parse out the ids from the structured names
+ boolean errors = false;
+ for (int i = 0; i < sequences.length; i++)
+ {
+ PDBEntry entry = new PDBEntry();
+ com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(
+ "PDB\\|([0-9A-z]{4})\\|(.)");
+ if (idbits.search(sequences[i].getName()))
+ {
+ String pdbid = idbits.substring(1);
+ String pdbccode = idbits.substring(2);
+ // Construct the PDBEntry
+ entry.setId(pdbid);
+ if (entry.getProperty() == null)
+ entry.setProperty(new Hashtable());
+ entry.getProperty().put("chains",
+ pdbccode
+ + "=" + sequences[i].getStart()
+ + "-" + sequences[i].getEnd());
+ sequences[i].getDatasetSequence().addPDBId(entry);
+
+ // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source
+ // JBPNote - PDB DBRefEntry should also carry the chain and mapping information
+ DBRefEntry dbentry = new DBRefEntry(jalview.datamodel.DBRefSource.PDB,"0",pdbid);
+ sequences[i].getDatasetSequence().addDBRef(dbentry);
+ }
+ else
+ {
+ // don't add an entry for this chain, but this is probably a bug
+ // that the user should know about.
+ jalview.bin.Cache.log.warn(
+ "No PDBEntry constructed for sequence " + i + " : " +
+ sequences[i].getName());
+ errors = true;
+ }
+ }
+ if (errors)
+ jalview.bin.Cache.log.warn(
+ "Query string that resulted in PDBEntry construction failure was :\n" +
+ textfield.getText());
+ }
+
+ }
+ else
+ showErrorMessage("Error retrieving " + textfield.getText()
+ + " from " + database.getSelectedItem());
+ }
+
+ return sequences;
+
+ }
+
+ void showErrorMessage(final String error)
+ {
+ resetDialog();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ error, "Error Retrieving Data",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+}
+
-/*\r
-* Jalview - A Sequence Alignment Editor and Viewer\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
-* as published by the Free Software Foundation; either version 2\r
-* of the License, or (at your option) any later version.\r
-*\r
-* This program is distributed in the hope that it will be useful,\r
-* but WITHOUT ANY WARRANTY; without even the implied warranty of\r
-* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
-* GNU General Public License for more details.\r
-*\r
-* You should have received a copy of the GNU General Public License\r
-* along with this program; if not, write to the Free Software\r
-* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
-*/\r
-package jalview.io;\r
-\r
-import java.io.*;\r
-\r
-import org.apache.axis.client.*;\r
-import org.apache.axis.encoding.XMLType;\r
-\r
-import javax.xml.namespace.QName;\r
-import javax.xml.rpc.ParameterMode;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class EBIFetchClient\r
-{\r
- Call call;\r
- String format = "default";\r
- String style = "raw";\r
-\r
- /**\r
- * Creates a new EBIFetchClient object.\r
- */\r
- public EBIFetchClient()\r
- {\r
- try\r
- {\r
- call = (Call) new Service().createCall();\r
- call.setTargetEndpointAddress(new java.net.URL(\r
- "http://www.ebi.ac.uk/ws/services/Dbfetch"));\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedDBs()\r
- {\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- return (String[]) call.invoke(new Object[] { });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedFormats()\r
- {\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- return (String[]) call.invoke(new Object[] { });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] getSupportedStyles()\r
- {\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- return (String[]) call.invoke(new Object[] { });\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-\r
- public static void main (String [] args)\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",\r
- "xml", null);\r
-\r
- try{\r
- java.io.PrintWriter out = new java.io.PrintWriter(\r
- new java.io.FileWriter("out.xml"));\r
-\r
-\r
- for(int i=0; i<result.length; i++)\r
- {\r
- out.println(result[i]);\r
- }\r
- out.close();\r
- }catch(Exception ex){ex.printStackTrace();}\r
-\r
- }\r
-\r
-\r
- public File fetchDataAsFile(String ids, String f, String s)\r
- {\r
- String [] data = fetchData(ids, f, s);\r
- File outFile = null;\r
- try{\r
- outFile = File.createTempFile("jalview", ".xml");\r
- outFile.deleteOnExit();\r
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
- int index=0;\r
- while( index < data.length )\r
- {\r
- out.println(data[index]);\r
- index++;\r
- }\r
- out.close();\r
- }catch(Exception ex){}\r
- return outFile;\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ids DOCUMENT ME!\r
- * @param f DOCUMENT ME!\r
- * @param s DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public String[] fetchData(String ids, String f, String s)\r
- {\r
- // ids should be of the form uniprot:25KD_SARPE;ADHR_DROPS;\r
- // max 50 ids can be added at one time\r
- try\r
- {\r
- call.setOperationName(new QName("urn:Dbfetch", "fetchData"));\r
- call.addParameter("query", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);\r
- call.setReturnType(XMLType.SOAP_ARRAY);\r
-\r
- if (f != null)\r
- {\r
- format = f;\r
- }\r
-\r
- if (s != null)\r
- {\r
- style = s;\r
- }\r
-\r
- try{\r
- return (String[]) call.invoke(new Object[]\r
- {ids, format, style});\r
- }catch(OutOfMemoryError er)\r
- {\r
- System.out.println("OUT OF MEMORY LOADING PDB FILE!!");\r
- }\r
- return null;\r
- }\r
- catch (Exception ex)\r
- {\r
- return null;\r
- }\r
- }\r
-}\r
+/*
+* Jalview - A Sequence Alignment Editor and Viewer
+* Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+*
+* This program is free software; you can redistribute it and/or
+* modify it under the terms of the GNU General Public License
+* as published by the Free Software Foundation; either version 2
+* of the License, or (at your option) any later version.
+*
+* This program is distributed in the hope that it will be useful,
+* but WITHOUT ANY WARRANTY; without even the implied warranty of
+* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+* GNU General Public License for more details.
+*
+* You should have received a copy of the GNU General Public License
+* along with this program; if not, write to the Free Software
+* Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+*/
+package jalview.io;
+
+import java.io.*;
+import java.util.Enumeration;
+import java.util.Hashtable;
+import java.util.StringTokenizer;
+
+import org.apache.axis.client.*;
+import org.apache.axis.encoding.XMLType;
+
+import javax.xml.namespace.QName;
+import javax.xml.rpc.ParameterMode;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class EBIFetchClient
+{
+ Call call;
+ String format = "default";
+ String style = "raw";
+
+ /**
+ * Creates a new EBIFetchClient object.
+ */
+ public EBIFetchClient()
+ {
+ try
+ {
+ call = (Call) new Service().createCall();
+ call.setTargetEndpointAddress(new java.net.URL(
+ "http://www.ebi.ac.uk/ws/services/Dbfetch"));
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedDBs()
+ {
+ try
+ {
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedDBs"));
+ call.setReturnType(XMLType.SOAP_ARRAY);
+
+ return (String[]) call.invoke(new Object[] { });
+ }
+ catch (Exception ex)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedFormats()
+ {
+ try
+ {
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedFormats"));
+ call.setReturnType(XMLType.SOAP_ARRAY);
+
+ return (String[]) call.invoke(new Object[] { });
+ }
+ catch (Exception ex)
+ {
+ return null;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public String[] getSupportedStyles()
+ {
+ try
+ {
+ call.setOperationName(new QName("urn:Dbfetch", "getSupportedStyles"));
+ call.setReturnType(XMLType.SOAP_ARRAY);
+
+ return (String[]) call.invoke(new Object[] { });
+ }
+ catch (Exception ex)
+ {
+ return null;
+ }
+ }
+
+ public static void main (String [] args)
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ String[] result = ebi.fetchData("uniprot:25KD_SARPE;G6PD_HUMAN",
+ "xml", null);
+
+ try{
+ java.io.PrintWriter out = new java.io.PrintWriter(
+ new java.io.FileWriter("out.xml"));
+
+
+ for(int i=0; i<result.length; i++)
+ {
+ out.println(result[i]);
+ }
+ out.close();
+ }catch(Exception ex){ex.printStackTrace();}
+
+ }
+
+
+ public File fetchDataAsFile(String ids, String f, String s)
+ {
+ String [] data = fetchData(ids, f, s);
+ File outFile = null;
+ try{
+ outFile = File.createTempFile("jalview", ".xml");
+ outFile.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ int index=0;
+ while( index < data.length )
+ {
+ out.println(data[index]);
+ index++;
+ }
+ out.close();
+ }catch(Exception ex){}
+ return outFile;
+ }
+
+ /**
+ * Single DB multiple record retrieval
+ *
+ * @param ids db:query1;query2;query3
+ * @param f raw/xml
+ * @param s ?
+ *
+ * @return Raw string array result of query set
+ */
+ public String[] fetchData(String ids, String f, String s)
+ {
+ // Need to split
+ // ids of the form uniprot:25KD_SARPE;ADHR_DROPS;
+
+ StringTokenizer queries=new StringTokenizer(ids,";");
+ String db=null;
+ StringBuffer querystring=null;
+ while (queries.hasMoreTokens()) {
+ String query=queries.nextToken();
+ int p;
+ if ((p=query.indexOf(':'))>-1 && (p+3<query.length())) {
+ db = query.substring(0,p);
+ query = query.substring(p+1);
+ }
+ if (querystring==null) {
+ querystring = new StringBuffer(query);
+ } else {
+ querystring.append(","+query);
+ }
+ }
+ if (db==null) {
+ System.err.println("Invalid Query string : '"+ids+"'\nShould be of form 'dbname:q1;q2;q3;q4'");
+ }
+ return fetchBatch(querystring.toString(), db, f, s);
+ }
+ public String[] fetchBatch(String ids, String db, String f, String s) {
+ // max 50 ids can be added at one time
+ try
+ {
+ //call.setOperationName(new QName("urn:Dbfetch", "fetchData"));
+ call.setOperationName(new QName("urn:Dbfetch", "fetchBatch"));
+ call.addParameter("ids", XMLType.XSD_STRING, ParameterMode.IN);
+ call.addParameter("db", XMLType.XSD_STRING, ParameterMode.IN);
+ call.addParameter("format", XMLType.XSD_STRING, ParameterMode.IN);
+ call.addParameter("style", XMLType.XSD_STRING, ParameterMode.IN);
+ call.setReturnType(XMLType.SOAP_ARRAY);
+
+ if (f != null)
+ {
+ format = f;
+ }
+
+ if (s != null)
+ {
+ style = s;
+ }
+
+ try{
+ return (String[]) call.invoke(new Object[]
+ {ids.toLowerCase(), db.toLowerCase(), format, style});
+ }catch(OutOfMemoryError er)
+ {
+ System.out.println("OUT OF MEMORY DOWNLOADING QUERY FROM "+db+":\n"+ids);
+ }
+ return null;
+ }
+ catch (Exception ex)
+ {
+ if (ex.getMessage().startsWith("uk.ac.ebi.jdbfetch.exceptions.DbfNoEntryFoundException"))
+ return null;
+ System.err.println("Unexpected exception when retrieving from "+db+"\nQuery was : '"+ids+"'");
+ ex.printStackTrace(System.err);
+ return null;
+ }
+ }
+}
git://source.jalview.org / jalview.git / commitdiff