-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 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 java.io.*;
-import java.util.*;
-
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import MCview.*;
-import jalview.datamodel.*;
-import jalview.datamodel.xdb.embl.*;
-import jalview.analysis.*;
-import java.io.File;
-import jalview.io.*;
-
-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"))
- {
- String DBRefSource = database.getSelectedItem().equals("EMBLCDS")
- ? jalview.datamodel.DBRefSource.EMBLCDS
- : jalview.datamodel.DBRefSource.EMBL;
-
- StringTokenizer st = new StringTokenizer(textfield.getText(), ";");
- SequenceI[] seqs = null;
- while(st.hasMoreTokens())
- {
- EBIFetchClient dbFetch = new EBIFetchClient();
-
- File reply = dbFetch.fetchDataAsFile(
- database.getSelectedItem().toString().toLowerCase(
- ) + ":" + st.nextToken(),
- "emblxml",null);
-
- jalview.datamodel.xdb.embl.EmblFile efile=null;
- if (reply != null && reply.exists())
- {
- efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);
- }
- if (efile!=null) {
- for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {
- EmblEntry entry = (EmblEntry) i.next();
- SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);
- if (seqparts!=null) {
- SequenceI[] newseqs = null;
- int si=0;
- if (seqs==null) {
- newseqs = new SequenceI[seqparts.length];
- } else {
- newseqs = new SequenceI[seqs.length+seqparts.length];
-
- for (;si<seqs.length; si++) {
- newseqs[si] = seqs[si];
- seqs[si] = null;
- }
- }
- for (int j=0;j<seqparts.length; si++, j++) {
- newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer
- }
- seqs=newseqs;
-
- }
- }
- } else {
- result=null;
- }
- }
- if (seqs!=null && seqs.length>0) {
- if (parseResult(new Alignment(seqs), null, null)!=null)
- result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");
- }
- }
- else if (database.getSelectedItem().equals("PDB"))
- {
- StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");
- String query;
- SequenceI[] seqs = null;
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))
- {
- SequenceI[] seqparts = getPDBFile(query.toUpperCase());
- if (seqparts != null)
- {
- if (seqs == null)
- {
- seqs = seqparts;
- }
- else
- {
- SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];
- int i=0;
- for (; i < seqs.length; i++)
- {
- newseqs[i] = seqs[i];
- seqs[i] = null;
- }
- for (int j=0;j<seqparts.length; i++, j++)
- {
- newseqs[i] = seqparts[j];
- }
- seqs=newseqs;
- }
- result.append("# Success for "+query.toUpperCase()+"\n");
- }
- }
- if (seqs != null && seqs.length > 0)
- {
- if (parseResult(new Alignment(seqs), null, null)!=null)
- {
- result.append(
- "# Successfully parsed the PDB File Queries into an Alignment");
- }
- }
- }
- 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
- Alignment al = 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())
- {
- al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(
- DBRefSource.UNIPROT,
- "0",
- en2.nextElement().toString()));
- }
-
-
-
-
- al.getSequenceAt(i).getDatasetSequence().setPDBId(onlyPdbEntries);
- if (entry.getFeature() != null)
- {
- e = entry.getFeature().elements();
- while (e.hasMoreElements())
- {
- SequenceFeature sf = (SequenceFeature) e.nextElement();
- sf.setFeatureGroup("Uniprot");
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );
- }
- }
- }
- }
- }
-
- SequenceI[] getPDBFile(String id)
- {
- Vector result = new Vector();
- 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))
- {
- PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);
- // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file
- SequenceI sq = pdbchain.sequence;
- // Specially formatted name for the PDB chain sequences retrieved from the PDB
- sq.setName("PDB|"+id+"|"+sq.getName());
- // Might need to add more metadata to the PDBEntry object
- // like below
- /*
- * PDBEntry entry = new PDBEntry();
- // Construct the PDBEntry
- entry.setId(id);
- if (entry.getProperty() == null)
- entry.setProperty(new Hashtable());
- entry.getProperty().put("chains",
- pdbchain.id
- + "=" + sq.getStart()
- + "-" + sq.getEnd());
- sq.getDatasetSequence().addPDBId(entry);
- */
- // Add PDB DB Refs
- // 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", id + pdbchain.id);
- sq.addDBRef(dbentry);
- // and add seuqence to the retrieved set
- result.addElement(sq.deriveSequence());
- }
- }
-
- if (result.size() < 1)
- {
- throw new Exception("WsDBFetch for PDB id resulted in zero result size");
- }
- }
- catch (Exception ex) // Problem parsing PDB file
- {
- jalview.bin.Cache.log.warn("Exception when retrieving " +
- textfield.getText() + " from " +
- database.getSelectedItem(), ex);
- return null;
- }
-
-
- SequenceI[] results = new SequenceI[result.size()];
- for (int i = 0, j = result.size(); i < j; i++)
- {
- results[i] = (SequenceI) result.elementAt(i);
- result.setElementAt(null,i);
- }
- return results;
- }
- Alignment parseResult(String result, String title)
- {
- String format = new IdentifyFile().Identify(result, "Paste");
- Alignment sequences = null;
- if (FormatAdapter.isValidFormat(format))
- {
- sequences = null;
- try
- {
- sequences = new FormatAdapter().readFile(result.toString(), "Paste",
- format);
- }
- catch (Exception ex)
- {}
-
- if (sequences!=null)
- {
- return parseResult(sequences, title, format);
- }
- }
- else
- {
- showErrorMessage("Error retrieving " + textfield.getText()
- + " from " + database.getSelectedItem());
- }
-
- return null;
- }
-
- Alignment parseResult(Alignment al, String title, String currentFileFormat)
- {
-
- if (al != null && al.getHeight() > 0)
- {
- if (alignFrame == null)
- {
- AlignFrame af = new AlignFrame(al,
- AlignFrame.DEFAULT_WIDTH,
- AlignFrame.DEFAULT_HEIGHT);
- if (currentFileFormat!=null)
- {
- af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?
- }
-
- 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 < al.getHeight(); i++)
- {
- alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries
- }
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.
- getHeight());
- alignFrame.viewport.alignment.getWidth();
- alignFrame.viewport.firePropertyChange("alignment", null,
- alignFrame.viewport.
- getAlignment().getSequences());
- }
- }
- return al;
- }
-
- 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) 2007 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 java.io.*;\r
+import java.util.*;\r
+\r
+import java.awt.*;\r
+import java.awt.event.*;\r
+import javax.swing.*;\r
+\r
+import MCview.*;\r
+import jalview.datamodel.*;\r
+import jalview.datamodel.xdb.embl.*;\r
+import java.io.File;\r
+import jalview.io.*;\r
+import java.awt.Rectangle;\r
+import java.awt.BorderLayout;\r
+import java.awt.Dimension;\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
+ {\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
+ }\r
+ else\r
+ {\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
+ }\r
+ }\r
+\r
+ private String getFrameTitle()\r
+ {\r
+ return ( (alignFrame == null) ? "New " : "Additional ") +\r
+ "Sequence Fetcher";\r
+ }\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+ this.setLayout(borderLayout2);\r
+\r
+ database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);\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();\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
+ textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
+ textArea.setLineWrap(true);\r
+ textArea.addKeyListener(new KeyAdapter()\r
+ {\r
+ public void keyPressed(KeyEvent e)\r
+ {\r
+ System.out.println(e.getKeyCode()+" "+KeyEvent.VK_ENTER);\r
+ if(e.getKeyCode()==KeyEvent.VK_ENTER)\r
+ ok_actionPerformed();\r
+ }\r
+ });\r
+ jPanel3.setLayout(borderLayout1);\r
+ borderLayout1.setVgap(5);\r
+ jPanel1.add(ok);\r
+ jPanel1.add(close);\r
+ jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);\r
+ jPanel2.add(database);\r
+ jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);\r
+ jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);\r
+ jScrollPane1.getViewport().add(textArea);\r
+\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
+ JTextArea textArea = new JTextArea();\r
+ JScrollPane jScrollPane1 = new JScrollPane();\r
+ JPanel jPanel2 = new JPanel();\r
+ JPanel jPanel3 = new JPanel();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ BorderLayout borderLayout2 = new BorderLayout();\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()\r
+ {\r
+ database.setEnabled(false);\r
+ textArea.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
+ textArea.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
+ {\r
+ error += "Please select the source database\n";\r
+ }\r
+ com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
+ textArea.setText(empty.replaceAll(textArea.getText()));\r
+ if (textArea.getText().length() == 0)\r
+ {\r
+ error += "Please enter a (semi-colon separated list of) database id(s)";\r
+ }\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(textArea.getText());\r
+ }\r
+ else if (database.getSelectedItem().equals("EMBL")\r
+ || database.getSelectedItem().equals("EMBLCDS"))\r
+ {\r
+ String DBRefSource = database.getSelectedItem().equals("EMBLCDS")\r
+ ? jalview.datamodel.DBRefSource.EMBLCDS\r
+ : jalview.datamodel.DBRefSource.EMBL;\r
+\r
+ StringTokenizer st = new StringTokenizer(textArea.getText(), ";");\r
+ SequenceI[] seqs = null;\r
+ while(st.hasMoreTokens())\r
+ {\r
+ EBIFetchClient dbFetch = new EBIFetchClient();\r
+\r
+ File reply = dbFetch.fetchDataAsFile(\r
+ database.getSelectedItem().toString().toLowerCase(\r
+ ) + ":" + st.nextToken(),\r
+ "emblxml",null);\r
+\r
+ jalview.datamodel.xdb.embl.EmblFile efile=null;\r
+ if (reply != null && reply.exists())\r
+ {\r
+ efile = jalview.datamodel.xdb.embl.EmblFile.getEmblFile(reply);\r
+ }\r
+ if (efile!=null) {\r
+ for (Iterator i=efile.getEntries().iterator(); i.hasNext(); ) {\r
+ EmblEntry entry = (EmblEntry) i.next();\r
+ SequenceI[] seqparts = entry.getSequences(false,true, DBRefSource);\r
+ if (seqparts!=null) {\r
+ SequenceI[] newseqs = null;\r
+ int si=0;\r
+ if (seqs==null) {\r
+ newseqs = new SequenceI[seqparts.length];\r
+ } else {\r
+ newseqs = new SequenceI[seqs.length+seqparts.length];\r
+\r
+ for (;si<seqs.length; si++) {\r
+ newseqs[si] = seqs[si];\r
+ seqs[si] = null;\r
+ }\r
+ }\r
+ for (int j=0;j<seqparts.length; si++, j++) {\r
+ newseqs[si] = seqparts[j].deriveSequence(); // place DBReferences on dataset and refer\r
+ }\r
+ seqs=newseqs;\r
+\r
+ }\r
+ }\r
+ } else {\r
+ result=null;\r
+ }\r
+ }\r
+ if (seqs!=null && seqs.length>0) {\r
+ if (parseResult(new Alignment(seqs), null, null)!=null)\r
+ result.append("# Successfully parsed the "+database.getSelectedItem()+" Queries into an Alignment");\r
+ }\r
+ }\r
+ else if (database.getSelectedItem().equals("PDB"))\r
+ {\r
+ StringTokenizer qset = new StringTokenizer(textArea.getText(), ";");\r
+ String query;\r
+ SequenceI[] seqs = null;\r
+ while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
+ {\r
+ SequenceI[] seqparts = getPDBFile(query.toUpperCase());\r
+ if (seqparts != null)\r
+ {\r
+ if (seqs == null)\r
+ {\r
+ seqs = seqparts;\r
+ }\r
+ else\r
+ {\r
+ SequenceI[] newseqs = new SequenceI[seqs.length+seqparts.length];\r
+ int i=0;\r
+ for (; i < seqs.length; i++)\r
+ {\r
+ newseqs[i] = seqs[i];\r
+ seqs[i] = null;\r
+ }\r
+ for (int j=0;j<seqparts.length; i++, j++)\r
+ {\r
+ newseqs[i] = seqparts[j];\r
+ }\r
+ seqs=newseqs;\r
+ }\r
+ result.append("# Success for "+query.toUpperCase()+"\n");\r
+ }\r
+ }\r
+ if (seqs != null && seqs.length > 0)\r
+ {\r
+ if (parseResult(new Alignment(seqs), null, null)!=null)\r
+ {\r
+ result.append(\r
+ "# Successfully parsed the PDB File Queries into an Alignment");\r
+ }\r
+ }\r
+ }\r
+ else if( database.getSelectedItem().equals("PFAM"))\r
+ {\r
+ try\r
+ {\r
+ result.append(new FastaFile(\r
+ "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
+ + textArea.getText().toUpperCase(), "URL").print()\r
+ );\r
+\r
+ if(result.length()>0)\r
+ {\r
+ parseResult( result.toString(), textArea.getText().toUpperCase() );\r
+ }\r
+\r
+ }\r
+ catch (java.io.IOException ex)\r
+ {\r
+ result = null;\r
+ }\r
+ }\r
+\r
+ if (result == null || result.length() == 0)\r
+ {\r
+ showErrorMessage("Error retrieving " + textArea.getText()\r
+ + " from " + database.getSelectedItem());\r
+ }\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
+ Alignment al = 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
+ {\r
+ continue;\r
+ }\r
+\r
+ onlyPdbEntries.addElement(pdb);\r
+ }\r
+\r
+ Enumeration en2 = entry.getAccession().elements();\r
+ while (en2.hasMoreElements())\r
+ {\r
+ al.getSequenceAt(i).getDatasetSequence().addDBRef(new DBRefEntry(\r
+ DBRefSource.UNIPROT,\r
+ "0",\r
+ en2.nextElement().toString()));\r
+ }\r
+\r
+\r
+\r
+\r
+ al.getSequenceAt(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
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature( sf );\r
+ }\r
+ }\r
+ }\r
+ }\r
+ }\r
+\r
+ SequenceI[] getPDBFile(String id)\r
+ {\r
+ Vector result = new Vector();\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").\r
+ getAbsolutePath();\r
+ if (file == null)\r
+ {\r
+ return null;\r
+ }\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
+ PDBChain pdbchain = (PDBChain) pdbfile.chains.elementAt(i);\r
+ // Get the Chain's Sequence - who's dataset includes any special features added from the PDB file\r
+ SequenceI sq = pdbchain.sequence;\r
+ // Specially formatted name for the PDB chain sequences retrieved from the PDB\r
+ sq.setName("PDB|"+id+"|"+sq.getName());\r
+ // Might need to add more metadata to the PDBEntry object\r
+ // like below\r
+ /*\r
+ * PDBEntry entry = new PDBEntry();\r
+ // Construct the PDBEntry\r
+ entry.setId(id);\r
+ if (entry.getProperty() == null)\r
+ entry.setProperty(new Hashtable());\r
+ entry.getProperty().put("chains",\r
+ pdbchain.id\r
+ + "=" + sq.getStart()\r
+ + "-" + sq.getEnd());\r
+ sq.getDatasetSequence().addPDBId(entry);\r
+ */\r
+ // Add PDB DB Refs\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,\r
+ "0", id + pdbchain.id);\r
+ sq.addDBRef(dbentry);\r
+ // and add seuqence to the retrieved set\r
+ result.addElement(sq.deriveSequence());\r
+ }\r
+ }\r
+\r
+ if (result.size() < 1)\r
+ {\r
+ throw new Exception("WsDBFetch for PDB id resulted in zero result size");\r
+ }\r
+ }\r
+ catch (Exception ex) // Problem parsing PDB file\r
+ {\r
+ jalview.bin.Cache.log.warn("Exception when retrieving " +\r
+ textArea.getText() + " from " +\r
+ database.getSelectedItem(), ex);\r
+ return null;\r
+ }\r
+\r
+\r
+ SequenceI[] results = new SequenceI[result.size()];\r
+ for (int i = 0, j = result.size(); i < j; i++)\r
+ {\r
+ results[i] = (SequenceI) result.elementAt(i);\r
+ result.setElementAt(null,i);\r
+ }\r
+ return results;\r
+ }\r
+ Alignment parseResult(String result, String title)\r
+ {\r
+ String format = new IdentifyFile().Identify(result, "Paste");\r
+ Alignment sequences = null;\r
+ if (FormatAdapter.isValidFormat(format))\r
+ {\r
+ sequences = null;\r
+ try\r
+ {\r
+ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
+ format);\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+\r
+ if (sequences!=null)\r
+ {\r
+ return parseResult(sequences, title, format);\r
+ }\r
+ }\r
+ else\r
+ {\r
+ showErrorMessage("Error retrieving " + textArea.getText()\r
+ + " from " + database.getSelectedItem());\r
+ }\r
+\r
+ return null;\r
+ }\r
+\r
+ Alignment parseResult(Alignment al, String title, String currentFileFormat)\r
+ {\r
+\r
+ if (al != null && al.getHeight() > 0)\r
+ {\r
+ if (alignFrame == null)\r
+ {\r
+ AlignFrame af = new AlignFrame(al,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+ if (currentFileFormat!=null)\r
+ {\r
+ af.currentFileFormat = currentFileFormat; // WHAT IS THE DEFAULT FORMAT FOR NON-FormatAdapter Sourced Alignments?\r
+ }\r
+\r
+ if(title==null)\r
+ {\r
+ title = "Retrieved from " + database.getSelectedItem();\r
+ }\r
+\r
+ Desktop.addInternalFrame(af,\r
+ title,\r
+ AlignFrame.DEFAULT_WIDTH,\r
+ AlignFrame.DEFAULT_HEIGHT);\r
+\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 < al.getHeight(); i++)\r
+ {\r
+ alignFrame.viewport.alignment.addSequence(al.getSequenceAt(i)); // this also creates dataset sequence entries\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
+ return al;\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
git://source.jalview.org / jalview.git / commitdiff