-/*\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
- 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
+/*
+ * 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 java.io.File;
+import jalview.io.*;
+import jalview.ws.DBRefFetcher;
+import jalview.ws.EBIFetchClient;
+
+import java.awt.Rectangle;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+
+public class SequenceFetcher
+extends JPanel implements Runnable
+{
+ jalview.ws.SequenceFetcher sfetch;
+ JInternalFrame frame;
+ AlignFrame alignFrame;
+ StringBuffer result;
+ final String noDbSelected = "-- Select Database --";
+ public SequenceFetcher(AlignFrame af)
+ {
+ alignFrame = af;
+ sfetch = new jalview.ws.SequenceFetcher();
+ database.addItem(noDbSelected);
+ /*
+ * Dynamically generated database list
+ * will need a translation function from
+ * internal source to externally distinct names.
+ * UNIPROT and UP_NAME are identical DB sources,
+ * and should be collapsed.
+ *
+
+ String dbs[] = sfetch.getSupportedDb();
+ for (int i=0; i<dbs.length;i++)
+ {
+ if (DBRefSource.isPrimaryDb(dbs[i]))
+ {
+ database.addItem(dbs[i]);
+ // should have some kind of human readable description of each database displayed when
+ * that combo is selected.
+ }
+ }*/
+ 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(borderLayout2);
+
+ database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText(
+ "Separate multiple accession ids with semi colon \";\"");
+ ok.setText("OK");
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ close.setText("Close");
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed(e);
+ }
+ });
+ textArea.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent e)
+ {
+ if(e.getKeyCode()==KeyEvent.VK_ENTER)
+ ok_actionPerformed();
+ }
+ });
+ jPanel3.setLayout(borderLayout1);
+ borderLayout1.setVgap(5);
+ jPanel1.add(ok);
+ jPanel1.add(close);
+ jPanel3.add(jPanel2, java.awt.BorderLayout.WEST);
+ jPanel2.add(database);
+ jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
+ jPanel3.add(jLabel1, java.awt.BorderLayout.NORTH);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ jScrollPane1.getViewport().add(textArea);
+
+ }
+
+ JComboBox database = new JComboBox();
+ JLabel jLabel1 = new JLabel();
+ JButton ok = new JButton();
+ JButton close = new JButton();
+ JPanel jPanel1 = new JPanel();
+ JTextArea textArea = new JTextArea();
+ JScrollPane jScrollPane1 = new JScrollPane();
+ JPanel jPanel2 = new JPanel();
+ JPanel jPanel3 = new JPanel();
+ BorderLayout borderLayout1 = new BorderLayout();
+ BorderLayout borderLayout2 = new BorderLayout();
+ public void close_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ }
+ catch (Exception ex)
+ {}
+ }
+
+ public void ok_actionPerformed()
+ {
+ database.setEnabled(false);
+ textArea.setEnabled(false);
+ ok.setEnabled(false);
+ close.setEnabled(false);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ private void resetDialog()
+ {
+ database.setEnabled(true);
+ textArea.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+", "");
+ textArea.setText(empty.replaceAll(textArea.getText()));
+ if (textArea.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(textArea.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(textArea.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(textArea.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="
+ + textArea.getText().toUpperCase(), "URL").print()
+ );
+
+ if(result.length()>0)
+ {
+ parseResult( result.toString(), textArea.getText().toUpperCase() );
+ }
+
+ }
+ catch (java.io.IOException ex)
+ {
+ result = null;
+ }
+ }
+
+ if (result == null || result.length() == 0)
+ {
+ showErrorMessage("Error retrieving " + textArea.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 " +
+ textArea.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 " + textArea.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);
+ }
+ });
+ }
+}
+
git://source.jalview.org / jalview.git / blobdiff