-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
-\r
-public class SequenceFetcher\r
- extends JPanel implements Runnable\r
-{\r
- JInternalFrame frame;\r
- AlignFrame alignFrame;\r
- StringBuffer result;\r
- public SequenceFetcher(AlignFrame af)\r
- {\r
- alignFrame = af;\r
- database.addItem("-- Select Database --");\r
- database.addItem("Uniprot");\r
- database.addItem("EMBL");\r
- database.addItem("EMBLCDS");\r
- database.addItem("PDB");\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, "Sequence Fetcher (WSDBfetch@EBI)", 400, 140);\r
- else\r
- Desktop.addInternalFrame(frame, "Sequence Fetcher (WSDBfetch@EBI)", 400, 125);\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
- cancel.setText("Cancel");\r
- cancel.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- cancel_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(cancel);\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.HORIZONTAL,\r
- new Insets(0, 0, 0, 6), 200, 1));\r
- }\r
-\r
- JComboBox database = new JComboBox();\r
- JLabel jLabel1 = new JLabel();\r
- JButton ok = new JButton();\r
- JButton cancel = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- JTextField textfield = new JTextField();\r
- GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- public void cancel_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
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI) - Fetching Sequence...");\r
- database.setEnabled(false);\r
- textfield.setEnabled(false);\r
- ok.setEnabled(false);\r
- cancel.setEnabled(false);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
- public void run()\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
- EBIFetchClient dbFetch = new EBIFetchClient();\r
- String[] reply = dbFetch.fetchData(\r
- database.getSelectedItem().toString().toLowerCase(\r
- ) + ":" + textfield.getText(),\r
- "fasta", "raw");\r
-\r
- for (int i = 0; i < reply.length; i++)\r
- result.append(reply[i] + "\n");\r
-\r
- parseResult(result.toString());\r
- }\r
- else if (database.getSelectedItem().equals("PDB"))\r
- {\r
- result = getPDBFile(textfield.getText().toUpperCase());\r
- parseResult(result.toString());\r
- }\r
-\r
-\r
- if (result == null || result.length() == 0)\r
- showErrorMessage("Error retrieving " + textfield.getText()\r
- + " from " + database.getSelectedItem());\r
-\r
-\r
- database.setEnabled(true);\r
- textfield.setEnabled(true);\r
- ok.setEnabled(true);\r
- cancel.setEnabled(true);\r
- frame.setTitle("Sequence Fetcher (WSDBfetch@EBI)");\r
- }\r
-\r
- void getUniprotFile(String id)\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\r
- SequenceFeatureFetcher sff = new SequenceFeatureFetcher();\r
- Vector entries = sff.getUniprotEntries(file);\r
-\r
- 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
- 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.getProteinName()!=null)\r
- name.append(" "+entry.getProteinName().elementAt(0));\r
-\r
- result.append(name +"\n"+entry.getUniprotSequence().getContent());\r
-\r
- }\r
-\r
- //Then read in the features and apply them to the dataset\r
- SequenceI [] sequence = parseResult(result.toString());\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
- sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- sequence[i].getDatasetSequence().setSequenceFeatures(entry.getFeature());\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[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
- try\r
- {\r
- PDBfile pdbfile = new PDBfile(reply);\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
- 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
- showErrorMessage("Error retrieving " + textfield.getText() + " from " +\r
- database.getSelectedItem());\r
- return null;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- SequenceI[] parseResult(String result)\r
- {\r
- String format = IdentifyFile.Identify(result, "Paste");\r
- SequenceI[] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- {\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
- if (sequences != null && sequences.length>0)\r
- {\r
- if(alignFrame==null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- Desktop.addInternalFrame(af, "Retrieved from "+database.getSelectedItem(),\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- af.statusBar.setText("Successfully pasted alignment file");\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
- //Datset 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.getAlignment().getSequences());\r
-\r
- }\r
-\r
- if (database.getSelectedItem().equals("PDB"))\r
- {\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- entry.setId(textfield.getText());\r
- sequences[i].getDatasetSequence().addPDBId(entry);\r
- }\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(String error)\r
- {\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data", JOptionPane.WARNING_MESSAGE);\r
- }\r
-}\r
-\r
-\r
-\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview 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 3 of the License, or (at your option) any later version.
+ *
+ * Jalview 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+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.ebi.EBIFetchClient;
+import jalview.ws.seqfetcher.ASequenceFetcher;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+import java.awt.Rectangle;
+import java.awt.BorderLayout;
+import java.awt.Dimension;
+
+public class SequenceFetcher extends JPanel implements Runnable
+{
+ // ASequenceFetcher sfetch;
+ JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
+
+ AlignFrame alignFrame;
+
+ StringBuffer result;
+
+ final String noDbSelected = "-- Select Database --";
+
+ Hashtable sources = new Hashtable();
+
+ private static jalview.ws.SequenceFetcher sfetch = null;
+
+ private static String dasRegistry = null;
+
+ private static boolean _initingFetcher = false;
+
+ private static Thread initingThread = null;
+
+ /**
+ * Blocking method that initialises and returns the shared instance of the
+ * SequenceFetcher client
+ *
+ * @param guiWindow
+ * - where the initialisation delay message should be shown
+ * @return the singleton instance of the sequence fetcher client
+ */
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton(
+ final IProgressIndicator guiWindow)
+ {
+ if (_initingFetcher && initingThread != null && initingThread.isAlive())
+ {
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ // initting happening on another thread - so wait around to see if it
+ // finishes.
+ while (_initingFetcher && initingThread != null
+ && initingThread.isAlive())
+ {
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception e)
+ {
+ }
+ ;
+ }
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar(
+ "Waiting for Sequence Database Fetchers to initialise",
+ Thread.currentThread().hashCode());
+ }
+ }
+ if (sfetch == null
+ || dasRegistry != DasSourceBrowser.getDasRegistryURL())
+ {
+ _initingFetcher = true;
+ initingThread = Thread.currentThread();
+ /**
+ * give a visual indication that sequence fetcher construction is occuring
+ */
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ Thread.currentThread().hashCode());
+ }
+ dasRegistry = DasSourceBrowser.getDasRegistryURL();
+ jalview.ws.SequenceFetcher sf = new jalview.ws.SequenceFetcher();
+ if (guiWindow != null)
+ {
+ guiWindow.setProgressBar("Initialising Sequence Database Fetchers",
+ Thread.currentThread().hashCode());
+ }
+ sfetch = sf;
+ _initingFetcher = false;
+ initingThread = null;
+ }
+ return sfetch;
+ }
+
+ public SequenceFetcher(IProgressIndicator guiIndic)
+ {
+ final IProgressIndicator guiWindow = guiIndic;
+ final SequenceFetcher us = this;
+ // launch initialiser thread
+ Thread sf = new Thread(new Runnable()
+ {
+
+ public void run()
+ {
+ if (getSequenceFetcherSingleton(guiWindow) != null)
+ {
+ us.initGui(guiWindow);
+ }
+ else
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane
+ .showInternalMessageDialog(
+ Desktop.desktop,
+ "Could not create the sequence fetcher client. Check error logs for details.",
+ "Couldn't create SequenceFetcher",
+ JOptionPane.ERROR_MESSAGE);
+ }
+ });
+
+ // raise warning dialog
+ }
+ }
+ });
+ sf.start();
+ }
+
+ /**
+ * called by thread spawned by constructor
+ *
+ * @param guiWindow
+ */
+ private void initGui(IProgressIndicator guiWindow)
+ {
+ this.guiWindow = guiWindow;
+ if (guiWindow instanceof AlignFrame)
+ {
+ alignFrame = (AlignFrame) guiWindow;
+ }
+
+ 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.getOrderedSupportedSources();
+ for (int i = 0; i < dbs.length; i++)
+ {
+ if (!sources.containsValue(dbs[i]))
+ {
+ String name = sfetch.getSourceProxy(dbs[i]).getDbName();
+ // duplicate source names are thrown away, here.
+ if (!sources.containsKey(name))
+ {
+ database.addItem(name);
+ }
+ // overwrite with latest version of the retriever for this source
+ sources.put(name, dbs[i]);
+ }
+ }
+ try
+ {
+ jbInit();
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ if (new jalview.util.Platform().isAMac())
+ {
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 240);
+ }
+ else
+ {
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 180);
+ }
+ }
+
+ private String getFrameTitle()
+ {
+ return ((alignFrame == null) ? "New " : "Additional ")
+ + "Sequence Fetcher";
+ }
+
+ private void jbInit() throws Exception
+ {
+ this.setLayout(borderLayout2);
+
+ database.setFont(JvSwingUtils.getLabelFont());
+ dbeg.setFont(new java.awt.Font("Verdana", Font.BOLD, 11));
+ jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.CENTER);
+ jLabel1.setText("Separate multiple accession ids with semi colon \";\"");
+
+ replacePunctuation.setHorizontalAlignment(SwingConstants.CENTER);
+ replacePunctuation
+ .setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));
+ replacePunctuation.setText("Replace commas with semi-colons");
+ ok.setText("OK");
+ ok.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ clear.setText("Clear");
+ clear.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ clear_actionPerformed();
+ }
+ });
+
+ example.setText("Example");
+ example.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ example_actionPerformed();
+ }
+ });
+ close.setText("Close");
+ close.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed(e);
+ }
+ });
+ textArea.setFont(JvSwingUtils.getLabelFont());
+ 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(example);
+ jPanel1.add(clear);
+ jPanel1.add(close);
+ jPanel3.add(jPanel2, java.awt.BorderLayout.CENTER);
+ jPanel2.setLayout(borderLayout3);
+
+ database.addActionListener(new ActionListener()
+ {
+
+ public void actionPerformed(ActionEvent e)
+ {
+ DbSourceProxy db = null;
+ try
+ {
+ db = sfetch.getSourceProxy((String) sources.get(database
+ .getSelectedItem()));
+ String eq = db.getTestQuery();
+ dbeg.setText("Example query: " + eq);
+ replacePunctuation.setEnabled(!(eq != null && eq.indexOf(",") > -1));
+ } catch (Exception ex)
+ {
+ dbeg.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ jPanel2.repaint();
+ }
+ });
+ dbeg.setText("");
+ jPanel2.add(database, java.awt.BorderLayout.NORTH);
+ jPanel2.add(dbeg, java.awt.BorderLayout.CENTER);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, java.awt.BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, java.awt.BorderLayout.SOUTH);
+ jPanel2.add(jPanel2a, java.awt.BorderLayout.SOUTH);
+ // jPanel2.setPreferredSize(new Dimension())
+ jPanel3.add(jScrollPane1, java.awt.BorderLayout.CENTER);
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);
+ this.add(jPanel3, java.awt.BorderLayout.CENTER);
+ this.add(jPanel2, java.awt.BorderLayout.NORTH);
+ jScrollPane1.getViewport().add(textArea);
+
+ }
+
+ protected void example_actionPerformed()
+ {
+ DbSourceProxy db = null;
+ try
+ {
+ db = sfetch.getSourceProxy((String) sources.get(database
+ .getSelectedItem()));
+ textArea.setText(db.getTestQuery());
+ } catch (Exception ex)
+ {
+ }
+ jPanel3.repaint();
+ }
+
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ jPanel3.repaint();
+ }
+
+ JLabel dbeg = new JLabel();
+
+ JComboBox database = new JComboBox();
+
+ JLabel jLabel1 = new JLabel();
+
+ JCheckBox replacePunctuation = new JCheckBox();
+
+ JButton ok = new JButton();
+
+ JButton clear = new JButton();
+
+ JButton example = 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();
+
+ JPanel jPanel4 = new JPanel();
+
+ BorderLayout borderLayout1 = new BorderLayout();
+
+ BorderLayout borderLayout2 = new BorderLayout();
+
+ BorderLayout borderLayout3 = 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";
+ }
+ // TODO: make this transformation more configurable
+ com.stevesoft.pat.Regex empty;
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ empty = new com.stevesoft.pat.Regex(
+ // replace commas and spaces with a semicolon
+ "(\\s|[,; ])+", ";");
+ }
+ else
+ {
+ // just turn spaces and semicolons into single semicolons
+ empty = new com.stevesoft.pat.Regex("(\\s|[; ])+", ";");
+ }
+ textArea.setText(empty.replaceAll(textArea.getText()));
+ // see if there's anthing to search with
+ if (!new com.stevesoft.pat.Regex("[A-Za-z0-9_.]").search(textArea
+ .getText()))
+ {
+ error += "Please enter a (semi-colon separated list of) database id(s)";
+ }
+ if (error.length() > 0)
+ {
+ showErrorMessage(error);
+ resetDialog();
+ return;
+ }
+ ArrayList<String> aresultq=new ArrayList<String>();
+ ArrayList<AlignmentI> aresult = new ArrayList<AlignmentI>();
+ Object source = database.getSelectedItem();
+ Enumeration en = new StringTokenizer(textArea.getText(), ";");
+ boolean isAliSource=false;
+ try
+ {
+ guiWindow.setProgressBar(
+ "Fetching Sequences from " + database.getSelectedItem(),
+ Thread.currentThread().hashCode());
+ DbSourceProxy proxy = sfetch.getSourceProxy((String) sources
+ .get(source));
+ isAliSource = proxy.isA(DBRefSource.ALIGNMENTDB);
+ if (proxy.getAccessionSeparator() == null)
+ {
+ while (en.hasMoreElements())
+ {
+ String item = (String) en.nextElement();
+ try
+ {
+ if (aresult != null)
+ {
+ try
+ {
+ // give the server a chance to breathe
+ Thread.sleep(5);
+ } catch (Exception e)
+ {
+ //
+ }
+
+ }
+
+ AlignmentI indres = null;
+ try
+ {
+ indres = proxy.getSequenceRecords(item);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + item + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(item);
+ aresult.add(indres);
+ }
+ } catch (Exception e)
+ {
+ jalview.bin.Cache.log.info("Error retrieving " + item
+ + " from " + source, e);
+ }
+ }
+ }
+ else
+ {
+ StringBuffer multiacc = new StringBuffer();
+ while (en.hasMoreElements())
+ {
+ multiacc.append(en.nextElement());
+ if (en.hasMoreElements())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+ try
+ {
+ aresultq.add(multiacc.toString());
+ aresult.add(proxy.getSequenceRecords(multiacc.toString()));
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + database.getSelectedItem(), oome, this);
+ }
+
+ }
+
+ } catch (Exception e)
+ {
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + database.getSelectedItem());
+ // error +="Couldn't retrieve sequences from "+database.getSelectedItem();
+ System.err.println("Retrieval failed for source ='"
+ + database.getSelectedItem() + "' and query\n'"
+ + textArea.getText() + "'\n");
+ e.printStackTrace();
+ } catch (OutOfMemoryError e)
+ {
+ // resets dialog box - so we don't use OOMwarning here.
+ showErrorMessage("Out of Memory when retrieving "
+ + textArea.getText()
+ + " from "
+ + database.getSelectedItem()
+ + "\nPlease see the Jalview FAQ for instructions for increasing the memory available to Jalview.\n");
+ e.printStackTrace();
+ } catch (Error e)
+ {
+ showErrorMessage("Serious Error retrieving " + textArea.getText()
+ + " from " + database.getSelectedItem());
+ e.printStackTrace();
+ }
+ if (aresult != null && aresult.size()>0)
+ {
+ AlignmentI ar=null;
+ if (isAliSource) {
+ // new window for each result
+ while (aresult.size()>0)
+ {
+ parseResult(aresult.remove(0), aresultq.remove(0)+" "+getDefaultRetrievalTitle(), null);
+ }
+ } else {
+ // concatenate all results in one window
+ while (aresult.size()>0)
+ {
+ if (ar==null) { ar = aresult.remove(0);}
+ else { ar.append(aresult.remove(0)); };
+ }
+ parseResult(ar, null, null);
+ }
+ }
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+ resetDialog();
+ }
+
+ /*
+ * 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(); String qry =
+ * database.getSelectedItem().toString().toLowerCase( ) + ":" +
+ * st.nextToken(); File reply = dbFetch.fetchDataAsFile( qry, "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.append("# no response for "+qry); } } 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; }
+ */
+ AlignmentI 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;
+ }
+
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently selected source and settings
+ */
+ public String getDefaultRetrievalTitle() {
+ return "Retrieved from " + database.getSelectedItem();
+ }
+ AlignmentI parseResult(AlignmentI 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 = getDefaultRetrievalTitle();
+ }
+ SequenceFeature[] sfs = null;
+ for (Enumeration sq = al.getSequences().elements(); sq
+ .hasMoreElements();)
+ {
+ if ((sfs = ((SequenceI) sq.nextElement()).getDatasetSequence()
+ .getSequenceFeatures()) != null)
+ {
+ if (sfs.length > 0)
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
+
+ }
+ 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