-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import javax.swing.*;\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-import jalview.io.EBIFetchClient;\r
-import MCview.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.AlignSeq;\r
-import java.io.File;\r
-import jalview.io.*;\r
-import java.util.*;\r
-\r
-public class SequenceFetcher\r
- extends JPanel implements Runnable\r
-{\r
- JInternalFrame frame;\r
- AlignFrame alignFrame;\r
- StringBuffer result;\r
- final String noDbSelected = "-- Select Database --";\r
- public SequenceFetcher(AlignFrame af)\r
- {\r
- alignFrame = af;\r
- database.addItem(noDbSelected);\r
- database.addItem("Uniprot");\r
- database.addItem("EMBL");\r
- database.addItem("EMBLCDS");\r
- database.addItem("PDB");\r
- database.addItem("PFAM");\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- frame = new JInternalFrame();\r
- frame.setContentPane(this);\r
- if (System.getProperty("os.name").startsWith("Mac"))\r
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
- else\r
- Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
- }\r
-\r
- private String getFrameTitle()\r
- {\r
- return ( (alignFrame == null) ? "New " : "Additional ") + "Sequence Fetcher";\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.setLayout(gridBagLayout1);\r
-\r
- database.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- database.setMinimumSize(new Dimension(160, 21));\r
- database.setPreferredSize(new Dimension(160, 21));\r
- jLabel1.setFont(new java.awt.Font("Verdana", Font.ITALIC, 11));\r
- jLabel1.setText(\r
- "Separate multiple accession ids with semi colon \";\"");\r
- ok.setText("OK");\r
- ok.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- close.setText("Close");\r
- close.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- close_actionPerformed(e);\r
- }\r
- });\r
- textfield.setFont(new java.awt.Font("Verdana", Font.PLAIN, 11));\r
- textfield.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- ok_actionPerformed(e);\r
- }\r
- });\r
- jPanel1.add(ok);\r
- jPanel1.add(close);\r
- this.add(jLabel1, new GridBagConstraints(0, 0, 2, 1, 0.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(7, 4, 0, 6), 77, 6));\r
- this.add(jPanel1, new GridBagConstraints(0, 2, 2, 1, 1.0, 1.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.BOTH,\r
- new Insets(7, -2, 7, 12), 241, -2));\r
- this.add(database, new GridBagConstraints(0, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.WEST,\r
- GridBagConstraints.NONE,\r
- new Insets(0, 4, 0, 0), 1, 0));\r
- this.add(textfield, new GridBagConstraints(1, 1, 1, 1, 1.0, 0.0\r
- , GridBagConstraints.CENTER,\r
- GridBagConstraints.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 close = new JButton();\r
- JPanel jPanel1 = new JPanel();\r
- JTextField textfield = new JTextField();\r
- GridBagLayout gridBagLayout1 = new GridBagLayout();\r
- public void close_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- frame.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {}\r
- }\r
-\r
- public void ok_actionPerformed(ActionEvent e)\r
- {\r
- database.setEnabled(false);\r
- textfield.setEnabled(false);\r
- ok.setEnabled(false);\r
- close.setEnabled(false);\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
- }\r
-\r
- private void resetDialog()\r
- {\r
- database.setEnabled(true);\r
- textfield.setEnabled(true);\r
- ok.setEnabled(true);\r
- close.setEnabled(true);\r
- }\r
-\r
- public void run()\r
- {\r
- String error = "";\r
- if (database.getSelectedItem().equals(noDbSelected))\r
- error += "Please select the source database\n";\r
- com.stevesoft.pat.Regex empty = new com.stevesoft.pat.Regex("\\s+", "");\r
- textfield.setText(empty.replaceAll(textfield.getText()));\r
- if (textfield.getText().length() == 0)\r
- error += "Please enter a (semi-colon separated list of) database id(s)";\r
- if (error.length() > 0)\r
- {\r
- showErrorMessage(error);\r
- resetDialog();\r
- return;\r
- }\r
-\r
- result = new StringBuffer();\r
- if (database.getSelectedItem().equals("Uniprot"))\r
- {\r
- getUniprotFile(textfield.getText());\r
- }\r
- else if (database.getSelectedItem().equals("EMBL")\r
- || database.getSelectedItem().equals("EMBLCDS"))\r
- {\r
- EBIFetchClient dbFetch = new EBIFetchClient();\r
- String[] reply = dbFetch.fetchData(\r
- database.getSelectedItem().toString().toLowerCase(\r
- ) + ":" + textfield.getText(),\r
- "fasta", "raw");\r
-\r
- if(reply!=null)\r
- {\r
- for (int i = 0; i < reply.length; i++)\r
- result.append(reply[i] + "\n");\r
-\r
- parseResult(result.toString(), null);\r
- }\r
- }\r
- else if (database.getSelectedItem().equals("PDB"))\r
- {\r
- StringTokenizer qset = new StringTokenizer(textfield.getText(), ";");\r
- String query;\r
- while (qset.hasMoreTokens() && ((query = qset.nextToken())!=null))\r
- {\r
- StringBuffer respart = getPDBFile(query.toUpperCase());\r
- if(respart!=null)\r
- result.append(respart);\r
- }\r
-\r
-\r
- if (result.length()>0)\r
- parseResult(result.toString(), null);\r
- }\r
- else if( database.getSelectedItem().equals("PFAM"))\r
- {\r
- try{\r
- result.append(new FastaFile(\r
- "http://www.sanger.ac.uk/cgi-bin/Pfam/getalignment.pl?format=fal&acc="\r
- + textfield.getText().toUpperCase(), "URL").print()\r
- );\r
-\r
- if(result.length()>0)\r
- parseResult( result.toString(), textfield.getText().toUpperCase() );\r
-\r
- }catch(java.io.IOException ex)\r
- { result = null; }\r
- }\r
-\r
- if (result == null || result.length() == 0)\r
- showErrorMessage("Error retrieving " + textfield.getText()\r
- + " from " + database.getSelectedItem());\r
-\r
- resetDialog();\r
- return;\r
- }\r
-\r
- void getUniprotFile(String id)\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:" + id, "xml", null);\r
- // File file = new File("H:/jalview/classes/fer1.xml");\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
-\r
- StringBuffer name = new StringBuffer(">UniProt/Swiss-Prot");\r
- Enumeration en2 = entry.getAccession().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
- en2 = entry.getName().elements();\r
- while (en2.hasMoreElements())\r
- {\r
- name.append("|");\r
- name.append(en2.nextElement());\r
- }\r
-\r
- if (entry.getProtein() != null)\r
- {\r
- name.append(" " + entry.getProtein().getName().elementAt(0));\r
- }\r
-\r
- result.append(name + "\n" + entry.getUniprotSequence().getContent() +\r
- "\n");\r
-\r
- }\r
-\r
- //Then read in the features and apply them to the dataset\r
- SequenceI[] sequence = parseResult(result.toString(), null);\r
- for (int i = 0; i < entries.size(); i++)\r
- {\r
- UniprotEntry entry = (UniprotEntry) entries.elementAt(i);\r
- Enumeration e = entry.getDbReference().elements();\r
- Vector onlyPdbEntries = new Vector();\r
- while (e.hasMoreElements())\r
- {\r
- PDBEntry pdb = (PDBEntry) e.nextElement();\r
- if (!pdb.getType().equals("PDB"))\r
- continue;\r
-\r
- onlyPdbEntries.addElement(pdb);\r
- }\r
-\r
- sequence[i].getDatasetSequence().setPDBId(onlyPdbEntries);\r
- if (entry.getFeature() != null)\r
- {\r
- e = entry.getFeature().elements();\r
- while (e.hasMoreElements())\r
- {\r
- SequenceFeature sf = (SequenceFeature) e.nextElement();\r
- sf.setFeatureGroup("Uniprot");\r
- sequence[i].getDatasetSequence().addSequenceFeature( sf );\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- StringBuffer getPDBFile(String id)\r
- {\r
- StringBuffer result = new StringBuffer();\r
- String chain = null;\r
- if (id.indexOf(":") > -1)\r
- {\r
- chain = id.substring(id.indexOf(":") + 1);\r
- id = id.substring(0, id.indexOf(":"));\r
- }\r
-\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] reply = ebi.fetchData("pdb:" + id, "pdb", "raw");\r
- if (reply == null)\r
- return null;\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
- jalview.bin.Cache.log.warn("Exception when retrieving " +\r
- textfield.getText() + " from " +\r
- database.getSelectedItem(), ex);\r
- return null;\r
- }\r
-\r
- return result;\r
- }\r
-\r
- SequenceI[] parseResult(String result, String title)\r
- {\r
- String format = new IdentifyFile().Identify(result, "Paste");\r
- SequenceI[] sequences = null;\r
-\r
- if (FormatAdapter.formats.contains(format))\r
- {\r
- sequences = null;\r
- try{ sequences = new FormatAdapter().readFile(result.toString(), "Paste",\r
- format);}\r
- catch(Exception ex){}\r
-\r
- if (sequences != null && sequences.length > 0)\r
- {\r
- if (alignFrame == null)\r
- {\r
- AlignFrame af = new AlignFrame(new Alignment(sequences));\r
- af.currentFileFormat = format;\r
- if(title==null)\r
- title = "Retrieved from " + database.getSelectedItem();\r
- Desktop.addInternalFrame(af,\r
- title,\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\r
- 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
- //Dataset needs extension;\r
- /////////////////////////////\r
- Sequence ds = new Sequence(sequences[i].getName(),\r
- AlignSeq.extractGaps("-. ",\r
- sequences[i].getSequence()),\r
- sequences[i].getStart(),\r
- sequences[i].getEnd());\r
- sequences[i].setDatasetSequence(ds);\r
- alignFrame.viewport.alignment.getDataset().addSequence(ds);\r
- }\r
- alignFrame.viewport.setEndSeq(alignFrame.viewport.alignment.\r
- getHeight());\r
- alignFrame.viewport.alignment.getWidth();\r
- alignFrame.viewport.firePropertyChange("alignment", null,\r
- alignFrame.viewport.\r
- getAlignment().getSequences());\r
-\r
- }\r
-\r
- if (database.getSelectedItem().equals("PDB"))\r
- {\r
- // Parse out the ids from the structured names\r
- boolean errors = false;\r
- for (int i = 0; i < sequences.length; i++)\r
- {\r
- PDBEntry entry = new PDBEntry();\r
- com.stevesoft.pat.Regex idbits = new com.stevesoft.pat.Regex(\r
- "PDB\\|([0-9A-z]{4})\\|(.)");\r
- if (idbits.search(sequences[i].getName()))\r
- {\r
- String pdbid = idbits.substring(1);\r
- String pdbccode = idbits.substring(2);\r
- // Construct the PDBEntry\r
- entry.setId(pdbid);\r
- if (entry.getProperty() == null)\r
- entry.setProperty(new Hashtable());\r
- entry.getProperty().put("chains",\r
- pdbccode\r
- + "=" + sequences[i].getStart()\r
- + "-" + sequences[i].getEnd());\r
- sequences[i].getDatasetSequence().addPDBId(entry);\r
-\r
- // We make a DBRefEtntry because we have obtained the PDB file from a verifiable source\r
- // JBPNote - PDB DBRefEntry should also carry the chain and mapping information\r
- DBRefEntry dbentry = new DBRefEntry("PDB","0",pdbid);\r
- sequences[i].getDatasetSequence().addDBRef(dbentry);\r
- }\r
- else\r
- {\r
- // don't add an entry for this chain, but this is probably a bug\r
- // that the user should know about.\r
- jalview.bin.Cache.log.warn(\r
- "No PDBEntry constructed for sequence " + i + " : " +\r
- sequences[i].getName());\r
- errors = true;\r
- }\r
- }\r
- if (errors)\r
- jalview.bin.Cache.log.warn(\r
- "Query string that resulted in PDBEntry construction failure was :\n" +\r
- textfield.getText());\r
- }\r
-\r
- }\r
- else\r
- showErrorMessage("Error retrieving " + textfield.getText()\r
- + " from " + database.getSelectedItem());\r
- }\r
-\r
- return sequences;\r
-\r
- }\r
-\r
- void showErrorMessage(String error)\r
- {\r
- resetDialog();\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- error, "Error Retrieving Data",\r
- JOptionPane.WARNING_MESSAGE);\r
- return;\r
- }\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.BorderLayout;
+import java.awt.Font;
+import java.awt.event.ActionEvent;
+import java.awt.event.ActionListener;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+
+import javax.swing.JButton;
+import javax.swing.JCheckBox;
+import javax.swing.JComboBox;
+import javax.swing.JInternalFrame;
+import javax.swing.JLabel;
+import javax.swing.JPanel;
+import javax.swing.JScrollPane;
+import javax.swing.JTextArea;
+import javax.swing.SwingConstants;
+
+import jalview.api.FeatureSettingsModelI;
+import jalview.bin.Cache;
+import jalview.bin.Console;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.SequenceI;
+import jalview.fts.core.GFTSPanel;
+import jalview.fts.service.pdb.PDBFTSPanel;
+import jalview.fts.service.threedbeacons.TDBeaconsFTSPanel;
+import jalview.fts.service.uniprot.UniprotFTSPanel;
+import jalview.io.FileFormatI;
+import jalview.io.gff.SequenceOntologyI;
+import jalview.util.DBRefUtils;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.seqfetcher.DbSourceProxy;
+
+/**
+ * A panel where the use may choose a database source, and enter one or more
+ * accessions, to retrieve entries from the database.
+ * <p>
+ * If the selected source is Uniprot or PDB, a free text search panel is opened
+ * instead to perform the search and selection.
+ */
+public class SequenceFetcher extends JPanel implements Runnable
+{
+ private class StringPair
+ {
+ private String key;
+
+ private String display;
+
+ public StringPair(String s1, String s2)
+ {
+ key = s1;
+ display = s2;
+ }
+
+ public StringPair(String s)
+ {
+ this(s, s);
+ }
+
+ public String getKey()
+ {
+ return key;
+ }
+
+ public String getDisplay()
+ {
+ return display;
+ }
+
+ @Override
+ public String toString()
+ {
+ return display;
+ }
+
+ public boolean equals(StringPair other)
+ {
+ return other.key == this.key;
+ }
+ }
+
+ private static jalview.ws.SequenceFetcher sfetch = null;
+
+ JLabel exampleAccession;
+
+ JComboBox<StringPair> database;
+
+ JCheckBox replacePunctuation;
+
+ JButton okBtn;
+
+ JButton exampleBtn;
+
+ JButton closeBtn;
+
+ JButton backBtn;
+
+ JTextArea textArea;
+
+ JInternalFrame frame;
+
+ IProgressIndicator guiWindow;
+
+ AlignFrame alignFrame;
+
+ GFTSPanel parentSearchPanel;
+
+ IProgressIndicator progressIndicator;
+
+ volatile boolean _isConstructing = false;
+
+ /**
+ * Returns the shared instance of the SequenceFetcher client
+ *
+ * @return
+ */
+ public static jalview.ws.SequenceFetcher getSequenceFetcherSingleton()
+ {
+ if (sfetch == null)
+ {
+ sfetch = new jalview.ws.SequenceFetcher();
+ }
+ return sfetch;
+ }
+
+ /**
+ * Constructor given a client to receive any status or progress messages
+ * (currently either the Desktop, or an AlignFrame panel)
+ *
+ * @param guiIndic
+ */
+ public SequenceFetcher(IProgressIndicator guiIndic)
+ {
+ this(guiIndic, null, null);
+ }
+
+ /**
+ * Constructor with specified database and accession(s) to retrieve
+ *
+ * @param guiIndic
+ * @param selectedDb
+ * @param queryString
+ */
+ public SequenceFetcher(IProgressIndicator guiIndic,
+ final String selectedDb, final String queryString)
+ {
+ this.progressIndicator = guiIndic;
+ getSequenceFetcherSingleton();
+ this.guiWindow = progressIndicator;
+
+ if (progressIndicator instanceof AlignFrame)
+ {
+ alignFrame = (AlignFrame) progressIndicator;
+ }
+
+ jbInit(selectedDb);
+ textArea.setText(queryString);
+
+ frame = new JInternalFrame();
+ frame.setContentPane(this);
+ frame.setFrameIcon(null);
+ Desktop.addInternalFrame(frame, getFrameTitle(), true, 400,
+ Platform.isAMacAndNotJS() ? 240 : 180);
+ }
+
+ private String getFrameTitle()
+ {
+ return ((alignFrame == null)
+ ? MessageManager.getString("label.new_sequence_fetcher")
+ : MessageManager
+ .getString("label.additional_sequence_fetcher"));
+ }
+
+ private void jbInit(String selectedDb)
+ {
+ this.setLayout(new BorderLayout());
+
+ database = new JComboBox<>();
+ database.setFont(JvSwingUtils.getLabelFont());
+ StringPair instructionItem = new StringPair(
+ MessageManager.getString("action.select_ddbb"));
+ database.setPrototypeDisplayValue(instructionItem);
+ String[] sources = new jalview.ws.SequenceFetcher().getSupportedDb();
+ Arrays.sort(sources, String.CASE_INSENSITIVE_ORDER);
+ database.addItem(instructionItem);
+ for (String source : sources)
+ {
+ List<DbSourceProxy> slist = sfetch.getSourceProxy(source);
+ if (slist.size() == 1 && slist.get(0) != null)
+ {
+ database.addItem(new StringPair(source, slist.get(0).getDbName()));
+ }
+ else
+ {
+ database.addItem(new StringPair(source));
+ }
+ }
+ setDatabaseSelectedItem(selectedDb);
+ if (database.getSelectedIndex() == -1)
+ {
+ database.setSelectedIndex(0);
+ }
+ database.setMaximumRowCount(database.getItemCount());
+ database.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ String currentSelection = ((StringPair) database.getSelectedItem())
+ .getKey();
+ updateExampleQuery(currentSelection);
+
+ if ("pdb".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new PDBFTSPanel(SequenceFetcher.this);
+ }
+ else if ("uniprot".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new UniprotFTSPanel(SequenceFetcher.this);
+ }
+ else if ("3d-beacons".equalsIgnoreCase(currentSelection))
+ {
+ frame.dispose();
+ new TDBeaconsFTSPanel(SequenceFetcher.this);
+ }
+ else
+ {
+ otherSourceAction();
+ }
+ }
+ });
+
+ exampleAccession = new JLabel("");
+ exampleAccession.setFont(new Font("Verdana", Font.BOLD, 11));
+ JLabel jLabel1 = new JLabel(MessageManager
+ .getString("label.separate_multiple_accession_ids"));
+ jLabel1.setFont(new Font("Verdana", Font.ITALIC, 11));
+ jLabel1.setHorizontalAlignment(SwingConstants.LEFT);
+
+ replacePunctuation = new JCheckBox(
+ MessageManager.getString("label.replace_commas_semicolons"));
+ replacePunctuation.setHorizontalAlignment(SwingConstants.LEFT);
+ replacePunctuation.setFont(new Font("Verdana", Font.ITALIC, 11));
+ okBtn = new JButton(MessageManager.getString("action.ok"));
+ okBtn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ ok_actionPerformed();
+ }
+ });
+ JButton clear = new JButton(MessageManager.getString("action.clear"));
+ clear.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ clear_actionPerformed();
+ }
+ });
+
+ exampleBtn = new JButton(MessageManager.getString("label.example"));
+ exampleBtn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ example_actionPerformed();
+ }
+ });
+ closeBtn = new JButton(MessageManager.getString("action.cancel"));
+ closeBtn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ close_actionPerformed(e);
+ }
+ });
+ backBtn = new JButton(MessageManager.getString("action.back"));
+ backBtn.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ parentSearchPanel.btn_back_ActionPerformed();
+ }
+ });
+ // back not visible unless embedded
+ backBtn.setVisible(false);
+
+ textArea = new JTextArea();
+ textArea.setFont(JvSwingUtils.getLabelFont());
+ textArea.setLineWrap(true);
+ textArea.addKeyListener(new KeyAdapter()
+ {
+ @Override
+ public void keyPressed(KeyEvent e)
+ {
+ if (e.getKeyCode() == KeyEvent.VK_ENTER)
+ {
+ ok_actionPerformed();
+ }
+ }
+ });
+
+ JPanel actionPanel = new JPanel();
+ actionPanel.add(backBtn);
+ actionPanel.add(exampleBtn);
+ actionPanel.add(clear);
+ actionPanel.add(okBtn);
+ actionPanel.add(closeBtn);
+
+ JPanel databasePanel = new JPanel();
+ databasePanel.setLayout(new BorderLayout());
+ databasePanel.add(database, BorderLayout.NORTH);
+ databasePanel.add(exampleAccession, BorderLayout.CENTER);
+ JPanel jPanel2a = new JPanel(new BorderLayout());
+ jPanel2a.add(jLabel1, BorderLayout.NORTH);
+ jPanel2a.add(replacePunctuation, BorderLayout.SOUTH);
+ databasePanel.add(jPanel2a, BorderLayout.SOUTH);
+
+ JPanel idsPanel = new JPanel();
+ idsPanel.setLayout(new BorderLayout(0, 5));
+ JScrollPane jScrollPane1 = new JScrollPane();
+ jScrollPane1.getViewport().add(textArea);
+ idsPanel.add(jScrollPane1, BorderLayout.CENTER);
+
+ this.add(actionPanel, BorderLayout.SOUTH);
+ this.add(idsPanel, BorderLayout.CENTER);
+ this.add(databasePanel, BorderLayout.NORTH);
+ }
+
+ private void setDatabaseSelectedItem(String db)
+ {
+ for (int i = 0; i < database.getItemCount(); i++)
+ {
+ StringPair sp = database.getItemAt(i);
+ if (sp != null && db != null && db.equals(sp.getKey()))
+ {
+ database.setSelectedIndex(i);
+ return;
+ }
+ }
+ }
+
+ /**
+ * Answers a semi-colon-delimited string with the example query or queries for
+ * the selected database
+ *
+ * @param db
+ * @return
+ */
+ protected String getExampleQueries(String db)
+ {
+ StringBuilder sb = new StringBuilder();
+ HashSet<String> hs = new HashSet<>();
+ for (DbSourceProxy dbs : sfetch.getSourceProxy(db))
+ {
+ String tq = dbs.getTestQuery();
+ if (hs.add(tq)) // not a duplicate source
+ {
+ if (sb.length() > 0)
+ {
+ sb.append(";");
+ }
+ sb.append(tq);
+ }
+ }
+ return sb.toString();
+ }
+
+ /**
+ * Action on selecting a database other than Uniprot or PDB is to enable or
+ * disable 'Replace commas', and await input in the query field
+ */
+ protected void otherSourceAction()
+ {
+ try
+ {
+ String eq = exampleAccession.getText();
+ // TODO this should be a property of the SequenceFetcher whether commas
+ // are allowed in the IDs...
+
+ boolean enablePunct = !(eq != null && eq.indexOf(",") > -1);
+ replacePunctuation.setEnabled(enablePunct);
+
+ } catch (Exception ex)
+ {
+ exampleAccession.setText("");
+ replacePunctuation.setEnabled(true);
+ }
+ repaint();
+ }
+
+ /**
+ * Sets the text of the example query to incorporate the example accession
+ * provided by the selected database source
+ *
+ * @param selectedDatabase
+ * @return
+ */
+ protected String updateExampleQuery(String selectedDatabase)
+ {
+ String eq = getExampleQueries(selectedDatabase);
+ exampleAccession.setText(MessageManager
+ .formatMessage("label.example_query_param", new String[]
+ { eq }));
+ return eq;
+ }
+
+ /**
+ * Action on clicking the 'Example' button is to write the example accession
+ * as the query text field value
+ */
+ protected void example_actionPerformed()
+ {
+ String eq = getExampleQueries(
+ ((StringPair) database.getSelectedItem()).getKey());
+ textArea.setText(eq);
+ repaint();
+ }
+
+ /**
+ * Clears the query input field
+ */
+ protected void clear_actionPerformed()
+ {
+ textArea.setText("");
+ repaint();
+ }
+
+ /**
+ * Action on Close button is to close this frame, and also (if it is embedded
+ * in a search panel) to close the search panel
+ *
+ * @param e
+ */
+ protected void close_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ frame.setClosed(true);
+ if (parentSearchPanel != null)
+ {
+ parentSearchPanel.btn_cancel_ActionPerformed();
+ }
+ } catch (Exception ex)
+ {
+ }
+ }
+
+ /**
+ * Action on OK is to start the fetch for entered accession(s)
+ */
+ public void ok_actionPerformed()
+ {
+ /*
+ * tidy inputs and check there is something to search for
+ */
+ String t0 = textArea.getText();
+ String text = t0.trim();
+ if (replacePunctuation.isEnabled() && replacePunctuation.isSelected())
+ {
+ text = text.replace(",", ";");
+ }
+ text = text.replaceAll("(\\s|[; ])+", ";");
+ if (!t0.equals(text))
+ {
+ textArea.setText(text);
+ }
+ if (text.isEmpty())
+ {
+ // todo i18n
+ showErrorMessage(
+ "Please enter a (semi-colon separated list of) database id(s)");
+ resetDialog();
+ return;
+ }
+ if (database.getSelectedIndex() == 0)
+ {
+ // todo i18n
+ showErrorMessage("Please choose a database");
+ resetDialog();
+ return;
+ }
+
+ exampleBtn.setEnabled(false);
+ textArea.setEnabled(false);
+ okBtn.setEnabled(false);
+ closeBtn.setEnabled(false);
+ backBtn.setEnabled(false);
+
+ Thread worker = new Thread(this);
+ worker.start();
+ }
+
+ private void resetDialog()
+ {
+ exampleBtn.setEnabled(true);
+ textArea.setEnabled(true);
+ okBtn.setEnabled(true);
+ closeBtn.setEnabled(true);
+ backBtn.setEnabled(parentSearchPanel != null);
+ }
+
+ @Override
+ public void run()
+ {
+ boolean addToLast = false;
+ List<String> aresultq = new ArrayList<>();
+ List<String> presultTitle = new ArrayList<>();
+ List<AlignmentI> presult = new ArrayList<>();
+ List<AlignmentI> aresult = new ArrayList<>();
+ List<DbSourceProxy> sources = sfetch.getSourceProxy(
+ ((StringPair) database.getSelectedItem()).getKey());
+ Iterator<DbSourceProxy> proxies = sources.iterator();
+ String[] qries = textArea.getText().trim().split(";");
+ List<String> nextFetch = Arrays.asList(qries);
+ Iterator<String> en = Arrays.asList(new String[0]).iterator();
+ int nqueries = qries.length;
+
+ FeatureSettingsModelI preferredFeatureColours = null;
+ while (proxies.hasNext() && (en.hasNext() || nextFetch.size() > 0))
+ {
+ if (!en.hasNext() && nextFetch.size() > 0)
+ {
+ en = nextFetch.iterator();
+ nqueries = nextFetch.size();
+ // save the remaining queries in the original array
+ qries = nextFetch.toArray(new String[nqueries]);
+ nextFetch = new ArrayList<>();
+ }
+
+ DbSourceProxy proxy = proxies.next();
+ try
+ {
+ // update status
+ guiWindow.setProgressBar(MessageManager.formatMessage(
+ "status.fetching_sequence_queries_from", new String[]
+ { Integer.valueOf(nqueries).toString(),
+ proxy.getDbName() }),
+ Thread.currentThread().hashCode());
+ if (proxy.getMaximumQueryCount() == 1)
+ {
+ /*
+ * proxy only handles one accession id at a time
+ */
+ while (en.hasNext())
+ {
+ String acc = en.next();
+ if (!fetchSingleAccession(proxy, acc, aresultq, aresult))
+ {
+ nextFetch.add(acc);
+ }
+ }
+ }
+ else
+ {
+ /*
+ * proxy can fetch multiple accessions at one time
+ */
+ fetchMultipleAccessions(proxy, en, aresultq, aresult, nextFetch);
+ }
+ } catch (Exception e)
+ {
+ showErrorMessage("Error retrieving " + textArea.getText() + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay());
+ // error
+ // +="Couldn't retrieve sequences from "+database.getSelectedItem();
+ System.err.println("Retrieval failed for source ='"
+ + ((StringPair) database.getSelectedItem()).getDisplay()
+ + "' and query\n'" + textArea.getText() + "'\n");
+ e.printStackTrace();
+ } catch (OutOfMemoryError e)
+ {
+ showErrorMessage("Out of Memory when retrieving "
+ + textArea.getText() + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay()
+ + "\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 "
+ + ((StringPair) database.getSelectedItem()).getDisplay());
+ e.printStackTrace();
+ }
+
+ // Stack results ready for opening in alignment windows
+ if (aresult != null && aresult.size() > 0)
+ {
+ FeatureSettingsModelI proxyColourScheme = proxy
+ .getFeatureColourScheme();
+ if (proxyColourScheme != null)
+ {
+ preferredFeatureColours = proxyColourScheme;
+ }
+
+ AlignmentI ar = null;
+ if (proxy.isAlignmentSource())
+ {
+ addToLast = false;
+ // new window for each result
+ while (aresult.size() > 0)
+ {
+ presult.add(aresult.remove(0));
+ presultTitle.add(
+ aresultq.remove(0) + " " + getDefaultRetrievalTitle());
+ }
+ }
+ else
+ {
+ String titl = null;
+ if (addToLast && presult.size() > 0)
+ {
+ ar = presult.remove(presult.size() - 1);
+ titl = presultTitle.remove(presultTitle.size() - 1);
+ }
+ // concatenate all results in one window
+ while (aresult.size() > 0)
+ {
+ if (ar == null)
+ {
+ ar = aresult.remove(0);
+ }
+ else
+ {
+ ar.append(aresult.remove(0));
+ }
+ }
+ addToLast = true;
+ presult.add(ar);
+ presultTitle.add(titl);
+ }
+ }
+ guiWindow.setProgressBar(
+ MessageManager.getString("status.finshed_querying"),
+ Thread.currentThread().hashCode());
+ }
+ guiWindow
+ .setProgressBar(
+ (presult.size() > 0)
+ ? MessageManager
+ .getString("status.parsing_results")
+ : MessageManager.getString("status.processing"),
+ Thread.currentThread().hashCode());
+ // process results
+ while (presult.size() > 0)
+ {
+ parseResult(presult.remove(0), presultTitle.remove(0), null,
+ preferredFeatureColours);
+ }
+ // only remove visual delay after we finished parsing.
+ guiWindow.setProgressBar(null, Thread.currentThread().hashCode());
+ if (nextFetch.size() > 0)
+ {
+ StringBuffer sb = new StringBuffer();
+ sb.append("Didn't retrieve the following "
+ + (nextFetch.size() == 1 ? "query"
+ : nextFetch.size() + " queries")
+ + ": \n");
+ int l = sb.length(), lr = 0;
+ for (String s : nextFetch)
+ {
+ if (l != sb.length())
+ {
+ sb.append("; ");
+ }
+ if (lr - sb.length() > 40)
+ {
+ sb.append("\n");
+ }
+ sb.append(s);
+ }
+ showErrorMessage(sb.toString());
+ }
+ resetDialog();
+ }
+
+ /**
+ * Tries to fetch one or more accession ids from the database proxy
+ *
+ * @param proxy
+ * @param accessions
+ * the queries to fetch
+ * @param aresultq
+ * a successful queries list to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @param nextFetch
+ * failed queries are added to this list
+ * @throws Exception
+ */
+ void fetchMultipleAccessions(DbSourceProxy proxy,
+ Iterator<String> accessions, List<String> aresultq,
+ List<AlignmentI> aresult, List<String> nextFetch) throws Exception
+ {
+ StringBuilder multiacc = new StringBuilder();
+ List<String> tosend = new ArrayList<>();
+ while (accessions.hasNext())
+ {
+ String nel = accessions.next();
+ tosend.add(nel);
+ multiacc.append(nel);
+ if (accessions.hasNext())
+ {
+ multiacc.append(proxy.getAccessionSeparator());
+ }
+ }
+
+ try
+ {
+ String query = multiacc.toString();
+ AlignmentI rslt = proxy.getSequenceRecords(query);
+ if (rslt == null || rslt.getHeight() == 0)
+ {
+ // no results - pass on all queries to next source
+ nextFetch.addAll(tosend);
+ }
+ else
+ {
+ aresultq.add(query);
+ aresult.add(rslt);
+ if (tosend.size() > 1)
+ {
+ checkResultForQueries(rslt, tosend, nextFetch, proxy);
+ }
+ }
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning("fetching " + multiacc + " from "
+ + ((StringPair) database.getSelectedItem()).getDisplay(),
+ oome, this);
+ }
+ }
+
+ /**
+ * Query for a single accession id via the database proxy
+ *
+ * @param proxy
+ * @param accession
+ * @param aresultq
+ * a list of successful queries to add to
+ * @param aresult
+ * a list of retrieved alignments to add to
+ * @return true if the fetch was successful, else false
+ */
+ boolean fetchSingleAccession(DbSourceProxy proxy, String accession,
+ List<String> aresultq, List<AlignmentI> aresult)
+ {
+ boolean success = false;
+ 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(accession);
+ } catch (OutOfMemoryError oome)
+ {
+ new OOMWarning(
+ "fetching " + accession + " from " + proxy.getDbName(),
+ oome, this);
+ }
+ if (indres != null)
+ {
+ aresultq.add(accession);
+ aresult.add(indres);
+ success = true;
+ }
+ } catch (Exception e)
+ {
+ Console.info("Error retrieving " + accession + " from "
+ + proxy.getDbName(), e);
+ }
+ return success;
+ }
+
+ /**
+ * Checks which of the queries were successfully retrieved by searching the
+ * DBRefs of the retrieved sequences for a match. Any not found are added to
+ * the 'nextFetch' list.
+ *
+ * @param rslt
+ * @param queries
+ * @param nextFetch
+ * @param proxy
+ */
+ void checkResultForQueries(AlignmentI rslt, List<String> queries,
+ List<String> nextFetch, DbSourceProxy proxy)
+ {
+ SequenceI[] rs = rslt.getSequencesArray();
+
+ for (String q : queries)
+ {
+ // BH 2019.01.25 dbr is never used.
+ // DBRefEntry dbr = new DBRefEntry();
+ // dbr.setSource(proxy.getDbSource());
+ // dbr.setVersion(null);
+ String accId = proxy.getAccessionIdFromQuery(q);
+ // dbr.setAccessionId(accId);
+ boolean rfound = false;
+ for (int r = 0, nr = rs.length; r < nr; r++)
+ {
+ if (rs[r] != null)
+ {
+ List<DBRefEntry> found = DBRefUtils.searchRefs(rs[r].getDBRefs(),
+ accId);
+ if (!found.isEmpty())
+ {
+ rfound = true;
+ break;
+ }
+ }
+ }
+ if (!rfound)
+ {
+ nextFetch.add(q);
+ }
+ }
+ }
+
+ /**
+ *
+ * @return a standard title for any results retrieved using the currently
+ * selected source and settings
+ */
+ public String getDefaultRetrievalTitle()
+ {
+ return "Retrieved from "
+ + ((StringPair) database.getSelectedItem()).getDisplay();
+ }
+
+ /**
+ * constructs an alignment frame given the data and metadata
+ *
+ * @param al
+ * @param title
+ * @param currentFileFormat
+ * @param preferredFeatureColours
+ * @return the alignment
+ */
+ public AlignmentI parseResult(AlignmentI al, String title,
+ FileFormatI currentFileFormat,
+ FeatureSettingsModelI preferredFeatureColours)
+ {
+
+ if (al != null && al.getHeight() > 0)
+ {
+ if (title == null)
+ {
+ title = getDefaultRetrievalTitle();
+ }
+ if (alignFrame == null)
+ {
+ AlignFrame af = new AlignFrame(al, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+ if (currentFileFormat != null)
+ {
+ af.currentFileFormat = currentFileFormat;
+ }
+
+ List<SequenceI> alsqs = al.getSequences();
+ synchronized (alsqs)
+ {
+ for (SequenceI sq : alsqs)
+ {
+ if (sq.getFeatures().hasFeatures())
+ {
+ af.setShowSeqFeatures(true);
+ break;
+ }
+ }
+ }
+
+ af.getViewport().applyFeaturesStyle(preferredFeatureColours);
+ if (Cache.getDefault("HIDE_INTRONS", true))
+ {
+ af.hideFeatureColumns(SequenceOntologyI.EXON, false);
+ }
+ Desktop.addInternalFrame(af, title, AlignFrame.DEFAULT_WIDTH,
+ AlignFrame.DEFAULT_HEIGHT);
+
+ af.setStatus(MessageManager
+ .getString("label.successfully_pasted_alignment_file"));
+
+ try
+ {
+ af.setMaximum(Cache.getDefault("SHOW_FULLSCREEN", false));
+ } catch (Exception ex)
+ {
+ }
+ }
+ else
+ {
+ alignFrame.viewport.addAlignment(al, title);
+ }
+ }
+ return al;
+ }
+
+ void showErrorMessage(final String error)
+ {
+ resetDialog();
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.desktop, error,
+ MessageManager.getString("label.error_retrieving_data"),
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+
+ public IProgressIndicator getProgressIndicator()
+ {
+ return progressIndicator;
+ }
+
+ public void setProgressIndicator(IProgressIndicator progressIndicator)
+ {
+ this.progressIndicator = progressIndicator;
+ }
+
+ /**
+ * Hide this panel (on clicking the database button to open the database
+ * chooser)
+ */
+ void hidePanel()
+ {
+ frame.setVisible(false);
+ }
+
+ public void setQuery(String ids)
+ {
+ textArea.setText(ids);
+ }
+
+ /**
+ * Called to modify the search panel for embedding as an alternative tab of a
+ * free text search panel. The database choice list is hidden (since the
+ * choice has been made), and a Back button is made visible (which reopens the
+ * Sequence Fetcher panel).
+ *
+ * @param parentPanel
+ */
+ public void embedIn(GFTSPanel parentPanel)
+ {
+ database.setVisible(false);
+ backBtn.setVisible(true);
+ parentSearchPanel = parentPanel;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff