-/*\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 MCview;\r
-\r
-import javax.swing.*;\r
-import java.awt.event.*;\r
-import jalview.datamodel.*;\r
-import jalview.schemes.*;\r
-import jalview.gui.*;\r
-import jalview.io.EBIFetchClient;\r
-import java.awt.event.ActionListener;\r
-import java.awt.event.ActionEvent;\r
-\r
-public class PDBViewer extends JInternalFrame implements Runnable\r
-{\r
- PDBEntry pdb;\r
- Sequence sequence;\r
- PDBCanvas pdbcanvas;\r
-\r
-\r
- public PDBViewer(PDBEntry entry,\r
- Sequence seq,\r
- SeqCanvas seqcanvas)\r
- {\r
- /*Uncomment this to modify in Jbuilder\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }*/\r
-\r
-\r
- pdb = entry;\r
- sequence = seq;\r
-\r
- Thread worker = new Thread(this);\r
- worker.start();\r
-\r
- pdbcanvas = new PDBCanvas(seqcanvas, seq);\r
-\r
- setContentPane(pdbcanvas);\r
- StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());\r
- if(pdb.getProperty()!=null)\r
- {\r
- title.append( " Method: " );\r
- title.append(pdb.getProperty().get("method"));\r
- title.append( " Chain:" );\r
- title.append( pdb.getProperty().get("chains"));\r
- }\r
-\r
- Desktop.addInternalFrame(this,title.toString(),400, 400);\r
- }\r
-\r
- public void run()\r
- {\r
- try\r
- {\r
- EBIFetchClient ebi = new EBIFetchClient();\r
- String[] result = ebi.fetchData("pdb:" + pdb.getId(), "default","raw");\r
-\r
- PDBfile pdbfile = new PDBfile(result);\r
-\r
- pdbcanvas.setPDBFile(pdbfile);\r
-\r
- try\r
- {\r
- jbInit();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- private void jbInit()\r
- throws Exception\r
- {\r
- this.addKeyListener(new KeyAdapter()\r
- {\r
- public void keyPressed(KeyEvent evt)\r
- {\r
- pdbcanvas.keyPressed(evt);\r
- }\r
- });\r
-\r
- this.setJMenuBar(jMenuBar1);\r
- fileMenu.setText("File");\r
- coloursMenu.setText("Colours");\r
- saveMenu.setActionCommand("Save Image");\r
- saveMenu.setText("Save As");\r
- png.setText("PNG");\r
- png.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- png_actionPerformed(e);\r
- }\r
- });\r
- eps.setText("EPS");\r
- eps.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- eps_actionPerformed(e);\r
- }\r
- });\r
- mapping.setText("View Mapping");\r
- mapping.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- mapping_actionPerformed(e);\r
- }\r
- });\r
- wire.setText("Wireframe");\r
- wire.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- wire_actionPerformed(e);\r
- }\r
- });\r
- depth.setSelected(true);\r
- depth.setText("Depthcue");\r
- depth.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- depth_actionPerformed(e);\r
- }\r
- });\r
- zbuffer.setSelected(true);\r
- zbuffer.setText("Z Buffering");\r
- zbuffer.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zbuffer_actionPerformed(e);\r
- }\r
- });\r
- charge.setText("Charge & Cysteine");\r
- charge.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- charge_actionPerformed(e);\r
- }\r
- });\r
- chain.setText("By Chain");\r
- chain.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- chain_actionPerformed(e);\r
- }\r
- });\r
- seqButton.setSelected(true);\r
- seqButton.setText("By Sequence");\r
- seqButton.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- seqButton_actionPerformed(e);\r
- }\r
- });\r
- allchains.setSelected(true);\r
- allchains.setText("Show All Chains");\r
- allchains.addItemListener(new ItemListener()\r
- {\r
- public void itemStateChanged(ItemEvent e)\r
- {\r
- allchains_itemStateChanged(e);\r
- }\r
- });\r
- zappo.setText("Zappo");\r
- zappo.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- zappo_actionPerformed(e);\r
- }\r
- });\r
- taylor.setText("Taylor");\r
- taylor.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- taylor_actionPerformed(e);\r
- }\r
- });\r
- hydro.setText("Hydro");\r
- hydro.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- hydro_actionPerformed(e);\r
- }\r
- });\r
- helix.setText("Helix");\r
- helix.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- helix_actionPerformed(e);\r
- }\r
- });\r
- strand.setText("Strand");\r
- strand.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- strand_actionPerformed(e);\r
- }\r
- });\r
- turn.setText("Turn");\r
- turn.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- turn_actionPerformed(e);\r
- }\r
- });\r
- buried.setText("Buried");\r
- buried.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- buried_actionPerformed(e);\r
- }\r
- });\r
- user.setText("User Defined...");\r
- user.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent e)\r
- {\r
- user_actionPerformed(e);\r
- }\r
- });\r
- viewMenu.setText("View");\r
- jMenuBar1.add(fileMenu);\r
- jMenuBar1.add(coloursMenu);\r
- jMenuBar1.add(viewMenu);\r
- fileMenu.add(saveMenu);\r
- fileMenu.add(mapping);\r
- saveMenu.add(png);\r
- saveMenu.add(eps);\r
- coloursMenu.add(seqButton);\r
- coloursMenu.add(chain);\r
- coloursMenu.add(charge);\r
- coloursMenu.add(zappo);\r
- coloursMenu.add(taylor);\r
- coloursMenu.add(hydro);\r
- coloursMenu.add(helix);\r
- coloursMenu.add(strand);\r
- coloursMenu.add(turn);\r
- coloursMenu.add(buried);\r
- coloursMenu.add(user);\r
- ButtonGroup bg = new ButtonGroup();\r
- bg.add(seqButton);\r
- bg.add(chain);\r
- bg.add(charge);\r
- bg.add(zappo);\r
- bg.add(taylor);\r
- bg.add(hydro);\r
- bg.add(helix);\r
- bg.add(strand);\r
- bg.add(turn);\r
- bg.add(buried);\r
- bg.add(user);\r
-\r
-\r
- if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)\r
- {\r
- java.util.Enumeration userColours = jalview.gui.UserDefinedColours.\r
- getUserColourSchemes().keys();\r
-\r
- while (userColours.hasMoreElements())\r
- {\r
- final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.\r
- nextElement().toString());\r
- radioItem.setName("USER_DEFINED");\r
- radioItem.addMouseListener(new MouseAdapter()\r
- {\r
- public void mousePressed(MouseEvent evt)\r
- {\r
- if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))\r
- {\r
- radioItem.removeActionListener(radioItem.getActionListeners()[0]);\r
-\r
- int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,\r
- "Remove from default list?",\r
- "Remove user defined colour",\r
- JOptionPane.YES_NO_OPTION);\r
- if(option == JOptionPane.YES_OPTION)\r
- {\r
- jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());\r
- coloursMenu.remove(radioItem);\r
- }\r
- else\r
- radioItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- user_actionPerformed(evt);\r
- }\r
- });\r
- }\r
- }\r
- });\r
- radioItem.addActionListener(new ActionListener()\r
- {\r
- public void actionPerformed(ActionEvent evt)\r
- {\r
- user_actionPerformed(evt);\r
- }\r
- });\r
- coloursMenu.add(radioItem);\r
- bg.add(radioItem);\r
- }\r
- }\r
-\r
- viewMenu.add(wire);\r
- viewMenu.add(depth);\r
- viewMenu.add(zbuffer);\r
- viewMenu.add(allchains);\r
- }\r
-\r
- JMenuBar jMenuBar1 = new JMenuBar();\r
- JMenu fileMenu = new JMenu();\r
- JMenu coloursMenu = new JMenu();\r
- JMenu saveMenu = new JMenu();\r
- JMenuItem png = new JMenuItem();\r
- JMenuItem eps = new JMenuItem();\r
- JMenuItem mapping = new JMenuItem();\r
- JCheckBoxMenuItem wire = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem depth = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();\r
- JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();\r
-\r
- JRadioButtonMenuItem charge = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem chain = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem user = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem buried = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem turn = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem strand = new JRadioButtonMenuItem();\r
- JRadioButtonMenuItem helix = new JRadioButtonMenuItem();\r
- JMenu viewMenu = new JMenu();\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void eps_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.EPS);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void png_actionPerformed(ActionEvent e)\r
- {\r
- makePDBImage(jalview.util.ImageMaker.PNG);\r
- }\r
-\r
- void makePDBImage(int type)\r
- {\r
- int width = pdbcanvas.getWidth();\r
- int height = pdbcanvas.getHeight();\r
-\r
- jalview.util.ImageMaker im;\r
-\r
- if (type == jalview.util.ImageMaker.PNG)\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.PNG,\r
- "Make PNG image from view",\r
- width, height,\r
- null, null);\r
- else\r
- im = new jalview.util.ImageMaker(this,\r
- jalview.util.ImageMaker.EPS,\r
- "Make EPS file from view",\r
- width, height,\r
- null, this.getTitle());\r
-\r
- if (im.getGraphics() != null)\r
- {\r
- pdbcanvas.drawAll(im.getGraphics(), width, height);\r
- im.writeImage();\r
- }\r
- }\r
- public void charge_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setChargeColours();\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void hydro_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new HydrophobicColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void chain_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setChainColours();\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void zbuffer_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void molecule_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void depth_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.depthcue = ! pdbcanvas.depthcue;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void wire_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.wire = ! pdbcanvas.wire;\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void seqButton_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = true;\r
- pdbcanvas.updateSeqColours();\r
- }\r
-\r
-\r
- public void mapping_actionPerformed(ActionEvent e)\r
- {\r
- jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();\r
- Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);\r
- cap.setText(pdbcanvas.mappingDetails.toString());\r
- }\r
-\r
- public void allchains_itemStateChanged(ItemEvent e)\r
- {\r
- pdbcanvas.setAllchainsVisible(allchains.getState());\r
- }\r
-\r
- public void zappo_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new ZappoColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void taylor_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new TaylorColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void helix_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new HelixColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void strand_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new StrandColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void turn_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new TurnColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void buried_actionPerformed(ActionEvent e)\r
- {\r
- pdbcanvas.bysequence = false;\r
- pdbcanvas.pdb.setColours(new BuriedColourScheme());\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
-\r
- public void user_actionPerformed(ActionEvent e)\r
- {\r
- if (e.getActionCommand().equals("User Defined..."))\r
- {\r
- new UserDefinedColours(pdbcanvas, null);\r
- }\r
- else\r
- {\r
- UserColourScheme udc = (UserColourScheme) UserDefinedColours.\r
- getUserColourSchemes().get(e.getActionCommand());\r
-\r
- pdbcanvas.pdb.setColours(udc);\r
- pdbcanvas.redrawneeded=true;\r
- pdbcanvas.repaint();\r
- }\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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 MCview;
+
+import javax.swing.*;
+import java.awt.event.*;
+import jalview.datamodel.*;
+import jalview.schemes.*;
+import jalview.gui.*;
+import jalview.io.EBIFetchClient;
+import java.awt.event.ActionListener;
+import java.awt.event.ActionEvent;
+
+public class PDBViewer extends JInternalFrame implements Runnable
+{
+ PDBEntry pdb;
+ Sequence sequence;
+ PDBCanvas pdbcanvas;
+
+
+ public PDBViewer(PDBEntry entry,
+ Sequence seq,
+ SeqCanvas seqcanvas)
+ {
+ /*Uncomment this to modify in Jbuilder
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }*/
+
+ if (entry==null)
+ return;
+ pdb = entry;
+ sequence = seq;
+
+ Thread worker = new Thread(this);
+ worker.start();
+
+ pdbcanvas = new PDBCanvas(seqcanvas, seq);
+
+ setContentPane(pdbcanvas);
+ StringBuffer title = new StringBuffer(sequence.getName() + ":" + pdb.getId());
+ if(pdb.getProperty()!=null)
+ {
+ if (pdb.getProperty().get("method")!=null)
+ {
+ title.append(" Method: ");
+ title.append(pdb.getProperty().get("method"));
+ }
+ if (pdb.getProperty().get("chains") != null)
+ {
+ title.append(" Chain:");
+ title.append(pdb.getProperty().get("chains"));
+ }
+ }
+ Desktop.addInternalFrame(this,title.toString(),400, 400);
+ }
+
+ public void run()
+ {
+ try
+ {
+ EBIFetchClient ebi = new EBIFetchClient();
+ String query = "pdb:" + pdb.getId();
+ String[] result = ebi.fetchData(query, "default","raw");
+ if (result!=null) {
+ PDBfile pdbfile = new PDBfile(result);
+ pdbcanvas.setPDBFile(pdbfile);
+ } else {
+ throw new Exception("Empty result for WSDbFetch Query: "+query);
+ }
+
+ try
+ {
+ jbInit();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ showErrorMessage("Failed to retrieve PDB structure.");
+// this.dispose();
+ }
+ }
+
+ private void jbInit()
+ throws Exception
+ {
+ this.addKeyListener(new KeyAdapter()
+ {
+ public void keyPressed(KeyEvent evt)
+ {
+ pdbcanvas.keyPressed(evt);
+ }
+ });
+
+ this.setJMenuBar(jMenuBar1);
+ fileMenu.setText("File");
+ coloursMenu.setText("Colours");
+ saveMenu.setActionCommand("Save Image");
+ saveMenu.setText("Save As");
+ png.setText("PNG");
+ png.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ png_actionPerformed(e);
+ }
+ });
+ eps.setText("EPS");
+ eps.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ eps_actionPerformed(e);
+ }
+ });
+ mapping.setText("View Mapping");
+ mapping.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ mapping_actionPerformed(e);
+ }
+ });
+ wire.setText("Wireframe");
+ wire.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ wire_actionPerformed(e);
+ }
+ });
+ depth.setSelected(true);
+ depth.setText("Depthcue");
+ depth.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ depth_actionPerformed(e);
+ }
+ });
+ zbuffer.setSelected(true);
+ zbuffer.setText("Z Buffering");
+ zbuffer.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zbuffer_actionPerformed(e);
+ }
+ });
+ charge.setText("Charge & Cysteine");
+ charge.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ charge_actionPerformed(e);
+ }
+ });
+ chain.setText("By Chain");
+ chain.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ chain_actionPerformed(e);
+ }
+ });
+ seqButton.setSelected(true);
+ seqButton.setText("By Sequence");
+ seqButton.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ seqButton_actionPerformed(e);
+ }
+ });
+ allchains.setSelected(true);
+ allchains.setText("Show All Chains");
+ allchains.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ allchains_itemStateChanged(e);
+ }
+ });
+ zappo.setText("Zappo");
+ zappo.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ zappo_actionPerformed(e);
+ }
+ });
+ taylor.setText("Taylor");
+ taylor.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ taylor_actionPerformed(e);
+ }
+ });
+ hydro.setText("Hydro");
+ hydro.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ hydro_actionPerformed(e);
+ }
+ });
+ helix.setText("Helix");
+ helix.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ helix_actionPerformed(e);
+ }
+ });
+ strand.setText("Strand");
+ strand.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ strand_actionPerformed(e);
+ }
+ });
+ turn.setText("Turn");
+ turn.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ turn_actionPerformed(e);
+ }
+ });
+ buried.setText("Buried");
+ buried.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ buried_actionPerformed(e);
+ }
+ });
+ user.setText("User Defined...");
+ user.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ user_actionPerformed(e);
+ }
+ });
+ viewMenu.setText("View");
+ jMenuBar1.add(fileMenu);
+ jMenuBar1.add(coloursMenu);
+ jMenuBar1.add(viewMenu);
+ fileMenu.add(saveMenu);
+ fileMenu.add(mapping);
+ saveMenu.add(png);
+ saveMenu.add(eps);
+ coloursMenu.add(seqButton);
+ coloursMenu.add(chain);
+ coloursMenu.add(charge);
+ coloursMenu.add(zappo);
+ coloursMenu.add(taylor);
+ coloursMenu.add(hydro);
+ coloursMenu.add(helix);
+ coloursMenu.add(strand);
+ coloursMenu.add(turn);
+ coloursMenu.add(buried);
+ coloursMenu.add(user);
+ ButtonGroup bg = new ButtonGroup();
+ bg.add(seqButton);
+ bg.add(chain);
+ bg.add(charge);
+ bg.add(zappo);
+ bg.add(taylor);
+ bg.add(hydro);
+ bg.add(helix);
+ bg.add(strand);
+ bg.add(turn);
+ bg.add(buried);
+ bg.add(user);
+
+
+ if(jalview.gui.UserDefinedColours.getUserColourSchemes()!=null)
+ {
+ java.util.Enumeration userColours = jalview.gui.UserDefinedColours.
+ getUserColourSchemes().keys();
+
+ while (userColours.hasMoreElements())
+ {
+ final JRadioButtonMenuItem radioItem = new JRadioButtonMenuItem(userColours.
+ nextElement().toString());
+ radioItem.setName("USER_DEFINED");
+ radioItem.addMouseListener(new MouseAdapter()
+ {
+ public void mousePressed(MouseEvent evt)
+ {
+ if(evt.isControlDown() || SwingUtilities.isRightMouseButton(evt))
+ {
+ radioItem.removeActionListener(radioItem.getActionListeners()[0]);
+
+ int option = JOptionPane.showInternalConfirmDialog(jalview.gui.Desktop.desktop,
+ "Remove from default list?",
+ "Remove user defined colour",
+ JOptionPane.YES_NO_OPTION);
+ if(option == JOptionPane.YES_OPTION)
+ {
+ jalview.gui.UserDefinedColours.removeColourFromDefaults(radioItem.getText());
+ coloursMenu.remove(radioItem);
+ }
+ else
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ user_actionPerformed(evt);
+ }
+ });
+ }
+ }
+ });
+ radioItem.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent evt)
+ {
+ user_actionPerformed(evt);
+ }
+ });
+ coloursMenu.add(radioItem);
+ bg.add(radioItem);
+ }
+ }
+
+ viewMenu.add(wire);
+ viewMenu.add(depth);
+ viewMenu.add(zbuffer);
+ viewMenu.add(allchains);
+ }
+
+ JMenuBar jMenuBar1 = new JMenuBar();
+ JMenu fileMenu = new JMenu();
+ JMenu coloursMenu = new JMenu();
+ JMenu saveMenu = new JMenu();
+ JMenuItem png = new JMenuItem();
+ JMenuItem eps = new JMenuItem();
+ JMenuItem mapping = new JMenuItem();
+ JCheckBoxMenuItem wire = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem depth = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem zbuffer = new JCheckBoxMenuItem();
+ JCheckBoxMenuItem allchains = new JCheckBoxMenuItem();
+
+ JRadioButtonMenuItem charge = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem chain = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem seqButton = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem hydro = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem taylor = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem zappo = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem user = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem buried = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem turn = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem strand = new JRadioButtonMenuItem();
+ JRadioButtonMenuItem helix = new JRadioButtonMenuItem();
+ JMenu viewMenu = new JMenu();
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void eps_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.EPS);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void png_actionPerformed(ActionEvent e)
+ {
+ makePDBImage(jalview.util.ImageMaker.PNG);
+ }
+
+ void makePDBImage(int type)
+ {
+ int width = pdbcanvas.getWidth();
+ int height = pdbcanvas.getHeight();
+
+ jalview.util.ImageMaker im;
+
+ if (type == jalview.util.ImageMaker.PNG)
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.PNG,
+ "Make PNG image from view",
+ width, height,
+ null, null);
+ else
+ im = new jalview.util.ImageMaker(this,
+ jalview.util.ImageMaker.EPS,
+ "Make EPS file from view",
+ width, height,
+ null, this.getTitle());
+
+ if (im.getGraphics() != null)
+ {
+ pdbcanvas.drawAll(im.getGraphics(), width, height);
+ im.writeImage();
+ }
+ }
+ public void charge_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChargeColours();
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void hydro_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new HydrophobicColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void chain_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setChainColours();
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void zbuffer_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.zbuffer = ! pdbcanvas.zbuffer;
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void molecule_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bymolecule = ! pdbcanvas.bymolecule;
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void depth_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.depthcue = ! pdbcanvas.depthcue;
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void wire_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.wire = ! pdbcanvas.wire;
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void seqButton_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = true;
+ pdbcanvas.updateSeqColours();
+ }
+
+
+ public void mapping_actionPerformed(ActionEvent e)
+ {
+ jalview.gui.CutAndPasteTransfer cap = new jalview.gui.CutAndPasteTransfer();
+ Desktop.addInternalFrame(cap, "PDB - Sequence Mapping", 550, 600);
+ cap.setText(pdbcanvas.mappingDetails.toString());
+ }
+
+ public void allchains_itemStateChanged(ItemEvent e)
+ {
+ pdbcanvas.setAllchainsVisible(allchains.getState());
+ }
+ void showErrorMessage(String error)
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ error, "PDB Viewer Error", JOptionPane.WARNING_MESSAGE);
+ }
+
+
+ public void zappo_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new ZappoColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void taylor_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new TaylorColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void helix_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new HelixColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void strand_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new StrandColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void turn_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new TurnColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void buried_actionPerformed(ActionEvent e)
+ {
+ pdbcanvas.bysequence = false;
+ pdbcanvas.pdb.setColours(new BuriedColourScheme());
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+
+ public void user_actionPerformed(ActionEvent e)
+ {
+ if (e.getActionCommand().equals("User Defined..."))
+ {
+ new UserDefinedColours(pdbcanvas, null);
+ }
+ else
+ {
+ UserColourScheme udc = (UserColourScheme) UserDefinedColours.
+ getUserColourSchemes().get(e.getActionCommand());
+
+ pdbcanvas.pdb.setColours(udc);
+ pdbcanvas.redrawneeded=true;
+ pdbcanvas.repaint();
+ }
+ }
+}
import jalview.io.*;\r
import java.util.*;\r
\r
-\r
public class SequenceFetcher\r
extends JPanel implements Runnable\r
{\r
\r
frame = new JInternalFrame();\r
frame.setContentPane(this);\r
- if(System.getProperty("os.name").startsWith("Mac"))\r
- Desktop.addInternalFrame(frame, ((af==null) ?\r
- "New " : "Additional ")+"Sequence Fetcher (WSDBfetch@EBI)", 400, 140);\r
+ if (System.getProperty("os.name").startsWith("Mac"))\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 140);\r
else\r
- Desktop.addInternalFrame(frame, ((af==null) ?\r
- "New " : "Additional ")+"Sequence Fetcher (WSDBfetch@EBI)", 400, 125);\r
+ Desktop.addInternalFrame(frame, getFrameTitle(), 400, 125);\r
+ }\r
+\r
+ private String getFrameTitle()\r
+ {\r
+ return ( (alignFrame == null) ? "New " : "Additional ") +\r
+ "Sequence Fetcher (WSDBfetch@EBI)";\r
}\r
\r
private void jbInit()\r
worker.start();\r
}\r
\r
- private void resetDialog() {\r
+ private void resetDialog()\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
+ frame.setTitle(getFrameTitle());\r
}\r
\r
public void run()\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
+ 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
+ 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
+ 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
+ || database.getSelectedItem().equals("EMBLCDS"))\r
{\r
EBIFetchClient dbFetch = new EBIFetchClient();\r
String[] reply = dbFetch.fetchData(\r
}\r
else if (database.getSelectedItem().equals("PDB"))\r
{\r
- result = getPDBFile(textfield.getText().toUpperCase());\r
- if (result!=null)\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
+ result.append(respart);\r
+\r
+ }\r
+\r
+ if (result != null)\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
void getUniprotFile(String id)\r
{\r
EBIFetchClient ebi = new EBIFetchClient();\r
- File file = ebi.fetchDataAsFile("uniprot:"+id,"xml", null);\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
+ 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
+ StringBuffer name = new StringBuffer(">Uniprot/Swiss-Prot");\r
Enumeration en2 = entry.getAccession().elements();\r
- while(en2.hasMoreElements())\r
+ while (en2.hasMoreElements())\r
{\r
name.append("|");\r
name.append(en2.nextElement());\r
}\r
en2 = entry.getName().elements();\r
- while(en2.hasMoreElements())\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
+ if (entry.getProteinName() != null)\r
+ name.append(" " + entry.getProteinName().elementAt(0));\r
\r
- result.append(name +"\n"+entry.getUniprotSequence().getContent());\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());\r
- for(int i=0; i<entries.size(); i++)\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
}\r
}\r
\r
- StringBuffer getPDBFile(String id)\r
+ StringBuffer getPDBFile(String id)\r
+ {\r
+ StringBuffer result = new StringBuffer();\r
+ String chain = null;\r
+ if (id.indexOf(":") > -1)\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
+ 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
+ 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
- jalview.bin.Cache.log.warn("Exception when retrieving " + textfield.getText() + " from " +\r
- database.getSelectedItem(), ex);\r
- return null;\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
- return result;\r
}\r
-\r
- SequenceI[] parseResult(String result)\r
+ catch (Exception ex) // Problem parsing PDB file\r
{\r
- String format = IdentifyFile.Identify(result, "Paste");\r
- SequenceI[] sequences = null;\r
+ jalview.bin.Cache.log.warn("Exception when retrieving " +\r
+ textfield.getText() + " from " +\r
+ database.getSelectedItem(), ex);\r
+ return null;\r
+ }\r
\r
- if (FormatAdapter.formats.contains(format))\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",\r
+ format);\r
+ if (sequences != null && sequences.length > 0)\r
{\r
- sequences = new FormatAdapter().readFile(result.toString(), "Paste", format);\r
- if (sequences != null && sequences.length>0)\r
+ if (alignFrame == null)\r
{\r
- if(alignFrame==null)\r
+ AlignFrame af = new AlignFrame(new Alignment(sequences));\r
+ af.currentFileFormat = format;\r
+ Desktop.addInternalFrame(af,\r
+ "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
- 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
+ af.setMaximum(jalview.bin.Cache.getDefault("SHOW_FULLSCREEN", false));\r
}\r
- else\r
+ catch (Exception ex)\r
+ {}\r
+ }\r
+ else\r
+ {\r
+ for (int i = 0; i < sequences.length; i++)\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
+ 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.\r
+ getAlignment().getSequences());\r
\r
- if (database.getSelectedItem().equals("PDB"))\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
- for (int i = 0; i < sequences.length; i++)\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
- PDBEntry entry = new PDBEntry();\r
- entry.setId(textfield.getText());\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
+ 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
-\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
- else\r
- showErrorMessage( "Error retrieving "+textfield.getText()\r
- +" from "+database.getSelectedItem());\r
+\r
}\r
+ else\r
+ showErrorMessage("Error retrieving " + textfield.getText()\r
+ + " from " + database.getSelectedItem());\r
+ }\r
\r
- return sequences;\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
+ error, "Error Retrieving Data",\r
+ JOptionPane.WARNING_MESSAGE);\r
}\r
}\r
\r
-\r
-\r
-\r
git://source.jalview.org / jalview.git / commitdiff