X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=4c38898604f817da581651a6f72f796f3a88c758;hb=5965127c38ff1a35d10d806c4b4537cdc1e39579;hp=fe12f404163c0cb8253913a5e1f0bbcb60b28344;hpb=c3b8fbc19c04c2daec702a2bffdfab5d10555143;p=jalview.git diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java index fe12f40..4c38898 100644 --- a/src/jalview/gui/ChimeraViewFrame.java +++ b/src/jalview/gui/ChimeraViewFrame.java @@ -26,9 +26,10 @@ import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; import jalview.datamodel.PDBEntry; import jalview.datamodel.SequenceI; +import jalview.ext.rbvi.chimera.ChimeraCommands; import jalview.ext.rbvi.chimera.JalviewChimeraBinding; import jalview.gui.StructureViewer.ViewerType; -import jalview.io.AppletFormatAdapter; +import jalview.io.DataSourceType; import jalview.io.JalviewFileChooser; import jalview.io.JalviewFileView; import jalview.io.StructureFile; @@ -47,8 +48,11 @@ import jalview.util.Platform; import jalview.ws.dbsources.Pdb; import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.awt.event.ItemEvent; import java.awt.event.ItemListener; +import java.awt.event.MouseAdapter; +import java.awt.event.MouseEvent; import java.io.BufferedReader; import java.io.File; import java.io.FileInputStream; @@ -58,6 +62,7 @@ import java.io.IOException; import java.io.InputStream; import java.io.PrintWriter; import java.util.ArrayList; +import java.util.Collections; import java.util.List; import java.util.Random; import java.util.Vector; @@ -66,6 +71,7 @@ import javax.swing.JCheckBoxMenuItem; import javax.swing.JColorChooser; import javax.swing.JInternalFrame; import javax.swing.JMenu; +import javax.swing.JMenuItem; import javax.swing.JOptionPane; import javax.swing.event.InternalFrameAdapter; import javax.swing.event.InternalFrameEvent; @@ -180,6 +186,97 @@ public class ChimeraViewFrame extends StructureViewerBase // TODO Auto-generated method stub } }); + + JMenuItem writeFeatures = new JMenuItem( + MessageManager.getString("label.create_chimera_attributes")); + writeFeatures.setToolTipText(MessageManager + .getString("label.create_chimera_attributes_tip")); + writeFeatures.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + sendFeaturesToChimera(); + } + }); + viewerActionMenu.add(writeFeatures); + + final JMenu fetchAttributes = new JMenu("Fetch Chimera attributes"); + fetchAttributes + .setToolTipText("Copy Chimera attribute to Jalview feature"); + fetchAttributes.addMouseListener(new MouseAdapter() + { + + @Override + public void mouseEntered(MouseEvent e) + { + buildAttributesMenu(fetchAttributes); + } + }); + viewerActionMenu.add(fetchAttributes); + + } + + /** + * Query Chimera for its residue attribute names and add them as items off the + * attributes menu + * + * @param attributesMenu + */ + protected void buildAttributesMenu(JMenu attributesMenu) + { + List atts = jmb.sendChimeraCommand("list resattr", true); + if (atts == null) + { + return; + } + attributesMenu.removeAll(); + Collections.sort(atts); + for (String att : atts) + { + final String attName = att.split(" ")[1]; + + /* + * ignore 'jv_*' attributes, as these are Jalview features that have + * been transferred to residue attributes in Chimera! + */ + if (!attName.startsWith(ChimeraCommands.NAMESPACE_PREFIX)) + { + JMenuItem menuItem = new JMenuItem(attName); + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + getChimeraAttributes(attName); + } + }); + attributesMenu.add(menuItem); + } + } + } + + /** + * Read residues in Chimera with the given attribute name, and set as features + * on the corresponding sequence positions (if any) + * + * @param attName + */ + protected void getChimeraAttributes(String attName) + { + jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel()); + } + + /** + * Send a command to Chimera to create residue attributes for Jalview features + *

+ * The syntax is: setattr r + *

+ * For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A + */ + protected void sendFeaturesToChimera() + { + jmb.sendFeaturesToViewer(getAlignmentPanel()); } /** @@ -246,7 +343,6 @@ public class ChimeraViewFrame extends StructureViewerBase SequenceI[][] seqs) { createProgressBar(); - // FIXME extractChains needs pdbentries to match IDs to PDBEntry(s) on seqs jmb = new JalviewChimeraBindingModel(this, ap.getStructureSelectionManager(), pdbentrys, seqs, null); addAlignmentPanel(ap); @@ -275,8 +371,6 @@ public class ChimeraViewFrame extends StructureViewerBase } - - /** * Create a new viewer from saved session state data including Chimera session * file @@ -370,17 +464,15 @@ public class ChimeraViewFrame extends StructureViewerBase */ void initChimera() { - jmb.setFinishedInit(false); - jalview.gui.Desktop.addInternalFrame(this, - jmb.getViewerTitle("Chimera", true), getBounds().width, - getBounds().height); + Desktop.addInternalFrame(this, jmb.getViewerTitle("Chimera", true), + getBounds().width, getBounds().height); if (!jmb.launchChimera()) { - JOptionPane.showMessageDialog(Desktop.desktop, + JvOptionPane.showMessageDialog(Desktop.desktop, MessageManager.getString("label.chimera_failed"), MessageManager.getString("label.error_loading_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); this.dispose(); return; } @@ -395,11 +487,64 @@ public class ChimeraViewFrame extends StructureViewerBase + chimeraSessionFile); } } - jmb.setFinishedInit(true); jmb.startChimeraListener(); } + /** + * If the list is not empty, add menu items for 'All' and each individual + * chain to the "View | Show Chain" sub-menu. Multiple selections are allowed. + * + * @param chainNames + */ + @Override + void setChainMenuItems(List chainNames) + { + chainMenu.removeAll(); + if (chainNames == null || chainNames.isEmpty()) + { + return; + } + JMenuItem menuItem = new JMenuItem( + MessageManager.getString("label.all")); + menuItem.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent evt) + { + allChainsSelected = true; + for (int i = 0; i < chainMenu.getItemCount(); i++) + { + if (chainMenu.getItem(i) instanceof JCheckBoxMenuItem) + { + ((JCheckBoxMenuItem) chainMenu.getItem(i)).setSelected(true); + } + } + showSelectedChains(); + allChainsSelected = false; + } + }); + + chainMenu.add(menuItem); + + for (String chainName : chainNames) + { + menuItem = new JCheckBoxMenuItem(chainName, true); + menuItem.addItemListener(new ItemListener() + { + @Override + public void itemStateChanged(ItemEvent evt) + { + if (!allChainsSelected) + { + showSelectedChains(); + } + } + }); + + chainMenu.add(menuItem); + } + } /** * Show only the selected chain(s) in the viewer @@ -441,18 +586,18 @@ public class ChimeraViewFrame extends StructureViewerBase "label.confirm_close_chimera", new Object[] { jmb.getViewerTitle("Chimera", false) }); prompt = JvSwingUtils.wrapTooltip(true, prompt); - int confirm = JOptionPane.showConfirmDialog(this, prompt, + int confirm = JvOptionPane.showConfirmDialog(this, prompt, MessageManager.getString("label.close_viewer"), - JOptionPane.YES_NO_CANCEL_OPTION); + JvOptionPane.YES_NO_CANCEL_OPTION); /* * abort closure if user hits escape or Cancel */ - if (confirm == JOptionPane.CANCEL_OPTION - || confirm == JOptionPane.CLOSED_OPTION) + if (confirm == JvOptionPane.CANCEL_OPTION + || confirm == JvOptionPane.CLOSED_OPTION) { return; } - closeChimera = confirm == JOptionPane.YES_OPTION; + closeChimera = confirm == JvOptionPane.YES_OPTION; } jmb.closeViewer(closeChimera); } @@ -541,15 +686,16 @@ public class ChimeraViewFrame extends StructureViewerBase if (errormsgs.length() > 0) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .formatMessage("label.pdb_entries_couldnt_be_retrieved", new Object[] { errormsgs.toString() }), MessageManager.getString("label.couldnt_load_file"), - JOptionPane.ERROR_MESSAGE); + JvOptionPane.ERROR_MESSAGE); } if (files.length() > 0) { + jmb.setFinishedInit(false); if (!addingStructures) { try @@ -575,12 +721,12 @@ public class ChimeraViewFrame extends StructureViewerBase jmb.openFile(pe); jmb.addSequence(pos, jmb.getSequence()[pos]); File fl = new File(pe.getFile()); - String protocol = AppletFormatAdapter.URL; + DataSourceType protocol = DataSourceType.URL; try { if (fl.exists()) { - protocol = AppletFormatAdapter.FILE; + protocol = DataSourceType.FILE; } } catch (Throwable e) { @@ -607,6 +753,7 @@ public class ChimeraViewFrame extends StructureViewerBase } } } + jmb.refreshGUI(); jmb.setFinishedInit(true); jmb.setLoadingFromArchive(false); @@ -965,10 +1112,10 @@ public class ChimeraViewFrame extends StructureViewerBase setChainMenuItems(jmb.getChainNames()); this.setTitle(jmb.getViewerTitle("Chimera", true)); - if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) - { + // if (jmb.getPdbFile().length > 1 && jmb.getSequence().length > 1) + // { viewerActionMenu.setVisible(true); - } + // } if (!jmb.isLoadingFromArchive()) { seqColour_actionPerformed(null);