label.align_structures = Align Structures
label.jmol = Jmol
label.chimera = Chimera
-label.create_chimera_attributes = Write Jalview features
-label.create_chimera_attributes_tip = Set Chimera residue attributes for visible features
+label.create_viewer_attributes = Write Jalview features
+label.create_viewer_attributes_tip = Create {0} attributes for visible features
+label.fetch_viewer_attributes = Fetch {0} attribute
+label.fetch_viewer_attributes_tip = Copy {0} attribute to Jalview feature
label.sort_alignment_by_tree = Sort Alignment By Tree
label.mark_unlinked_leaves = Mark Unlinked Leaves
label.associate_leaves_with = Associate Leaves With
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewerBase;
import jalview.structure.StructureMapping;
import jalview.structure.StructureMappingcommandSet;
import jalview.structure.StructureSelectionManager;
*/
public class ChimeraCommands
{
-
- public static final String NAMESPACE_PREFIX = "jv_";
-
/**
* Constructs Chimera commands to colour residues as per the Jalview alignment
*
sb.append(Character.isLetterOrDigit(c) ? c : '_');
}
}
- String attName = NAMESPACE_PREFIX + sb.toString();
+ String attName = StructureViewerBase.NAMESPACE_PREFIX + sb.toString();
/*
* Chimera treats an attribute name ending in 'color' as colour-valued;
}
return -1;
}
+
+ /**
+ * Queries Chimera for its list of residue attributes and returns their names
+ *
+ * @return
+ */
+ public List<String> getResidueAttributes()
+ {
+ List<String> result = new ArrayList<String>();
+ List<String> atts = sendChimeraCommand("list resattr", true);
+ for (String att : atts)
+ {
+ /*
+ * expect lines like "resattr chi1" - we just one the second bit
+ */
+ String[] tokens = att.split(" ");
+ result.add(tokens[tokens.length - 1]);
+ }
+ return result;
+ }
}
import java.awt.Graphics;
import java.awt.Rectangle;
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.FileOutputStream;
import javax.swing.JColorChooser;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
-import javax.swing.JOptionPane;
+import javax.swing.JMenuItem;
import javax.swing.JPanel;
import javax.swing.JSplitPane;
import javax.swing.SwingUtilities;
private void initMenus()
{
+ String jmol = MessageManager.getString("label.jmol");
+ viewerActionMenu.setText(jmol);
seqColour.setSelected(jmb.isColourBySequence());
viewerColour.setSelected(!jmb.isColourBySequence());
if (_colourwith == null)
}
});
+
+ JMenuItem writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_viewer_attributes"));
+ writeFeatures.setToolTipText(MessageManager.formatMessage(
+ "label.create_viewer_attributes_tip", jmol));
+ writeFeatures.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ sendFeaturesToViewer();
+ }
+ });
+ viewerActionMenu.add(writeFeatures);
+
+ final JMenu fetchAttributes = new JMenu(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes", jmol));
+ fetchAttributes.setToolTipText(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes_tip", jmol));
+ fetchAttributes.addMouseListener(new MouseAdapter()
+ {
+
+ @Override
+ public void mouseEntered(MouseEvent e)
+ {
+ buildAttributesMenu(fetchAttributes);
+ }
+ });
+ viewerActionMenu.add(fetchAttributes);
}
IProgressIndicator progressBar = null;
setChainMenuItems(jmb.getChainNames());
this.setTitle(jmb.getViewerTitle());
- 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);
return jmb;
}
+ @Override
+ protected void sendFeaturesToViewer()
+ {
+ /*
+ * Atom properties may also be set directly using {atom expression}.xxxx = y.
+ */
+ }
+
+ @Override
+ protected void getResidueAttributes(String attName)
+ {
+ /*
+ * getproperty atominfo returns properties for all atoms
+ * - could parse this for unique/specific property names?
+ *
+ * _ipt atomID atomIndex atomno bondCount chain clickabilityFlags colix color coord
+ * element elemno formalCharge groupID info model name occupancy partialCharge
+ * polymerLength radius resname resno shape spacefill structure sym temp
+ * visibilityFlags visible x y z
+ *
+ * getproperty chaininfo is residue level info
+ * no sign of average bfactor for a residue :-(
+ */
+ }
+
+ @Override
+ protected List<String> getResidueAttributeNames()
+ {
+ // TODO Auto-generated method stub
+ return null;
+ }
+
}
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.DataSourceType;
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;
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;
import javax.swing.event.MenuEvent;
*/
public class ChimeraViewFrame extends StructureViewerBase
{
- private JalviewChimeraBinding jmb;
+ JalviewChimeraBinding jmb;
private boolean allChainsSelected = false;
*/
private void initMenus()
{
- viewerActionMenu.setText(MessageManager.getString("label.chimera"));
+ String chimera = MessageManager.getString("label.chimera");
+ viewerActionMenu.setText(chimera);
viewerColour.setText(MessageManager
.getString("label.colour_with_chimera"));
viewerColour.setToolTipText(MessageManager
viewerActionMenu.add(alpanels);
viewerActionMenu.addMenuListener(new MenuListener()
{
-
@Override
public void menuSelected(MenuEvent e)
{
handler.itemStateChanged(null);
}
-
@Override
public void menuDeselected(MenuEvent e)
{
- // TODO Auto-generated method stub
}
-
@Override
public void menuCanceled(MenuEvent e)
{
- // TODO Auto-generated method stub
}
});
JMenuItem writeFeatures = new JMenuItem(
- MessageManager.getString("label.create_chimera_attributes"));
- writeFeatures.setToolTipText(MessageManager
- .getString("label.create_chimera_attributes_tip"));
+ MessageManager.getString("label.create_viewer_attributes"));
+ writeFeatures.setToolTipText(MessageManager.formatMessage(
+ "label.create_viewer_attributes_tip", chimera));
writeFeatures.addActionListener(new ActionListener()
{
@Override
public void actionPerformed(ActionEvent e)
{
- sendFeaturesToChimera();
+ sendFeaturesToViewer();
}
});
viewerActionMenu.add(writeFeatures);
- final JMenu fetchAttributes = new JMenu("Fetch Chimera attributes");
- fetchAttributes
- .setToolTipText("Copy Chimera attribute to Jalview feature");
+ final JMenu fetchAttributes = new JMenu(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes", chimera));
+ fetchAttributes.setToolTipText(MessageManager.formatMessage(
+ "label.fetch_viewer_attributes_tip", chimera));
fetchAttributes.addMouseListener(new MouseAdapter()
{
}
});
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<String> 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)
+ * Asks Chimera for residues with the given attribute name, and set as
+ * features on the corresponding sequence positions (if any)
*
* @param attName
*/
- protected void getChimeraAttributes(String attName)
+ @Override
+ protected void getResidueAttributes(String attName)
{
jmb.copyStructureAttributesToFeatures(attName, getAlignmentPanel());
}
* <p>
* For example: setattr r jv:chain "Ferredoxin-1, Chloroplastic" #0:94.A
*/
- protected void sendFeaturesToChimera()
+ @Override
+ protected void sendFeaturesToViewer()
{
jmb.sendFeaturesToViewer(getAlignmentPanel());
}
{
return jmb;
}
+
+ @Override
+ protected List<String> getResidueAttributeNames()
+ {
+ return jmb.getResidueAttributes();
+ }
}
.size()][]);
String newViewId = viewerData.getKey();
- ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
+ StructureViewerBase cvf = new ChimeraViewFrame(chimeraSessionFile,
af.alignPanel, pdbArray, seqsArray, colourByChimera,
colourBySequence, newViewId);
cvf.setSize(data.getWidth(), data.getHeight());
import java.awt.event.ItemEvent;
import java.awt.event.ItemListener;
import java.util.ArrayList;
+import java.util.Collections;
import java.util.List;
import java.util.Vector;
import javax.swing.JCheckBoxMenuItem;
+import javax.swing.JMenu;
import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
/**
* Base class with common functionality for JMol, Chimera or other structure
public abstract class StructureViewerBase extends GStructureViewer
implements Runnable, ViewSetProvider
{
+ /*
+ * prefix for attributes on structure which are derived from Jalview features
+ */
+ public static final String NAMESPACE_PREFIX = "jv_";
/**
* list of sequenceSet ids associated with the view
abstract void showSelectedChains();
+ /**
+ * Send a command to the structure viewer to create residue attributes for
+ * Jalview features
+ */
+ abstract protected void sendFeaturesToViewer();
+
+ /**
+ * Query the structure viewer for its residue attribute names and add them as
+ * sub-items of the attributes menu. Names of the form "jv_*" are ignored as
+ * these originated from Jalview so no need to copy them back.
+ *
+ * @param attributesMenu
+ */
+ protected void buildAttributesMenu(JMenu attributesMenu)
+ {
+ List<String> atts = getResidueAttributeNames();
+ if (atts == null)
+ {
+ return;
+ }
+ attributesMenu.removeAll();
+ Collections.sort(atts);
+ for (final String att : atts)
+ {
+ /*
+ * ignore 'jv_*' attributes, as these are Jalview features that have
+ * been transferred to residue attributes in Chimera!
+ */
+ if (!att.startsWith(StructureViewerBase.NAMESPACE_PREFIX))
+ {
+ JMenuItem menuItem = new JMenuItem(att);
+ menuItem.addActionListener(new ActionListener()
+ {
+ @Override
+ public void actionPerformed(ActionEvent e)
+ {
+ getResidueAttributes(att);
+ }
+ });
+ attributesMenu.add(menuItem);
+ }
+ }
+ }
+
+ /**
+ * Queries the structure viewer for residues with the given attribute, and
+ * creates sequence features in Jalview for the corresponding mapped positions
+ *
+ * @param attName
+ */
+ protected abstract void getResidueAttributes(String attName);
+
+ /**
+ * Returns a list of residue attributes in the structure viewer, excluding any
+ * with prefix "jv_"
+ *
+ * @return
+ */
+ protected abstract List<String> getResidueAttributeNames();
+
}
alignStructs_actionPerformed(actionEvent);
}
});
- viewerActionMenu.setText(MessageManager.getString("label.jmol"));
menuBar.add(fileMenu);
menuBar.add(viewMenu);
menuBar.add(colourMenu);
git://source.jalview.org / jalview.git / commitdiff