X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FChimeraViewFrame.java;h=3a17ea35bfeaa69b3551be289b53ce99988d936a;hb=b7cd96eaeb85474ee2ddec1de92181a3b88ceece;hp=8fcea0c8d0167092ae49755010fd1366db2eaa28;hpb=d85a2741994c169e1b81db8f9166f5214ff1f561;p=jalview.git
diff --git a/src/jalview/gui/ChimeraViewFrame.java b/src/jalview/gui/ChimeraViewFrame.java
index 8fcea0c..3a17ea3 100644
--- a/src/jalview/gui/ChimeraViewFrame.java
+++ b/src/jalview/gui/ChimeraViewFrame.java
@@ -25,10 +25,10 @@ import java.awt.event.ActionListener;
import java.awt.event.MouseAdapter;
import java.awt.event.MouseEvent;
import java.io.File;
-import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.List;
+import java.util.Map;
import javax.swing.JInternalFrame;
import javax.swing.JMenu;
@@ -38,15 +38,17 @@ import javax.swing.event.InternalFrameEvent;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
-import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.StructureViewerModel;
+import jalview.datamodel.StructureViewerModel.StructureData;
import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.gui.StructureViewer.ViewerType;
import jalview.io.DataSourceType;
import jalview.io.StructureFile;
import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker.TYPE;
import jalview.util.MessageManager;
import jalview.util.Platform;
@@ -71,7 +73,10 @@ public class ChimeraViewFrame extends StructureViewerBase
private int myHeight = 150;
- /**
+ private JMenuItem writeFeatures=null;
+
+ private JMenu fetchAttributes=null;
+/**
* Initialise menu options.
*/
@Override
@@ -79,16 +84,13 @@ public class ChimeraViewFrame extends StructureViewerBase
{
super.initMenus();
- viewerActionMenu.setText(MessageManager.getString("label.chimera"));
-
- helpItem.setText(MessageManager.getString("label.chimera_help"));
savemenu.setVisible(false); // not yet implemented
viewMenu.add(fitToWindow);
- JMenuItem writeFeatures = new JMenuItem(
- MessageManager.getString("label.create_chimera_attributes"));
+ writeFeatures = new JMenuItem(
+ MessageManager.getString("label.create_viewer_attributes"));
writeFeatures.setToolTipText(MessageManager
- .getString("label.create_chimera_attributes_tip"));
+ .getString("label.create_viewer_attributes_tip"));
writeFeatures.addActionListener(new ActionListener()
{
@Override
@@ -99,10 +101,10 @@ public class ChimeraViewFrame extends StructureViewerBase
});
viewerActionMenu.add(writeFeatures);
- final JMenu fetchAttributes = new JMenu(
- MessageManager.getString("label.fetch_chimera_attributes"));
+ fetchAttributes = new JMenu(
+ MessageManager.formatMessage("label.fetch_viewer_attributes",getViewerName()));
fetchAttributes.setToolTipText(
- MessageManager.getString("label.fetch_chimera_attributes_tip"));
+ MessageManager.formatMessage("label.fetch_viewer_attributes_tip",getViewerName()));
fetchAttributes.addMouseListener(new MouseAdapter()
{
@@ -114,10 +116,18 @@ public class ChimeraViewFrame extends StructureViewerBase
});
viewerActionMenu.add(fetchAttributes);
}
-
+ @Override
+ protected void buildActionMenu()
+ {
+ super.buildActionMenu();
+ // add these back in after menu is refreshed
+ viewerActionMenu.add(writeFeatures);
+ viewerActionMenu.add(fetchAttributes);
+
+ };
/**
- * Query Chimera for its residue attribute names and add them as items off the
- * attributes menu
+ * Query the structure viewer for its residue attribute names and add them as
+ * items off the attributes menu
*
* @param attributesMenu
*/
@@ -134,7 +144,11 @@ public class ChimeraViewFrame extends StructureViewerBase
@Override
public void actionPerformed(ActionEvent e)
{
- getChimeraAttributes(attName);
+ if (getBinding().copyStructureAttributesToFeatures(attName,
+ getAlignmentPanel()) > 0)
+ {
+ getAlignmentPanel().getFeatureRenderer().featuresAdded();
+ }
}
});
attributesMenu.add(menuItem);
@@ -142,28 +156,15 @@ public class ChimeraViewFrame extends StructureViewerBase
}
/**
- * 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 <attName> <attValue> <atomSpec>
- *
- * For example: setattr r jv_chain "Ferredoxin-1, Chloroplastic" #0:94.A
+ * Sends command(s) to the structure viewer to create residue attributes for
+ * visible Jalview features
*/
protected void sendFeaturesToChimera()
{
+ // todo pull up?
int count = jmb.sendFeaturesToViewer(getAlignmentPanel());
statusBar.setText(
- MessageManager.formatMessage("label.attributes_set", count));
+ MessageManager.formatMessage("label.attributes_set", count, getViewerName()));
}
/**
@@ -246,22 +247,34 @@ public class ChimeraViewFrame extends StructureViewerBase
* @param colourBySequence
* @param newViewId
*/
- public ChimeraViewFrame(String chimeraSessionFile,
- AlignmentPanel alignPanel, PDBEntry[] pdbArray,
- SequenceI[][] seqsArray, boolean colourByChimera,
- boolean colourBySequence, String newViewId)
+ public ChimeraViewFrame(StructureViewerModel viewerData,
+ AlignmentPanel alignPanel, String sessionFile, String vid)
{
this();
- setViewId(newViewId);
- this.chimeraSessionFile = chimeraSessionFile;
+ setViewId(vid);
+ this.chimeraSessionFile = sessionFile;
+ Map pdbData = viewerData.getFileData();
+ PDBEntry[] pdbArray = new PDBEntry[pdbData.size()];
+ SequenceI[][] seqsArray = new SequenceI[pdbData.size()][];
+ int i = 0;
+ for (StructureData data : pdbData.values())
+ {
+ PDBEntry pdbentry = new PDBEntry(data.getPdbId(), null,
+ PDBEntry.Type.PDB, data.getFilePath());
+ pdbArray[i] = pdbentry;
+ List sequencesForPdb = data.getSeqList();
+ seqsArray[i] = sequencesForPdb
+ .toArray(new SequenceI[sequencesForPdb.size()]);
+ i++;
+ }
openNewChimera(alignPanel, pdbArray, seqsArray);
- if (colourByChimera)
+ if (viewerData.isColourByViewer())
{
jmb.setColourBySequence(false);
seqColour.setSelected(false);
viewerColour.setSelected(true);
}
- else if (colourBySequence)
+ else if (viewerData.isColourWithAlignPanel())
{
jmb.setColourBySequence(true);
seqColour.setSelected(true);
@@ -318,6 +331,7 @@ public class ChimeraViewFrame extends StructureViewerBase
getViewerName()),
MessageManager.getString("label.error_loading_file"),
JvOptionPane.ERROR_MESSAGE);
+ jmb.closeViewer(true);
this.dispose();
return;
}
@@ -428,9 +442,15 @@ public class ChimeraViewFrame extends StructureViewerBase
initChimera();
} catch (Exception ex)
{
- Cache.log.error("Couldn't open Chimera viewer!", ex);
+ Console.error("Couldn't open Chimera viewer!", ex);
}
}
+ if (!jmb.isViewerRunning())
+ {
+ // nothing to do
+ // TODO: ensure we tidy up JAL-3619
+ return;
+ }
int num = -1;
for (PDBEntry pe : filePDB)
{
@@ -473,12 +493,12 @@ public class ChimeraViewFrame extends StructureViewerBase
oomerror);
} catch (Exception ex)
{
- Cache.log.error(
+ Console.error(
"Couldn't open " + pe.getFile() + " in Chimera viewer!",
ex);
} finally
{
- Cache.log.debug("File locations are " + files);
+ Console.debug("File locations are " + files);
}
}
}
@@ -489,7 +509,8 @@ public class ChimeraViewFrame extends StructureViewerBase
/*
* ensure that any newly discovered features (e.g. RESNUM)
- * are added to any open feature settings dialog
+ * are notified to the FeatureRenderer (and added to any
+ * open feature settings dialog)
*/
FeatureRenderer fr = getBinding().getFeatureRenderer(null);
if (fr != null)
@@ -521,31 +542,10 @@ public class ChimeraViewFrame extends StructureViewerBase
}
@Override
- public void eps_actionPerformed()
- {
- throw new Error(MessageManager
- .getString("error.eps_generation_not_implemented"));
- }
-
- @Override
- public void png_actionPerformed()
- {
- throw new Error(MessageManager
- .getString("error.png_generation_not_implemented"));
- }
-
- @Override
- public void showHelp_actionPerformed()
+ public void makePDBImage(TYPE imageType)
{
- try
- {
- String url = jmb.getHelpURL();
- BrowserLauncher.openURL(url);
- } catch (IOException ex)
- {
- System.err
- .println("Show Chimera help failed with: " + ex.getMessage());
- }
+ throw new UnsupportedOperationException(
+ "Image export for Chimera is not implemented");
}
@Override
@@ -555,12 +555,6 @@ public class ChimeraViewFrame extends StructureViewerBase
}
@Override
- protected void fitToWindow_actionPerformed()
- {
- jmb.focusView();
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.CHIMERA;