*/
package jalview.ext.jmol;
-import jalview.api.FeatureRenderer;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.IProgressIndicator;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.io.DataSourceType;
-import jalview.io.StructureFile;
-import jalview.structure.AtomSpec;
-import jalview.structure.StructureCommand;
-import jalview.structure.StructureCommandI;
-import jalview.structure.StructureSelectionManager;
-import jalview.structures.models.AAStructureBindingModel;
-
import java.awt.Container;
import java.awt.event.ComponentEvent;
import java.awt.event.ComponentListener;
import org.jmol.c.CBK;
import org.jmol.viewer.Viewer;
+import jalview.api.FeatureRenderer;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.IProgressIndicator;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.io.DataSourceType;
+import jalview.io.StructureFile;
+import jalview.structure.AtomSpec;
+import jalview.structure.StructureCommand;
+import jalview.structure.StructureCommandI;
+import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+
public abstract class JalviewJmolBinding extends AAStructureBindingModel
implements JmolStatusListener, JmolSelectionListener,
ComponentListener
{
return String.valueOf(pdbfnum + 1);
}
+
+ /**
+ * Returns ".spt" - the Jmol session file extension
+ *
+ * @return
+ * @see https://chemapps.stolaf.edu/jmol/docs/#writemodel
+ */
+ @Override
+ public String getSessionFileExtension()
+ {
+ return ".spt";
+ }
}
*/
package jalview.ext.jmol;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.structure.StructureSelectionManager;
import jalview.util.Comparison;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Map;
-
/**
* Routines for generating Jmol commands for Jalview/Jmol binding
*
public StructureCommandI saveSession(String filepath)
{
/*
- * https://chemapps.stolaf.edu/jmol/docs/#write
- * not currently used in Jalview
+ * https://chemapps.stolaf.edu/jmol/docs/#writemodel
*/
- return new StructureCommand("write \"" + filepath + "\"");
+ return new StructureCommand("write STATE \"" + filepath + "\"");
}
@Override
package jalview.ext.pymol;
+import java.awt.Color;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.structure.AtomSpecModel;
import jalview.structure.StructureCommand;
import jalview.structure.StructureCommandI;
import jalview.structure.StructureCommandsBase;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.List;
-
/**
* A class that generates commands to send to PyMol over its XML-RPC interface.
* <p>
@Override
public StructureCommandI openCommandFile(String path)
{
- // where is this documented by PyMol?
- // todo : xml-rpc answers 'method "@" is not supported'
- return new StructureCommand("@" + path); // should be .pml
+ // https://pymolwiki.org/index.php/Run
+ return new StructureCommand("run", path); // should be .pml
}
@Override
*/
package jalview.ext.rbvi.chimera;
+import java.io.File;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.PrintWriter;
+import java.net.BindException;
+import java.util.ArrayList;
+import java.util.Collections;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.api.AlignmentViewPanel;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.PrintWriter;
-import java.net.BindException;
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraManager;
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
public abstract class JalviewChimeraBinding extends AAStructureBindingModel
{
public static final String CHIMERA_FEATURE_GROUP = "Chimera";
}
/**
- * Returns the file extension to use for a saved viewer session file
+ * Returns the file extension to use for a saved viewer session file (.py)
*
* @return
*/
+ @Override
public String getSessionFileExtension()
{
return ".py";
*/
package jalview.gui;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.structure.StructureCommand;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.BrowserLauncher;
-import jalview.util.ImageMaker;
-import jalview.util.MessageManager;
-import jalview.util.Platform;
-import jalview.ws.dbsources.Pdb;
-
import java.awt.BorderLayout;
import java.awt.Color;
import java.awt.Dimension;
import javax.swing.event.InternalFrameAdapter;
import javax.swing.event.InternalFrameEvent;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.structure.StructureCommand;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.BrowserLauncher;
+import jalview.util.ImageMaker;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.ws.dbsources.Pdb;
+
public class AppJmol extends StructureViewerBase
{
// ms to wait for Jmol to load files
}
@Override
- public String getStateInfo()
- {
- return jmb == null ? null : jmb.jmolViewer.getStateInfo();
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.JMOL;
*/
package jalview.gui;
-import jalview.api.AlignmentViewPanel;
-import jalview.api.structures.JalviewStructureDisplayI;
-import jalview.bin.Cache;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.ext.jmol.JalviewJmolBinding;
-import jalview.io.DataSourceType;
-import jalview.structure.StructureSelectionManager;
-
import java.awt.Container;
+import java.io.File;
+import java.io.FileWriter;
+import java.io.IOException;
import java.util.Map;
import javax.swing.JComponent;
import org.jmol.java.BS;
import org.openscience.jmol.app.jmolpanel.console.AppConsole;
+import jalview.api.AlignmentViewPanel;
+import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.ext.jmol.JalviewJmolBinding;
+import jalview.io.DataSourceType;
+import jalview.structure.StructureSelectionManager;
+
public class AppJmolBinding extends JalviewJmolBinding
{
public AppJmolBinding(AppJmol appJmol, StructureSelectionManager sSm,
// TODO Auto-generated method stub
return null;
}
+
+ /**
+ * Overrides the default method to save a session to file, in order to
+ * guarantee it is done synchronously. Jmol command 'write STATE path' would
+ * execute asynchronously, so instead we get the state and write it directly
+ * here.
+ */
+ @Override
+ protected void saveSession(File f)
+ {
+ String state = jmolViewer.getStateInfo();
+ if (state != null)
+ {
+ try
+ {
+ FileWriter fw = new FileWriter(f);
+ fw.write(state);
+ fw.close();
+ } catch (IOException e)
+ {
+ Cache.log.error("Error writing Jmol state: " + e.toString());
+ }
+ }
+ else
+ {
+ Cache.log.error("Error requesting Jmol state to save");
+ }
+ }
}
return jmb;
}
- /**
- * Ask Chimera to save its session to the designated file path, or to a
- * temporary file if the path is null. Returns the file path if successful,
- * else null.
- *
- * @param filepath
- * @see getStateInfo
- */
- protected String saveSession(String filepath)
- {
- String pathUsed = filepath;
- try
- {
- if (pathUsed == null)
- {
- String suffix = jmb.getSessionFileExtension();
- File tempFile = File.createTempFile("chimera", suffix);
- tempFile.deleteOnExit();
- pathUsed = tempFile.getPath();
- }
- boolean result = jmb.saveSession(pathUsed);
- if (result)
- {
- this.chimeraSessionFile = pathUsed;
- return pathUsed;
- }
- } catch (IOException e)
- {
- }
- return null;
- }
-
- /**
- * Returns a string representing the state of the Chimera session. This is
- * done by requesting Chimera to save its session to a temporary file, then
- * reading the file contents. Returns an empty string on any error.
- */
- @Override
- public String getStateInfo()
- {
- String sessionFile = saveSession(null);
- if (sessionFile == null)
- {
- return "";
- }
- InputStream is = null;
- try
- {
- File f = new File(sessionFile);
- byte[] bytes = new byte[(int) f.length()];
- is = new FileInputStream(sessionFile);
- is.read(bytes);
- return new String(bytes);
- } catch (IOException e)
- {
- return "";
- } finally
- {
- if (is != null)
- {
- try
- {
- is.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- }
- }
-
@Override
protected void fitToWindow_actionPerformed()
{
package jalview.gui;
+import java.util.List;
+
+import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
+import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.ext.rbvi.chimera.ChimeraXCommands;
import jalview.structure.StructureCommand;
import jalview.structure.StructureSelectionManager;
-import java.util.List;
-
-import ext.edu.ucsf.rbvi.strucviz2.ChimeraModel;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
-import ext.edu.ucsf.rbvi.strucviz2.StructureManager.ModelType;
-
public class JalviewChimeraXBindingModel extends JalviewChimeraBindingModel
{
}
/**
- * Returns the file extension to use for a saved viewer session file
+ * Returns the file extension to use for a saved viewer session file (.cxs)
*
* @return
+ * @see https://www.cgl.ucsf.edu/chimerax/docs/user/commands/save.html#sesformat
*/
@Override
public String getSessionFileExtension()
package jalview.gui;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
import jalview.api.AlignmentViewPanel;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
import jalview.structure.StructureSelectionManager;
import jalview.structures.models.AAStructureBindingModel;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
public class PymolBindingModel extends AAStructureBindingModel
{
private PymolManager pymolManager;
protected List<String> executeCommand(StructureCommandI command,
boolean getReply)
{
- System.out.println(command.toString()); // debug
+ // System.out.println(command.toString()); // debug
return pymolManager.sendCommand(command, getReply);
}
{
pymolManager.exitPymol();
}
- // if (this.pymolListener != null)
- // {
- // pymolListener.shutdown();
- // pymolListener = null;
- // }
pymolManager = null;
if (pymolMonitor != null)
return file;
}
+ /**
+ * Returns the file extension to use for a saved viewer session file (.pse)
+ *
+ * @return
+ * @see https://pymolwiki.org/index.php/Save
+ */
+ @Override
+ public String getSessionFileExtension()
+ {
+ return ".pse";
+ }
+
}
package jalview.gui;
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.bin.Cache;
import jalview.structures.models.AAStructureBindingModel;
import jalview.util.MessageManager;
-import java.io.File;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.swing.JInternalFrame;
-import javax.swing.event.InternalFrameAdapter;
-import javax.swing.event.InternalFrameEvent;
-
public class PymolViewer extends StructureViewerBase
{
private static final int myWidth = 500;
openNewPymol(ap, pe, seqs);
}
+ /**
+ * Constructor given a session file to be restored
+ *
+ * @param sessionFile
+ * @param alignPanel
+ * @param pdbArray
+ * @param seqsArray
+ * @param colourByPymol
+ * @param colourBySequence
+ * @param newViewId
+ */
+ public PymolViewer(String sessionFile, AlignmentPanel alignPanel,
+ PDBEntry[] pdbArray, SequenceI[][] seqsArray,
+ boolean colourByPymol, boolean colourBySequence, String newViewId)
+ {
+ // TODO convert to base/factory class method
+ this();
+ setViewId(newViewId);
+ this.pymolSessionFile = sessionFile;
+ openNewPymol(alignPanel, pdbArray, seqsArray);
+ if (colourByPymol)
+ {
+ binding.setColourBySequence(false);
+ seqColour.setSelected(false);
+ viewerColour.setSelected(true);
+ }
+ else if (colourBySequence)
+ {
+ binding.setColourBySequence(true);
+ seqColour.setSelected(true);
+ viewerColour.setSelected(false);
+ }
+ }
+
private void openNewPymol(AlignmentPanel ap, PDBEntry[] pe,
SequenceI[][] seqs)
{
}
@Override
- public String getStateInfo()
- {
- return null;
- }
-
- @Override
public ViewerType getViewerType()
{
return ViewerType.PYMOL;
*/
package jalview.gui;
-import jalview.api.AlignmentViewPanel;
-import jalview.bin.Cache;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.PDBEntry;
-import jalview.datamodel.SequenceI;
-import jalview.gui.StructureViewer.ViewerType;
-import jalview.gui.ViewSelectionMenu.ViewSetProvider;
-import jalview.io.DataSourceType;
-import jalview.io.JalviewFileChooser;
-import jalview.io.JalviewFileView;
-import jalview.jbgui.GStructureViewer;
-import jalview.schemes.ColourSchemeI;
-import jalview.schemes.ColourSchemes;
-import jalview.structure.StructureMapping;
-import jalview.structures.models.AAStructureBindingModel;
-import jalview.util.MessageManager;
-import jalview.ws.dbsources.Pdb;
-
import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import javax.swing.event.MenuEvent;
import javax.swing.event.MenuListener;
+import jalview.api.AlignmentViewPanel;
+import jalview.bin.Cache;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
+import jalview.datamodel.SequenceI;
+import jalview.gui.StructureViewer.ViewerType;
+import jalview.gui.ViewSelectionMenu.ViewSetProvider;
+import jalview.io.DataSourceType;
+import jalview.io.JalviewFileChooser;
+import jalview.io.JalviewFileView;
+import jalview.jbgui.GStructureViewer;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemes;
+import jalview.structure.StructureMapping;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.ws.dbsources.Pdb;
+
/**
* Base class with common functionality for JMol, Chimera or other structure
* viewers.
this.viewId = viewId;
}
- public abstract String getStateInfo();
-
protected void buildActionMenu()
{
if (_alignwith == null)
return filePath;
}
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file, else returns null
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ // TODO: a wait loop to ensure the file is written fully before returning?
+ return getBinding() == null ? null : getBinding().saveSession();
+ }
+
}
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+import java.awt.Color;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStream;
+import java.io.InputStreamReader;
+import java.io.OutputStream;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.math.BigInteger;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.Enumeration;
+import java.util.GregorianCalendar;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.SwingUtilities;
+import javax.xml.bind.JAXBContext;
+import javax.xml.bind.JAXBElement;
+import javax.xml.bind.Marshaller;
+import javax.xml.datatype.DatatypeConfigurationException;
+import javax.xml.datatype.DatatypeFactory;
+import javax.xml.datatype.XMLGregorianCalendar;
+import javax.xml.stream.XMLInputFactory;
+import javax.xml.stream.XMLStreamReader;
+
import jalview.analysis.Conservation;
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.gui.OOMWarning;
import jalview.gui.PCAPanel;
import jalview.gui.PaintRefresher;
+import jalview.gui.PymolViewer;
import jalview.gui.SplitFrame;
import jalview.gui.StructureViewer;
import jalview.gui.StructureViewer.ViewerType;
import jalview.xml.binding.jalview.ThresholdType;
import jalview.xml.binding.jalview.VAMSAS;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.Rectangle;
-import java.io.BufferedReader;
-import java.io.DataInputStream;
-import java.io.DataOutputStream;
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.OutputStreamWriter;
-import java.io.PrintWriter;
-import java.lang.reflect.InvocationTargetException;
-import java.math.BigInteger;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.Enumeration;
-import java.util.GregorianCalendar;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Hashtable;
-import java.util.IdentityHashMap;
-import java.util.Iterator;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Set;
-import java.util.Vector;
-import java.util.jar.JarEntry;
-import java.util.jar.JarInputStream;
-import java.util.jar.JarOutputStream;
-
-import javax.swing.JInternalFrame;
-import javax.swing.SwingUtilities;
-import javax.xml.bind.JAXBContext;
-import javax.xml.bind.JAXBElement;
-import javax.xml.bind.Marshaller;
-import javax.xml.datatype.DatatypeConfigurationException;
-import javax.xml.datatype.DatatypeFactory;
-import javax.xml.datatype.XMLGregorianCalendar;
-import javax.xml.stream.XMLInputFactory;
-import javax.xml.stream.XMLStreamReader;
-
/**
* Write out the current jalview desktop state as a Jalview XML stream.
*
if (!storeDS && !viewIds.contains(viewId))
{
viewIds.add(viewId);
- try
+ File viewerState = viewFrame.saveSession();
+ if (viewerState != null)
{
- String viewerState = viewFrame.getStateInfo();
- writeJarEntry(jout, getViewerJarEntryName(viewId),
- viewerState.getBytes());
- } catch (IOException e)
+ copyFileToJar(jout, viewerState.getPath(),
+ getViewerJarEntryName(viewId));
+ }
+ else
{
- System.err.println(
- "Error saving viewer state: " + e.getMessage());
+ Cache.log.error("Failed to save viewer state for "
+ +
+ viewFrame.getViewerType().toString());
}
}
}
protected void copyFileToJar(JarOutputStream jout, String infilePath,
String jarEntryName)
{
- DataInputStream dis = null;
- try
+ try (InputStream is = new FileInputStream(infilePath))
{
File file = new File(infilePath);
if (file.exists() && jout != null)
{
- dis = new DataInputStream(new FileInputStream(file));
- byte[] data = new byte[(int) file.length()];
- dis.readFully(data);
- writeJarEntry(jout, jarEntryName, data);
+ System.out.println("Writing jar entry " + jarEntryName);
+ jout.putNextEntry(new JarEntry(jarEntryName));
+ copyAll(is, jout);
+ jout.closeEntry();
+ // dis = new DataInputStream(new FileInputStream(file));
+ // byte[] data = new byte[(int) file.length()];
+ // dis.readFully(data);
+ // writeJarEntry(jout, jarEntryName, data);
}
} catch (Exception ex)
{
ex.printStackTrace();
- } finally
- {
- if (dis != null)
- {
- try
- {
- dis.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
}
}
}
/**
+ * Copies input to output, in 4K buffers; handles any data (text or binary)
+ *
+ * @param in
+ * @param out
+ * @throws IOException
+ */
+ protected void copyAll(InputStream in, OutputStream out)
+ throws IOException
+ {
+ byte[] buffer = new byte[4096];
+ int bytesRead = 0;
+ while ((bytesRead = in.read(buffer)) != -1)
+ {
+ out.write(buffer, 0, bytesRead);
+ }
+ }
+
+ /**
* Save the state of a structure viewer
*
* @param ap
protected String copyJarEntry(jarInputStreamProvider jprovider,
String jarEntryName, String prefix, String suffixModel)
{
- BufferedReader in = null;
- PrintWriter out = null;
String suffix = ".tmp";
if (suffixModel == null)
{
{
suffix = "." + suffixModel.substring(sfpos + 1);
}
- try
- {
- JarInputStream jin = jprovider.getJarInputStream();
- /*
- * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
- * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
- * FileInputStream(jprovider)); }
- */
+ try (JarInputStream jin = jprovider.getJarInputStream())
+ {
JarEntry entry = null;
do
{
entry = jin.getNextJarEntry();
} while (entry != null && !entry.getName().equals(jarEntryName));
+
if (entry != null)
{
- in = new BufferedReader(new InputStreamReader(jin, UTF_8));
+ // in = new BufferedReader(new InputStreamReader(jin, UTF_8));
File outFile = File.createTempFile(prefix, suffix);
outFile.deleteOnExit();
- out = new PrintWriter(new FileOutputStream(outFile));
- String data;
-
- while ((data = in.readLine()) != null)
+ try (OutputStream os = new FileOutputStream(outFile))
{
- out.println(data);
+ copyAll(jin, os);
}
- out.flush();
String t = outFile.getAbsolutePath();
return t;
}
} catch (Exception ex)
{
ex.printStackTrace();
- } finally
- {
- if (in != null)
- {
- try
- {
- in.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
- if (out != null)
- {
- out.close();
- }
}
return null;
* From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
* "viewer_"+stateData.viewId
*/
- if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
+ String viewerType = stateData.getType();
+ if (ViewerType.CHIMERA.toString().equals(viewerType))
{
createChimeraViewer(viewerData, af, jprovider);
}
+ if (ViewerType.PYMOL.toString().equals(viewerType))
+ {
+ createPymolViewer(viewerData, af, jprovider);
+ }
else
{
/*
}
/**
+ * Create a new PyMol viewer
+ *
+ * @param data
+ * @param af
+ * @param jprovider
+ */
+ protected void createPymolViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ jarInputStreamProvider jprovider)
+ {
+ StructureViewerModel data = viewerData.getValue();
+ String pymolSessionFile = data.getStateData();
+
+ /*
+ * Copy PyMol session from jar entry "viewer_"+viewId to a temporary file
+ *
+ * NB this is the 'saved' viewId as in the project file XML, _not_ the
+ * 'uniquified' sviewid used to reconstruct the viewer here
+ */
+ String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
+ pymolSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
+ "pymol", ".pse");
+
+ Set<Entry<File, StructureData>> fileData = data.getFileData()
+ .entrySet();
+ List<PDBEntry> pdbs = new ArrayList<>();
+ List<SequenceI[]> allseqs = new ArrayList<>();
+ for (Entry<File, StructureData> pdb : fileData)
+ {
+ String filePath = pdb.getValue().getFilePath();
+ String pdbId = pdb.getValue().getPdbId();
+ // pdbs.add(new PDBEntry(filePath, pdbId));
+ pdbs.add(new PDBEntry(pdbId, null, PDBEntry.Type.PDB, filePath));
+ final List<SequenceI> seqList = pdb.getValue().getSeqList();
+ SequenceI[] seqs = seqList.toArray(new SequenceI[seqList.size()]);
+ allseqs.add(seqs);
+ }
+
+ boolean colourByPymol = data.isColourByViewer();
+ boolean colourBySequence = data.isColourWithAlignPanel();
+
+ // TODO use StructureViewer as a factory here, see JAL-1761
+ final PDBEntry[] pdbArray = pdbs.toArray(new PDBEntry[pdbs.size()]);
+ final SequenceI[][] seqsArray = allseqs
+ .toArray(new SequenceI[allseqs.size()][]);
+ String newViewId = viewerData.getKey();
+
+ PymolViewer pv = new PymolViewer(pymolSessionFile,
+ af.alignPanel, pdbArray, seqsArray, colourByPymol,
+ colourBySequence, newViewId);
+ pv.setSize(data.getWidth(), data.getHeight());
+ pv.setLocation(data.getX(), data.getY());
+ }
+
+ /**
* Populates an XML model of the feature colour scheme for one feature type
*
* @param featureType
*/
package jalview.structures.models;
+import java.awt.Color;
+import java.io.File;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.BitSet;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.List;
+import java.util.Map;
+
+import javax.swing.SwingUtilities;
+
import jalview.api.AlignViewportI;
import jalview.api.AlignmentViewPanel;
import jalview.api.FeatureRenderer;
import jalview.api.SequenceRenderer;
import jalview.api.StructureSelectionManagerProvider;
import jalview.api.structures.JalviewStructureDisplayI;
+import jalview.bin.Cache;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.HiddenColumns;
import jalview.datamodel.PDBEntry;
import jalview.util.Comparison;
import jalview.util.MessageManager;
-import java.awt.Color;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.BitSet;
-import java.util.HashMap;
-import java.util.LinkedHashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.SwingUtilities;
-
/**
*
* A base class to hold common function for protein structure model binding.
atomSpec.addRange(model, startPos, endPos, chain);
}
+
+ /**
+ * Returns the file extension (including '.' separator) to use for a saved
+ * viewer session file. Default is to return null (not supported), override as
+ * required.
+ *
+ * @return
+ */
+ public String getSessionFileExtension()
+ {
+ return null;
+ }
+
+ /**
+ * If supported, saves the state of the structure viewer to a temporary file
+ * and returns the file. Returns null and logs an error on any failure.
+ *
+ * @return
+ */
+ public File saveSession()
+ {
+ String prefix = getViewerType().toString();
+ String suffix = getSessionFileExtension();
+ File f = null;
+ try
+ {
+ f = File.createTempFile(prefix, suffix);
+ saveSession(f);
+ } catch (IOException e)
+ {
+ Cache.log.error(String.format("Error saving %s session: %s",
+ prefix, e.toString()));
+ }
+
+ return f;
+ }
+
+ /**
+ * Saves the structure viewer session to the given file
+ *
+ * @param f
+ */
+ protected void saveSession(File f)
+ {
+ StructureCommandI cmd = commandGenerator
+ .saveSession(f.getPath());
+ if (cmd != null)
+ {
+ executeCommand(cmd, false);
+ }
+ }
}
git://source.jalview.org / jalview.git / commitdiff