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.ByteArrayInputStream;
+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.datamodel.features.FeatureMatcherI;
import jalview.datamodel.features.FeatureMatcherSet;
import jalview.datamodel.features.FeatureMatcherSetI;
+import jalview.ext.rbvi.chimera.JalviewChimeraBinding;
import jalview.ext.varna.RnaModel;
import jalview.gui.AlignFrame;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.AppVarna;
import jalview.gui.ChimeraViewFrame;
+import jalview.gui.ChimeraXViewFrame;
import jalview.gui.Desktop;
+import jalview.gui.JalviewChimeraXBindingModel;
import jalview.gui.JvOptionPane;
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.ByteArrayInputStream;
-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
final String viewId = viewFrame.getViewId();
state.setViewId(viewId);
state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
- state.setColourwithAlignPanel(viewFrame.isUsedforcolourby(ap));
+ state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
state.setColourByJmol(viewFrame.isColouredByViewer());
state.setType(viewFrame.getViewerType().toString());
// pdb.addStructureState(state);
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 type = stateData.getType();
+ if (type == null)
{
- createChimeraViewer(viewerData, af, jprovider);
+ type = ViewerType.JMOL.toString();
}
- else
+ try
{
- /*
- * else Jmol (if pre-2.9, stateData contains JMOL state string)
- */
- createJmolViewer(viewerData, af, jprovider);
+ ViewerType viewerType = ViewerType.valueOf(type);
+ switch (viewerType)
+ {
+ case CHIMERA:
+ createChimeraViewer(viewerData, af, jprovider, false);
+ break;
+ case CHIMERAX:
+ createChimeraViewer(viewerData, af, jprovider, true);
+ break;
+ case PYMOL:
+ createPymolViewer(viewerData, af, jprovider);
+ break;
+ case JMOL:
+ createJmolViewer(viewerData, af, jprovider);
+ }
+ } catch (IllegalArgumentException | NullPointerException e)
+ {
+ Cache.log.error(
+ "Invalid structure viewer type: " + type);
}
}
/**
- * Create a new Chimera viewer.
+ * Create a new Chimera or ChimeraX viewer
*
* @param data
* @param af
* @param jprovider
+ * @param isChimeraX
*/
protected void createChimeraViewer(
Entry<String, StructureViewerModel> viewerData, AlignFrame af,
- jarInputStreamProvider jprovider)
+ jarInputStreamProvider jprovider, boolean isChimeraX)
{
StructureViewerModel data = viewerData.getValue();
String chimeraSessionFile = data.getStateData();
* 'uniquified' sviewid used to reconstruct the viewer here
*/
String viewerJarEntryName = getViewerJarEntryName(data.getViewId());
+ String extension = isChimeraX
+ ? JalviewChimeraXBindingModel.CHIMERAX_SESSION_EXTENSION
+ : JalviewChimeraBinding.CHIMERA_SESSION_EXTENSION;
chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera", ".py");
+ "chimera", extension);
Set<Entry<File, StructureData>> fileData = data.getFileData()
.entrySet();
.toArray(new SequenceI[allseqs.size()][]);
String newViewId = viewerData.getKey();
- ChimeraViewFrame cvf = new ChimeraViewFrame(chimeraSessionFile,
- af.alignPanel, pdbArray, seqsArray, colourByChimera,
- colourBySequence, newViewId);
+ ChimeraViewFrame cvf = isChimeraX
+ ? new ChimeraXViewFrame(chimeraSessionFile, af.alignPanel,
+ pdbArray, seqsArray, colourByChimera, colourBySequence,
+ newViewId)
+ : new ChimeraViewFrame(chimeraSessionFile, af.alignPanel,
+ pdbArray, seqsArray, colourByChimera, colourBySequence,
+ newViewId);
cvf.setSize(data.getWidth(), data.getHeight());
cvf.setLocation(data.getX(), data.getY());
}
}
/**
+ * 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
git://source.jalview.org / jalview.git / blobdiff