import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+import java.awt.Color;
+import java.awt.Dimension;
+import java.awt.Font;
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.ByteArrayInputStream;
+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.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLocus;
import jalview.datamodel.GraphLine;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.Point;
import jalview.gui.AlignViewport;
import jalview.gui.AlignmentPanel;
import jalview.gui.AppVarna;
-import jalview.gui.ChimeraViewFrame;
import jalview.gui.Desktop;
-import jalview.gui.FeatureRenderer;
import jalview.gui.JvOptionPane;
import jalview.gui.OOMWarning;
+import jalview.gui.OverviewPanel;
import jalview.gui.PCAPanel;
import jalview.gui.PaintRefresher;
import jalview.gui.SplitFrame;
import jalview.gui.StructureViewer.ViewerType;
import jalview.gui.StructureViewerBase;
import jalview.gui.TreePanel;
+import jalview.io.BackupFiles;
import jalview.io.DataSourceType;
import jalview.io.FileFormat;
import jalview.io.NewickFile;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.PCAModel;
import jalview.viewmodel.ViewportRanges;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import jalview.viewmodel.seqfeatures.FeaturesDisplayed;
import jalview.ws.jws2.Jws2Discoverer;
import jalview.xml.binding.jalview.JalviewModel.Viewport;
import jalview.xml.binding.jalview.JalviewModel.Viewport.CalcIdParam;
import jalview.xml.binding.jalview.JalviewModel.Viewport.HiddenColumns;
+import jalview.xml.binding.jalview.JalviewModel.Viewport.Overview;
import jalview.xml.binding.jalview.JalviewUserColours;
import jalview.xml.binding.jalview.JalviewUserColours.Colour;
import jalview.xml.binding.jalview.MapListType.MapListFrom;
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.
*
*/
public class Jalview2XML
{
+
+ // BH 2018 we add the .jvp binary extension to J2S so that
+ // it will declare that binary when we do the file save from the browser
+
+ static
+ {
+ Platform.addJ2SBinaryType(".jvp?");
+ }
+
private static final String VIEWER_PREFIX = "viewer_";
private static final String RNA_PREFIX = "rna_";
public boolean isResolvable()
{
return super.isResolvable() && mp.getTo() != null;
- };
+ }
@Override
boolean resolve()
public void saveState(File statefile)
{
FileOutputStream fos = null;
+
try
{
+
fos = new FileOutputStream(statefile);
+
JarOutputStream jout = new JarOutputStream(fos);
saveState(jout);
+ fos.close();
} catch (Exception e)
{
+ Cache.log.error("Couln't write Jalview state to " + statefile, e);
// TODO: inform user of the problem - they need to know if their data was
// not saved !
if (errorMessage == null)
{
- errorMessage = "Couldn't write Jalview Archive to output file '"
+ errorMessage = "Did't write Jalview Archive to output file '"
+ statefile + "' - See console error log for details";
}
else
{
- errorMessage += "(output file was '" + statefile + "')";
+ errorMessage += "(Didn't write Jalview Archive to output file '"
+ + statefile + ")";
}
e.printStackTrace();
} finally
} catch (Exception foo)
{
}
- ;
jout.close();
} catch (Exception ex)
{
{
try
{
- FileOutputStream fos = new FileOutputStream(jarFile);
+ // create backupfiles object and get new temp filename destination
+ boolean doBackup = BackupFiles.getEnabled();
+ BackupFiles backupfiles = doBackup ? new BackupFiles(jarFile) : null;
+ FileOutputStream fos = new FileOutputStream(doBackup ?
+ backupfiles.getTempFilePath() : jarFile);
+
JarOutputStream jout = new JarOutputStream(fos);
List<AlignFrame> frames = new ArrayList<>();
} catch (Exception foo)
{
}
- ;
jout.close();
- return true;
+ boolean success = true;
+
+ if (doBackup)
+ {
+ backupfiles.setWriteSuccess(success);
+ success = backupfiles.rollBackupsAndRenameTempFile();
+ }
+
+ return success;
} catch (Exception ex)
{
errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
if (frames[f] instanceof StructureViewerBase)
{
StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- matchedFile = saveStructureState(ap, jds, pdb, entry, viewIds,
+ matchedFile = saveStructureViewer(ap, jds, pdb, entry, viewIds,
matchedFile, viewFrame);
/*
* Only store each structure viewer's state once in the project
* jar. First time through only (storeDS==false)
*/
String viewId = viewFrame.getViewId();
+ String viewerType = viewFrame.getViewerType().toString();
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), viewerType);
+ }
+ else
{
- System.err.println(
- "Error saving viewer state: " + e.getMessage());
+ Cache.log.error("Failed to save viewer state for "
+ +
+ viewerType);
}
}
}
if (!pdbfiles.contains(pdbId))
{
pdbfiles.add(pdbId);
- copyFileToJar(jout, matchedFile, pdbId);
+ copyFileToJar(jout, matchedFile, pdbId, pdbId);
}
}
view.setStartRes(vpRanges.getStartRes());
view.setStartSeq(vpRanges.getStartSeq());
+ OverviewPanel ov = ap.getOverviewPanel();
+ if (ov != null)
+ {
+ Overview overview = new Overview();
+ Rectangle bounds = ov.getBounds();
+ overview.setXpos(bounds.x);
+ overview.setYpos(bounds.y);
+ overview.setWidth(bounds.width);
+ overview.setHeight(bounds.height);
+ overview.setShowHidden(ov.isShowHiddenRegions());
+ overview.setGapColour(ov.getCanvas().getGapColour().getRGB());
+ overview.setResidueColour(ov.getCanvas().getResidueColour().getRGB());
+ overview.setHiddenColour(ov.getCanvas().getHiddenColour().getRGB());
+ String title = ((JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, ov)).getTitle();
+ overview.setTitle(title);
+ view.setOverview(overview);
+ }
if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
view.setFollowHighlight(av.isFollowHighlight());
view.setFollowSelection(av.followSelection);
view.setIgnoreGapsinConsensus(av.isIgnoreGapsConsensus());
+ view.setShowComplementFeatures(av.isShowComplementFeatures());
+ view.setShowComplementFeaturesOnTop(
+ av.isShowComplementFeaturesOnTop());
if (av.getFeaturesDisplayed() != null)
{
FeatureSettings fs = new FeatureSettings();
- FeatureRenderer fr = ap.getSeqPanel().seqCanvas
+ FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
.getFeatureRenderer();
String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
// using save and then load
try
{
+ fileName = fileName.replace('\\', '/');
System.out.println("Writing jar entry " + fileName);
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
String varnaStateFile = varna.getStateInfo(model.rna);
jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
- copyFileToJar(jout, varnaStateFile, jarEntryName);
+ copyFileToJar(jout, varnaStateFile, jarEntryName, "Varna");
rnaSessions.put(model, jarEntryName);
}
SecondaryStructure ss = new SecondaryStructure();
* @param jout
* @param infilePath
* @param jarEntryName
+ * @param msg
+ * additional identifying info to log to the console
*/
protected void copyFileToJar(JarOutputStream jout, String infilePath,
- String jarEntryName)
+ String jarEntryName, String msg)
{
- 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 + " (" + msg + ")");
+ 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
- }
- }
}
}
/**
- * Write the data to a new entry of given name in the output jar file
+ * Copies input to output, in 4K buffers; handles any data (text or binary)
*
- * @param jout
- * @param jarEntryName
- * @param data
+ * @param in
+ * @param out
* @throws IOException
*/
- protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
- byte[] data) throws IOException
+ protected void copyAll(InputStream in, OutputStream out)
+ throws IOException
{
- if (jout != null)
+ byte[] buffer = new byte[4096];
+ int bytesRead = 0;
+ while ((bytesRead = in.read(buffer)) != -1)
{
- System.out.println("Writing jar entry " + jarEntryName);
- jout.putNextEntry(new JarEntry(jarEntryName));
- DataOutputStream dout = new DataOutputStream(jout);
- dout.write(data, 0, data.length);
- dout.flush();
- jout.closeEntry();
+ out.write(buffer, 0, bytesRead);
}
}
* @param viewFrame
* @return
*/
- protected String saveStructureState(AlignmentPanel ap, SequenceI jds,
+ protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
Pdbids pdb, PDBEntry entry, List<String> viewIds,
String matchedFile, StructureViewerBase viewFrame)
{
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);
vamsasSeq.setName(jds.getName());
vamsasSeq.setSequence(jds.getSequenceAsString());
vamsasSeq.setDescription(jds.getDescription());
- jalview.datamodel.DBRefEntry[] dbrefs = null;
+ List<DBRefEntry> dbrefs = null;
if (jds.getDatasetSequence() != null)
{
vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
parentseq = jds;
}
}
+
+ /*
+ * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+ */
if (dbrefs != null)
{
- for (int d = 0; d < dbrefs.length; d++)
+ for (int d = 0, nd = dbrefs.size(); d < nd; d++)
{
DBRef dbref = new DBRef();
- dbref.setSource(dbrefs[d].getSource());
- dbref.setVersion(dbrefs[d].getVersion());
- dbref.setAccessionId(dbrefs[d].getAccessionId());
- if (dbrefs[d].hasMap())
+ DBRefEntry ref = dbrefs.get(d);
+ dbref.setSource(ref.getSource());
+ dbref.setVersion(ref.getVersion());
+ dbref.setAccessionId(ref.getAccessionId());
+ if (ref instanceof GeneLocus)
{
- Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ dbref.setLocus(true);
+ }
+ if (ref.hasMap())
+ {
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
jds, recurse);
dbref.setMapping(mp);
}
- // vamsasSeq.addDBRef(dbref);
vamsasSeq.getDBRef().add(dbref);
}
}
* @param file
* - HTTP URL or filename
*/
- public AlignFrame loadJalviewAlign(final String file)
+ public AlignFrame loadJalviewAlign(final Object file)
{
jalview.gui.AlignFrame af = null;
public void run()
{
setLoadingFinishedForNewStructureViewers();
- };
+ }
});
} catch (Exception x)
{
return af;
}
- private jarInputStreamProvider createjarInputStreamProvider(
- final String file) throws MalformedURLException
- {
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (file.startsWith("http://"))
- {
- url = new URL(file);
- }
- final URL _url = url;
- return new jarInputStreamProvider()
- {
-
- @Override
- public JarInputStream getJarInputStream() throws IOException
- {
- if (_url != null)
- {
- return new JarInputStream(_url.openStream());
- }
- else
- {
- return new JarInputStream(new FileInputStream(file));
- }
- }
-
- @Override
- public String getFilename()
- {
- return file;
- }
- };
- }
+ @SuppressWarnings("unused")
+ private jarInputStreamProvider createjarInputStreamProvider(final Object ofile) throws MalformedURLException {
+
+ // BH 2018 allow for bytes already attached to File object
+ try {
+ String file = (ofile instanceof File ? ((File) ofile).getCanonicalPath() : ofile.toString());
+ byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
+ : null;
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (file.startsWith("http://")) {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider() {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException {
+ if (bytes != null) {
+// System.out.println("Jalview2XML: opening byte jarInputStream for bytes.length=" + bytes.length);
+ return new JarInputStream(new ByteArrayInputStream(bytes));
+ }
+ if (_url != null) {
+// System.out.println("Jalview2XML: opening url jarInputStream for " + _url);
+ return new JarInputStream(_url.openStream());
+ } else {
+// System.out.println("Jalview2XML: opening file jarInputStream for " + file);
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ @Override
+ public String getFilename() {
+ return file;
+ }
+ };
+ } catch (IOException e) {
+ e.printStackTrace();
+ return null;
+ }
+ }
/**
* Recover jalview session from a jalview project archive. Caller may
if (jarentry != null && jarentry.getName().endsWith(".xml"))
{
- InputStreamReader in = new InputStreamReader(jin, UTF_8);
- // JalviewModel object = new JalviewModel();
-
JAXBContext jc = JAXBContext
.newInstance("jalview.xml.binding.jalview");
XMLStreamReader streamReader = XMLInputFactory.newInstance()
.unmarshal(streamReader, JalviewModel.class);
JalviewModel object = jbe.getValue();
- /*
- Unmarshaller unmar = new Unmarshaller(object);
- unmar.setValidation(false);
- object = (JalviewModel) unmar.unmarshal(in);
- */
if (true) // !skipViewport(object))
{
_af = loadFromObject(object, file, true, jprovider);
* @param prefix
* a prefix for the temporary file name, must be at least three
* characters long
- * @param origFile
+ * @param suffixModel
* null or original file - so new file can be given the same suffix
* as the old one
* @return
*/
protected String copyJarEntry(jarInputStreamProvider jprovider,
- String jarEntryName, String prefix, String origFile)
+ String jarEntryName, String prefix, String suffixModel)
{
- BufferedReader in = null;
- PrintWriter out = null;
String suffix = ".tmp";
- if (origFile == null)
+ if (suffixModel == null)
{
- origFile = jarEntryName;
+ suffixModel = jarEntryName;
}
- int sfpos = origFile.lastIndexOf(".");
- if (sfpos > -1 && sfpos < (origFile.length() - 3))
+ int sfpos = suffixModel.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
{
- suffix = "." + origFile.substring(sfpos + 1);
+ 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;
|| tmpSeq.getEnd() != jseq.getEnd())
{
System.err.println(
- "Warning JAL-2154 regression: updating start/end for sequence "
- + tmpSeq.toString() + " to " + jseq);
+ String.format("Warning JAL-2154 regression: updating start/end for sequence %s from %d/%d to %d/%d",
+ tmpSeq.getName(), tmpSeq.getStart(),
+ tmpSeq.getEnd(), jseq.getStart(),
+ jseq.getEnd()));
}
}
else
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al,
+ cs = ColourSchemeProperty.getColourScheme(null, al,
jGroup.getColour());
}
}
}
/*
- * Load any trees, PDB structures and viewers
+ * Load any trees, PDB structures and viewers, Overview
*
* Not done if flag is false (when this method is used for New View)
*/
loadPCAViewers(jalviewModel, ap);
loadPDBStructures(jprovider, jseqs, af, ap);
loadRnaViewers(jprovider, jseqs, ap);
+ loadOverview(view, af);
}
// and finally return.
return af;
}
/**
+ * Load Overview window, restoring colours, 'show hidden regions' flag, title
+ * and geometry as saved
+ *
+ * @param view
+ * @param af
+ */
+ protected void loadOverview(Viewport view, AlignFrame af)
+ {
+ Overview overview = view.getOverview();
+ if (overview != null)
+ {
+ OverviewPanel overviewPanel = af
+ .openOverviewPanel(overview.isShowHidden());
+ overviewPanel.setBounds(overview.getXpos(), overview.getYpos(),
+ overview.getWidth(), overview.getHeight());
+ overviewPanel.setPreferredSize(
+ new Dimension(overview.getWidth(), overview.getHeight()));
+ Color gap = new Color(overview.getGapColour());
+ Color residue = new Color(overview.getResidueColour());
+ Color hidden = new Color(overview.getHiddenColour());
+ overviewPanel.getCanvas().setColours(gap, residue, hidden);
+ ((JInternalFrame) SwingUtilities
+ .getAncestorOfClass(JInternalFrame.class, overviewPanel))
+ .setTitle(overview.getTitle());
+ }
+ }
+
+ /**
* Instantiate and link any saved RNA (Varna) viewers. The state of the Varna
* panel is restored from separate jar entries, two (gapped and trimmed) per
* sequence and secondary structure.
// TODO: verify 'associate with all views' works still
tp.getTreeCanvas().setViewport(av); // af.viewport;
tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
- // FIXME: should we use safeBoolean here ?
- tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
}
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
if (tp == null)
{
warn("There was a problem recovering stored Newick tree: \n"
}
if (!structureViewers.containsKey(sviewid))
{
+ String viewerType = structureState.getType();
+ if (viewerType == null) // pre Jalview 2.9
+ {
+ viewerType = ViewerType.JMOL.toString();
+ }
structureViewers.put(sviewid,
new StructureViewerModel(x, y, width, height, false,
false, true, structureState.getViewId(),
- structureState.getType()));
+ viewerType));
// Legacy pre-2.7 conversion JAL-823 :
// do not assume any view has to be linked for colour by
// sequence
return;
}
- /*
- * From 2.9: stateData.type contains JMOL or CHIMERA, data is in jar entry
- * "viewer_"+stateData.viewId
- */
- if (ViewerType.CHIMERA.toString().equals(stateData.getType()))
- {
- createChimeraViewer(viewerData, af, jprovider);
- }
- else
- {
- /*
- * else Jmol (if pre-2.9, stateData contains JMOL state string)
- */
- createJmolViewer(viewerData, af, jprovider);
- }
- }
-
- /**
- * Create a new Chimera viewer.
- *
- * @param data
- * @param af
- * @param jprovider
- */
- protected void createChimeraViewer(
- Entry<String, StructureViewerModel> viewerData, AlignFrame af,
- jarInputStreamProvider jprovider)
- {
- StructureViewerModel data = viewerData.getValue();
- String chimeraSessionFile = data.getStateData();
-
- /*
- * Copy Chimera 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());
- chimeraSessionFile = copyJarEntry(jprovider, viewerJarEntryName,
- "chimera", null);
-
- 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 colourByChimera = 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();
-
- ChimeraViewFrame cvf = 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 Jmol window. First parse the Jmol state to translate filenames
- * loaded into the view, and record the order in which files are shown in the
- * Jmol view, so we can add the sequence mappings in same order.
- *
- * @param viewerData
- * @param af
- * @param jprovider
- */
- protected void createJmolViewer(
- final Entry<String, StructureViewerModel> viewerData,
- AlignFrame af, jarInputStreamProvider jprovider)
- {
- final StructureViewerModel svattrib = viewerData.getValue();
- String state = svattrib.getStateData();
-
- /*
- * Pre-2.9: state element value is the Jmol state string
- *
- * 2.9+: @type is "JMOL", state data is in a Jar file member named "viewer_"
- * + viewId
- */
- if (ViewerType.JMOL.toString().equals(svattrib.getType()))
- {
- state = readJarEntry(jprovider,
- getViewerJarEntryName(svattrib.getViewId()));
- }
-
- List<String> pdbfilenames = new ArrayList<>();
- List<SequenceI[]> seqmaps = new ArrayList<>();
- List<String> pdbids = new ArrayList<>();
- StringBuilder newFileLoc = new StringBuilder(64);
- int cp = 0, ncp, ecp;
- Map<File, StructureData> oldFiles = svattrib.getFileData();
- while ((ncp = state.indexOf("load ", cp)) > -1)
- {
- do
- {
- // look for next filename in load statement
- newFileLoc.append(state.substring(cp,
- ncp = (state.indexOf("\"", ncp + 1) + 1)));
- String oldfilenam = state.substring(ncp,
- ecp = state.indexOf("\"", ncp));
- // recover the new mapping data for this old filename
- // have to normalize filename - since Jmol and jalview do
- // filename
- // translation differently.
- StructureData filedat = oldFiles.get(new File(oldfilenam));
- if (filedat == null)
- {
- String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
- filedat = oldFiles.get(new File(reformatedOldFilename));
- }
- newFileLoc.append(Platform.escapeString(filedat.getFilePath()));
- pdbfilenames.add(filedat.getFilePath());
- pdbids.add(filedat.getPdbId());
- seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
- newFileLoc.append("\"");
- cp = ecp + 1; // advance beyond last \" and set cursor so we can
- // look for next file statement.
- } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
- }
- if (cp > 0)
- {
- // just append rest of state
- newFileLoc.append(state.substring(cp));
- }
- else
- {
- System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
- newFileLoc = new StringBuilder(state);
- newFileLoc.append("; load append ");
- for (File id : oldFiles.keySet())
- {
- // add this and any other pdb files that should be present in
- // the viewer
- StructureData filedat = oldFiles.get(id);
- newFileLoc.append(filedat.getFilePath());
- pdbfilenames.add(filedat.getFilePath());
- pdbids.add(filedat.getPdbId());
- seqmaps.add(filedat.getSeqList().toArray(new SequenceI[0]));
- newFileLoc.append(" \"");
- newFileLoc.append(filedat.getFilePath());
- newFileLoc.append("\"");
-
- }
- newFileLoc.append(";");
- }
-
- if (newFileLoc.length() == 0)
- {
- return;
- }
- int histbug = newFileLoc.indexOf("history = ");
- if (histbug > -1)
- {
- /*
- * change "history = [true|false];" to "history = [1|0];"
- */
- histbug += 10;
- int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";", histbug);
- String val = (diff == -1) ? null
- : newFileLoc.substring(histbug, diff);
- if (val != null && val.length() >= 4)
- {
- if (val.contains("e")) // eh? what can it be?
- {
- if (val.trim().equals("true"))
- {
- val = "1";
- }
- else
- {
- val = "0";
- }
- newFileLoc.replace(histbug, diff, val);
- }
- }
- }
-
- final String[] pdbf = pdbfilenames
- .toArray(new String[pdbfilenames.size()]);
- final String[] id = pdbids.toArray(new String[pdbids.size()]);
- final SequenceI[][] sq = seqmaps
- .toArray(new SequenceI[seqmaps.size()][]);
- final String fileloc = newFileLoc.toString();
- final String sviewid = viewerData.getKey();
- final AlignFrame alf = af;
- final Rectangle rect = new Rectangle(svattrib.getX(), svattrib.getY(),
- svattrib.getWidth(), svattrib.getHeight());
+ String type = stateData.getType();
try
{
- javax.swing.SwingUtilities.invokeAndWait(new Runnable()
- {
- @Override
- public void run()
- {
- JalviewStructureDisplayI sview = null;
- try
- {
- sview = new StructureViewer(
- alf.alignPanel.getStructureSelectionManager())
- .createView(StructureViewer.ViewerType.JMOL,
- pdbf, id, sq, alf.alignPanel, svattrib,
- fileloc, rect, sviewid);
- addNewStructureViewer(sview);
- } catch (OutOfMemoryError ex)
- {
- new OOMWarning("restoring structure view for PDB id " + id,
- (OutOfMemoryError) ex.getCause());
- if (sview != null && sview.isVisible())
- {
- sview.closeViewer(false);
- sview.setVisible(false);
- sview.dispose();
- }
- }
- }
- });
- } catch (InvocationTargetException ex)
+ ViewerType viewerType = ViewerType.valueOf(type);
+ createStructureViewer(viewerType, viewerData, af, jprovider);
+ } catch (IllegalArgumentException | NullPointerException e)
{
- warn("Unexpected error when opening Jmol view.", ex);
-
- } catch (InterruptedException e)
- {
- // e.printStackTrace();
+ // TODO JAL-3619 show error dialog / offer an alternative viewer
+ Cache.log.error(
+ "Invalid structure viewer type: " + type);
}
-
}
/**
{
AlignFrame af = null;
af = new AlignFrame(al, safeInt(view.getWidth()),
- safeInt(view.getHeight()), uniqueSeqSetId, viewId);
+ safeInt(view.getHeight()), uniqueSeqSetId, viewId)
+// {
+//
+// @Override
+// protected void processKeyEvent(java.awt.event.KeyEvent e) {
+// System.out.println("Jalview2XML AF " + e);
+// super.processKeyEvent(e);
+//
+// }
+//
+// }
+ ;
af.setFileName(file, FileFormat.Jalview);
}
else
{
- cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
+ cs = ColourSchemeProperty.getColourScheme(af.getViewport(), al,
+ view.getBgColour());
}
}
+ /*
+ * turn off 'alignment colour applies to all groups'
+ * while restoring global colour scheme
+ */
+ viewport.setColourAppliesToAllGroups(false);
viewport.setGlobalColourScheme(cs);
viewport.getResidueShading().setThreshold(pidThreshold,
view.isIgnoreGapsinConsensus());
viewport.getResidueShading()
.setConsensus(viewport.getSequenceConsensusHash());
- viewport.setColourAppliesToAllGroups(false);
-
if (safeBoolean(view.isConservationSelected()) && cs != null)
{
viewport.getResidueShading()
.setConservationInc(safeInt(view.getConsThreshold()));
}
-
af.changeColour(cs);
-
viewport.setColourAppliesToAllGroups(true);
viewport
viewport.setShowNPFeats(safeBoolean(view.isShowNPfeatureTooltip()));
viewport.setShowGroupConsensus(view.isShowGroupConsensus());
viewport.setShowGroupConservation(view.isShowGroupConservation());
+ viewport.setShowComplementFeatures(view.isShowComplementFeatures());
+ viewport.setShowComplementFeaturesOnTop(
+ view.isShowComplementFeaturesOnTop());
// recover feature settings
if (jm.getFeatureSettings() != null)
{
- FeatureRenderer fr = af.alignPanel.getSeqPanel().seqCanvas
+ FeatureRendererModel fr = af.alignPanel.getSeqPanel().seqCanvas
.getFeatureRenderer();
FeaturesDisplayed fdi;
viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed());
float min = safeFloat(safeFloat(setting.getMin()));
float max = setting.getMax() == null ? 1f
: setting.getMax().floatValue();
- FeatureColourI gc = new FeatureColour(minColour, maxColour,
+ FeatureColourI gc = new FeatureColour(maxColour, minColour,
+ maxColour,
noValueColour, min, max);
if (setting.getAttributeName().size() > 0)
{
}
else
{
- featureOrder.put(featureType, new Float(
+ featureOrder.put(featureType, Float.valueOf(
fs / jm.getFeatureSettings().getSetting().size()));
}
if (safeBoolean(setting.isDisplay()))
for (int gs = 0; gs < jm.getFeatureSettings().getGroup().size(); gs++)
{
Group grp = jm.getFeatureSettings().getGroup().get(gs);
- fgtable.put(grp.getName(), new Boolean(grp.isDisplay()));
+ fgtable.put(grp.getName(), Boolean.valueOf(grp.isDisplay()));
}
// FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
// fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ?
{
splitFrameCandidates.put(view, af);
}
+
return af;
}
else
{
cs = new AnnotationColourGradient(matchedAnnotation,
- ColourSchemeProperty.getColourScheme(al,
+ ColourSchemeProperty.getColourScheme(af.getViewport(), al,
viewAnnColour.getColourScheme()),
safeInt(viewAnnColour.getAboveThreshold()));
}
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
}
- Vector dseqs = null;
+ Vector<SequenceI> dseqs = null;
if (!ignoreUnrefed)
{
// recovering an alignment View
// try even harder to restore dataset
AlignmentI xtantDS = checkIfHasDataset(vamsasSet.getSequence());
// create a list of new dataset sequences
- dseqs = new Vector();
+ dseqs = new Vector<>();
}
for (int i = 0, iSize = vamsasSet.getSequence().size(); i < iSize; i++)
{
* vamsasSeq array ordering, to preserve ordering of dataset
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs, boolean ignoreUnrefed, int vseqpos)
+ AlignmentI ds, Vector<SequenceI> dseqs, boolean ignoreUnrefed,
+ int vseqpos)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
return datasetId;
}
+ /**
+ * Add any saved DBRefEntry's to the sequence. An entry flagged as 'locus' is
+ * constructed as a special subclass GeneLocus.
+ *
+ * @param datasetSequence
+ * @param sequence
+ */
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
for (int d = 0; d < sequence.getDBRef().size(); d++)
{
DBRef dr = sequence.getDBRef().get(d);
- jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
- dr.getSource(), dr.getVersion(), dr.getAccessionId());
+ DBRefEntry entry;
+ if (dr.isLocus())
+ {
+ entry = new GeneLocus(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
+ else
+ {
+ entry = new DBRefEntry(dr.getSource(), dr.getVersion(),
+ dr.getAccessionId());
+ }
if (dr.getMapping() != null)
{
entry.setMap(addMapping(dr.getMapping()));
jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto, fr,
fto, m.getMapFromUnit().intValue(),
m.getMapToUnit().intValue());
- // if (m.getMappingChoice() != null)
- // {
- // MappingChoice mc = m.getMappingChoice();
+
+ /*
+ * (optional) choice of dseqFor or Sequence
+ */
if (m.getDseqFor() != null)
{
String dsfor = m.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
- /**
+ /*
* recover from hash
*/
jmap.setTo(seqRefIds.get(dsfor));
frefedSequence.add(newMappingRef(dsfor, jmap));
}
}
- else
+ else if (m.getSequence() != null)
{
- /**
+ /*
* local sequence definition
*/
Sequence ms = m.getSequence();
}
/**
+ * Creates a new structure viewer window
+ *
+ * @param viewerType
+ * @param viewerData
+ * @param af
+ * @param jprovider
+ */
+ protected void createStructureViewer(
+ ViewerType viewerType, final Entry<String, StructureViewerModel> viewerData,
+ AlignFrame af, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel viewerModel = viewerData.getValue();
+ String sessionFilePath = null;
+
+ if (viewerType == ViewerType.JMOL)
+ {
+ sessionFilePath = rewriteJmolSession(viewerModel, jprovider);
+ }
+ else
+ {
+ String viewerJarEntryName = getViewerJarEntryName(
+ viewerModel.getViewId());
+ sessionFilePath = copyJarEntry(jprovider,
+ viewerJarEntryName,
+ "viewerSession", ".tmp");
+ }
+ final String sessionPath = sessionFilePath;
+ final String sviewid = viewerData.getKey();
+ try
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JalviewStructureDisplayI sview = null;
+ try
+ {
+ sview = StructureViewer.createView(viewerType, af.alignPanel,
+ viewerModel, sessionPath, sviewid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("Restoring structure view for "
+ + viewerType,
+ (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer(false);
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
+ }
+ });
+ } catch (InvocationTargetException | InterruptedException ex)
+ {
+ warn("Unexpected error when opening " + viewerType
+ + " structure viewer", ex);
+ }
+ }
+
+ /**
+ * Rewrites a Jmol session script, saves it to a temporary file, and returns
+ * the path of the file. "load file" commands are rewritten to change the
+ * original PDB file names to those created as the Jalview project is loaded.
+ *
+ * @param svattrib
+ * @param jprovider
+ * @return
+ */
+ private String rewriteJmolSession(StructureViewerModel svattrib,
+ jarInputStreamProvider jprovider)
+ {
+ String state = svattrib.getStateData(); // Jalview < 2.9
+ if (state == null || state.isEmpty()) // Jalview >= 2.9
+ {
+ String jarEntryName = getViewerJarEntryName(svattrib.getViewId());
+ state = readJarEntry(jprovider, jarEntryName);
+ }
+ // TODO or simpler? for each key in oldFiles,
+ // replace key.getPath() in state with oldFiles.get(key).getFilePath()
+ // (allowing for different path escapings)
+ StringBuilder rewritten = new StringBuilder(state.length());
+ int cp = 0, ncp, ecp;
+ Map<File, StructureData> oldFiles = svattrib.getFileData();
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ do
+ {
+ // look for next filename in load statement
+ rewritten.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename translation differently.
+ StructureData filedat = oldFiles.get(new File(oldfilenam));
+ if (filedat == null)
+ {
+ String reformatedOldFilename = oldfilenam.replaceAll("/", "\\\\");
+ filedat = oldFiles.get(new File(reformatedOldFilename));
+ }
+ rewritten
+ .append(Platform.escapeBackslashes(filedat.getFilePath()));
+ rewritten.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ rewritten.append(state.substring(cp));
+ }
+ else
+ {
+ System.err.print("Ignoring incomplete Jmol state for PDB ids: ");
+ rewritten = new StringBuilder(state);
+ rewritten.append("; load append ");
+ for (File id : oldFiles.keySet())
+ {
+ // add pdb files that should be present in the viewer
+ StructureData filedat = oldFiles.get(id);
+ rewritten.append(" \"").append(filedat.getFilePath()).append("\"");
+ }
+ rewritten.append(";");
+ }
+
+ if (rewritten.length() == 0)
+ {
+ return null;
+ }
+ final String history = "history = ";
+ int historyIndex = rewritten.indexOf(history);
+ if (historyIndex > -1)
+ {
+ /*
+ * change "history = [true|false];" to "history = [1|0];"
+ */
+ historyIndex += history.length();
+ String val = rewritten.substring(historyIndex, historyIndex + 5);
+ if (val.startsWith("true"))
+ {
+ rewritten.replace(historyIndex, historyIndex + 4, "1");
+ }
+ else if (val.startsWith("false"))
+ {
+ rewritten.replace(historyIndex, historyIndex + 5, "0");
+ }
+ }
+
+ try
+ {
+ File tmp = File.createTempFile("viewerSession", ".tmp");
+ try (OutputStream os = new FileOutputStream(tmp))
+ {
+ InputStream is = new ByteArrayInputStream(
+ rewritten.toString().getBytes());
+ copyAll(is, os);
+ return tmp.getAbsolutePath();
+ }
+ } catch (IOException e)
+ {
+ Cache.log.error("Error restoring Jmol session: " + e.toString());
+ }
+ return null;
+ }
+
+ /**
* Populates an XML model of the feature colour scheme for one feature type
*
* @param featureType
noValueColour = maxcol;
}
- colour = new FeatureColour(mincol, maxcol, noValueColour,
+ colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
final List<String> attributeName = colourModel.getAttributeName();