*/
package jalview.project;
+
import static jalview.math.RotatableMatrix.Axis.X;
import static jalview.math.RotatableMatrix.Axis.Y;
import static jalview.math.RotatableMatrix.Axis.Z;
+
import jalview.analysis.Conservation;
import jalview.analysis.PCA;
import jalview.analysis.scoremodels.ScoreModels;
import jalview.api.analysis.SimilarityParamsI;
import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
+import jalview.bin.Console;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
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.math.BigInteger;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Locale;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
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_";
+ // 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
- private static final String HMMER_PREFIX = "hmmer_";
- private static final String UTF_8 = "UTF-8";
+ static
+ {
+ Platform.addJ2SBinaryType(".jvp?");
+ }
- /**
- * prefix for recovering datasets for alignments with multiple views where
- * non-existent dataset IDs were written for some views
- */
- private static final String UNIQSEQSETID = "uniqueSeqSetId.";
+ private static final String VIEWER_PREFIX = "viewer_";
- // use this with nextCounter() to make unique names for entities
- private int counter = 0;
+ private static final String RNA_PREFIX = "rna_";
- /*
- * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
- * of sequence objects are created.
- */
- IdentityHashMap<SequenceI, String> seqsToIds = null;
+ private static final String HMMER_PREFIX = "hmmer_";
+ private static final String UTF_8 = "UTF-8";
- /**
- * jalview XML Sequence ID to jalview sequence object reference (both dataset
- * and alignment sequences. Populated as XML reps of sequence objects are
- * created.)
- */
- Map<String, SequenceI> seqRefIds = null;
+ /**
+ * prefix for recovering datasets for alignments with multiple views where
+ * non-existent dataset IDs were written for some views
+ */
+ private static final String UNIQSEQSETID = "uniqueSeqSetId.";
- Map<String, SequenceI> incompleteSeqs = null;
+ // use this with nextCounter() to make unique names for entities
+ private int counter = 0;
- List<SeqFref> frefedSequence = null;
+ /*
+ * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
+ * of sequence objects are created.
+ */
+ IdentityHashMap<SequenceI, String> seqsToIds = null;
- boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+ /**
+ * jalview XML Sequence ID to jalview sequence object reference (both dataset
+ * and alignment sequences. Populated as XML reps of sequence objects are
+ * created.)
+ */
+ Map<String, SequenceI> seqRefIds = null;
- /*
- * Map of reconstructed AlignFrame objects that appear to have come from
- * SplitFrame objects (have a dna/protein complement view).
- */
- private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
+ Map<String, SequenceI> incompleteSeqs = null;
- /*
- * Map from displayed rna structure models to their saved session state jar
- * entry names
- */
- private Map<RnaModel, String> rnaSessions = new HashMap<>();
+ List<SeqFref> frefedSequence = null;
- /**
- * contains last error message (if any) encountered by XML loader.
- */
- String errorMessage = null;
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
- /**
- * flag to control whether the Jalview2XML_V1 parser should be deferred to if
- * exceptions are raised during project XML parsing
- */
- public boolean attemptversion1parse = false;
+ /*
+ * Map of reconstructed AlignFrame objects that appear to have come from
+ * SplitFrame objects (have a dna/protein complement view).
+ */
+ private Map<Viewport, AlignFrame> splitFrameCandidates = new HashMap<>();
- /*
- * JalviewJS only -- to allow read file bytes to be saved in the
- * created AlignFrame, allowing File | Reload of a project file to work
- *
- * BH 2019 JAL-3436
- */
- private File jarFile;
+ /*
+ * Map from displayed rna structure models to their saved session state jar
+ * entry names
+ */
+ private Map<RnaModel, String> rnaSessions = new HashMap<>();
- /**
- * A helper method for safely using the value of an optional attribute that
- * may be null if not present in the XML. Answers the boolean value, or false
- * if null.
- *
- * @param b
- * @return
- */
- public static boolean safeBoolean(Boolean b)
- {
- return b == null ? false : b.booleanValue();
- }
+ /**
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
- /**
- * A helper method for safely using the value of an optional attribute that
- * may be null if not present in the XML. Answers the integer value, or zero
- * if null.
- *
- * @param i
- * @return
- */
- public static int safeInt(Integer i)
- {
- return i == null ? 0 : i.intValue();
- }
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = false;
- /**
- * A helper method for safely using the value of an optional attribute that
- * may be null if not present in the XML. Answers the float value, or zero if
- * null.
- *
- * @param f
- * @return
- */
- public static float safeFloat(Float f)
- {
- return f == null ? 0f : f.floatValue();
- }
+ /*
+ * JalviewJS only -- to allow read file bytes to be saved in the
+ * created AlignFrame, allowing File | Reload of a project file to work
+ *
+ * BH 2019 JAL-3436
+ */
+ private File jarFile;
- /**
- * create/return unique hash string for sq
- *
- * @param sq
- * @return new or existing unique string for sq
- */
- String seqHash(SequenceI sq)
- {
- if (seqsToIds == null)
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the boolean value, or false
+ * if null.
+ *
+ * @param b
+ * @return
+ */
+ public static boolean safeBoolean(Boolean b)
{
- initSeqRefs();
+ return b == null ? false : b.booleanValue();
}
- if (seqsToIds.containsKey(sq))
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the integer value, or zero
+ * if null.
+ *
+ * @param i
+ * @return
+ */
+ public static int safeInt(Integer i)
{
- return seqsToIds.get(sq);
+ return i == null ? 0 : i.intValue();
}
- else
+
+ /**
+ * A helper method for safely using the value of an optional attribute that
+ * may be null if not present in the XML. Answers the float value, or zero if
+ * null.
+ *
+ * @param f
+ * @return
+ */
+ public static float safeFloat(Float f)
{
- // create sequential key
- String key = "sq" + (seqsToIds.size() + 1);
- key = makeHashCode(sq, key); // check we don't have an external reference
- // for it already.
- seqsToIds.put(sq, key);
- return key;
+ return f == null ? 0f : f.floatValue();
}
- }
- void initSeqRefs()
- {
- if (seqsToIds == null)
+ /**
+ * create/return unique hash string for sq
+ *
+ * @param sq
+ * @return new or existing unique string for sq
+ */
+ String seqHash(SequenceI sq)
{
- seqsToIds = new IdentityHashMap<>();
+ if (seqsToIds == null)
+ {
+ initSeqRefs();
+ }
+ if (seqsToIds.containsKey(sq))
+ {
+ return seqsToIds.get(sq);
+ }
+ else
+ {
+ // create sequential key
+ String key = "sq" + (seqsToIds.size() + 1);
+ key = makeHashCode(sq, key); // check we don't have an external reference
+ // for it already.
+ seqsToIds.put(sq, key);
+ return key;
+ }
}
- if (seqRefIds == null)
+
+ void initSeqRefs()
{
- seqRefIds = new HashMap<>();
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap<>();
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new HashMap<>();
+ }
+ if (incompleteSeqs == null)
+ {
+ incompleteSeqs = new HashMap<>();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new ArrayList<>();
+ }
}
- if (incompleteSeqs == null)
+
+ public Jalview2XML()
{
- incompleteSeqs = new HashMap<>();
}
- if (frefedSequence == null)
+
+ public Jalview2XML(boolean raiseGUI)
{
- frefedSequence = new ArrayList<>();
+ this.raiseGUI = raiseGUI;
}
- }
- public Jalview2XML()
- {
- }
+ /**
+ * base class for resolving forward references to sequences by their ID
+ *
+ * @author jprocter
+ *
+ */
+ abstract class SeqFref
+ {
+ String sref;
+
+ String type;
+
+ public SeqFref(String _sref, String type)
+ {
+ sref = _sref;
+ this.type = type;
+ }
+
+ public String getSref()
+ {
+ return sref;
+ }
+
+ public SequenceI getSrefSeq()
+ {
+ return seqRefIds.get(sref);
+ }
+
+ public boolean isResolvable()
+ {
+ return seqRefIds.get(sref) != null;
+ }
+
+ public SequenceI getSrefDatasetSeq()
+ {
+ SequenceI sq = seqRefIds.get(sref);
+ if (sq != null)
+ {
+ while (sq.getDatasetSequence() != null)
+ {
+ sq = sq.getDatasetSequence();
+ }
+ }
+ return sq;
+ }
+
+ /**
+ * @return true if the forward reference was fully resolved
+ */
+ abstract boolean resolve();
+
+ @Override
+ public String toString()
+ {
+ return type + " reference to " + sref;
+ }
+ }
- public Jalview2XML(boolean raiseGUI)
- {
- this.raiseGUI = raiseGUI;
- }
+ /**
+ * create forward reference for a mapping
+ *
+ * @param sref
+ * @param _jmap
+ * @return
+ */
+ protected SeqFref newMappingRef(final String sref,
+ final jalview.datamodel.Mapping _jmap)
+ {
+ SeqFref fref = new SeqFref(sref, "Mapping")
+ {
+ public jalview.datamodel.Mapping jmap = _jmap;
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ jmap.setTo(seq);
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ protected SeqFref newAlcodMapRef(final String sref,
+ final AlignedCodonFrame _cf,
+ final jalview.datamodel.Mapping _jmap)
+ {
+
+ SeqFref fref = new SeqFref(sref, "Codon Frame")
+ {
+ AlignedCodonFrame cf = _cf;
+
+ public jalview.datamodel.Mapping mp = _jmap;
+
+ @Override
+ public boolean isResolvable()
+ {
+ return super.isResolvable() && mp.getTo() != null;
+ }
+
+ @Override
+ boolean resolve()
+ {
+ SequenceI seq = getSrefDatasetSeq();
+ if (seq == null)
+ {
+ return false;
+ }
+ cf.addMap(seq, mp.getTo(), mp.getMap());
+ return true;
+ }
+ };
+ return fref;
+ }
+
+ protected void resolveFrefedSequences()
+ {
+ Iterator<SeqFref> nextFref = frefedSequence.iterator();
+ int toresolve = frefedSequence.size();
+ int unresolved = 0, failedtoresolve = 0;
+ while (nextFref.hasNext())
+ {
+ SeqFref ref = nextFref.next();
+ if (ref.isResolvable())
+ {
+ try
+ {
+ if (ref.resolve())
+ {
+ nextFref.remove();
+ }
+ else
+ {
+ failedtoresolve++;
+ }
+ } catch (Exception x)
+ {
+ System.err.println(
+ "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
+ + ref.getSref());
+ x.printStackTrace();
+ failedtoresolve++;
+ }
+ }
+ else
+ {
+ unresolved++;
+ }
+ }
+ if (unresolved > 0)
+ {
+ System.err.println("Jalview Project Import: There were " + unresolved
+ + " forward references left unresolved on the stack.");
+ }
+ if (failedtoresolve > 0)
+ {
+ System.err.println("SERIOUS! " + failedtoresolve
+ + " resolvable forward references failed to resolve.");
+ }
+ if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+ {
+ System.err.println(
+ "Jalview Project Import: There are " + incompleteSeqs.size()
+ + " sequences which may have incomplete metadata.");
+ if (incompleteSeqs.size() < 10)
+ {
+ for (SequenceI s : incompleteSeqs.values())
+ {
+ System.err.println(s.toString());
+ }
+ }
+ else
+ {
+ System.err.println(
+ "Too many to report. Skipping output of incomplete sequences.");
+ }
+ }
+ }
- /**
- * base class for resolving forward references to sequences by their ID
- *
- * @author jprocter
- *
- */
- abstract class SeqFref
- {
- String sref;
+ /**
+ * This maintains a map of viewports, the key being the seqSetId. Important to
+ * set historyItem and redoList for multiple views
+ */
+ Map<String, AlignViewport> viewportsAdded = new HashMap<>();
- String type;
+ Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
- public SeqFref(String _sref, String type)
- {
- sref = _sref;
- this.type = type;
+ String uniqueSetSuffix = "";
+
+ /**
+ * List of pdbfiles added to Jar
+ */
+ List<String> pdbfiles = null;
+
+ // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
+ 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)
+ {
+ Console.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 = "Did't write Jalview Archive to output file '"
+ + statefile + "' - See console error log for details";
+ }
+ else
+ {
+ errorMessage += "(Didn't write Jalview Archive to output file '"
+ + statefile + ")";
+ }
+ e.printStackTrace();
+ } finally
+ {
+ if (fos != null)
+ {
+ try
+ {
+ fos.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ reportErrors();
}
- public String getSref()
+ /**
+ * Writes a jalview project archive to the given Jar output stream.
+ *
+ * @param jout
+ */
+ public void saveState(JarOutputStream jout)
{
- return sref;
+ AlignFrame[] frames = Desktop.getAlignFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+ saveAllFrames(Arrays.asList(frames), jout);
}
- public SequenceI getSrefSeq()
- {
- return seqRefIds.get(sref);
+ /**
+ * core method for storing state for a set of AlignFrames.
+ *
+ * @param frames
+ * - frames involving all data to be exported (including those
+ * contained in splitframes, though not the split frames themselves)
+ * @param jout
+ * - project output stream
+ */
+ private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
+ {
+ Hashtable<String, AlignFrame> dsses = new Hashtable<>();
+
+ /*
+ * ensure cached data is clear before starting
+ */
+ // todo tidy up seqRefIds, seqsToIds initialisation / reset
+ rnaSessions.clear();
+ splitFrameCandidates.clear();
+
+ try
+ {
+
+ // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+ // //////////////////////////////////////////////////
+
+ List<String> shortNames = new ArrayList<>();
+ List<String> viewIds = new ArrayList<>();
+
+ // REVERSE ORDER
+ for (int i = frames.size() - 1; i > -1; i--)
+ {
+ AlignFrame af = frames.get(i);
+ AlignViewport vp = af.getViewport();
+ // skip ?
+ if (skipList != null && skipList
+ .containsKey(vp.getSequenceSetId()))
+ {
+ continue;
+ }
+
+ String shortName = makeFilename(af, shortNames);
+
+ AlignmentI alignment = vp.getAlignment();
+ List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
+ int apSize = panels.size();
+
+ for (int ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
+ {
+ fileName = fileName + ".xml";
+ }
+
+ saveState(apanel, fileName, jout, viewIds);
+
+ }
+ if (apSize > 0)
+ {
+ // BH moved next bit out of inner loop, not that it really matters.
+ // so we are testing to make sure we actually have an alignment,
+ // apparently.
+ String dssid = getDatasetIdRef(alignment.getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ // We have not already covered this data by reference from another
+ // frame.
+ dsses.put(dssid, af);
+ }
+ }
+ }
+
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ jout.close();
+ } catch (Exception ex)
+ {
+ // 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 - see error output for details";
+ }
+ ex.printStackTrace();
+ }
}
- public boolean isResolvable()
- {
- return seqRefIds.get(sref) != null;
+ /**
+ * Generates a distinct file name, based on the title of the AlignFrame, by
+ * appending _n for increasing n until an unused name is generated. The new
+ * name (without its extension) is added to the list.
+ *
+ * @param af
+ * @param namesUsed
+ * @return the generated name, with .xml extension
+ */
+ protected String makeFilename(AlignFrame af, List<String> namesUsed)
+ {
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName
+ .substring(shortName.lastIndexOf(File.separatorChar) + 1);
+ }
+
+ int count = 1;
+
+ while (namesUsed.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
+ {
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));
+ }
+
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
+
+ namesUsed.add(shortName);
+
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
+ return shortName;
+ }
+
+ // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+ public boolean saveAlignment(AlignFrame af, String jarFile,
+ String fileName)
+ {
+ try
+ {
+ // 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<>();
+
+ // resolve splitframes
+ if (af.getViewport().getCodingComplement() != null)
+ {
+ frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
+ }
+ else
+ {
+ frames.add(af);
+ }
+ saveAllFrames(frames, jout);
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ jout.close();
+ 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";
+ ex.printStackTrace();
+ return false;
+ }
}
- public SequenceI getSrefDatasetSeq()
+ /**
+ * Each AlignFrame has a single data set associated with it. Note that none of
+ * these frames are split frames, because Desktop.getAlignFrames() collects
+ * top and bottom separately here.
+ *
+ * @param dsses
+ * @param fileName
+ * @param jout
+ */
+ private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
+ String fileName, JarOutputStream jout)
{
- SequenceI sq = seqRefIds.get(sref);
- if (sq != null)
- {
- while (sq.getDatasetSequence() != null)
- {
- sq = sq.getDatasetSequence();
- }
- }
- return sq;
+
+ // Note that in saveAllFrames we have associated each specific dataset to
+ // ONE of its associated frames.
+ for (String dssids : dsses.keySet())
+ {
+ AlignFrame _af = dsses.get(dssids);
+ String jfileName = fileName + " Dataset for " + _af.getTitle();
+ if (!jfileName.endsWith(".xml"))
+ {
+ jfileName = jfileName + ".xml";
+ }
+ saveState(_af.alignPanel, jfileName, true, jout, null);
+ }
}
/**
- * @return true if the forward reference was fully resolved
+ * create a JalviewModel from an alignment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param jout
+ * jar output stream
+ * @param viewIds
+ * @param out
+ * jar entry name
*/
- abstract boolean resolve();
-
- @Override
- public String toString()
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
+ JarOutputStream jout, List<String> viewIds)
{
- return type + " reference to " + sref;
+ return saveState(ap, fileName, false, jout, viewIds);
}
- }
- /**
- * create forward reference for a mapping
- *
- * @param sref
- * @param _jmap
- * @return
- */
- protected SeqFref newMappingRef(final String sref,
- final jalview.datamodel.Mapping _jmap)
- {
- SeqFref fref = new SeqFref(sref, "Mapping")
- {
- public jalview.datamodel.Mapping jmap = _jmap;
+ /**
+ * create a JalviewModel from an alignment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param storeDS
+ * when true, only write the dataset for the alignment, not the data
+ * associated with the view.
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
+ */
+ protected JalviewModel saveState(AlignmentPanel ap, String fileName,
+ boolean storeDS, JarOutputStream jout, List<String> viewIds)
+ {
+ if (viewIds == null)
+ {
+ viewIds = new ArrayList<>();
+ }
+
+ initSeqRefs();
+
+ List<UserColourScheme> userColours = new ArrayList<>();
+
+ AlignViewport av = ap.av;
+ ViewportRanges vpRanges = av.getRanges();
+
+ final ObjectFactory objectFactory = new ObjectFactory();
+ JalviewModel object = objectFactory.createJalviewModel();
+ object.setVamsasModel(new VAMSAS());
+
+ // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ try
+ {
+ GregorianCalendar c = new GregorianCalendar();
+ DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
+ XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
+ object.setCreationDate(now);
+ } catch (DatatypeConfigurationException e)
+ {
+ System.err.println("error writing date: " + e.toString());
+ }
+ object.setVersion(Cache.getDefault("VERSION", "Development Build"));
+
+ /**
+ * rjal is full height alignment, jal is actual alignment with full metadata
+ * but excludes hidden sequences.
+ */
+ jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
+
+ if (av.hasHiddenRows())
+ {
+ rjal = jal.getHiddenSequences().getFullAlignment();
+ }
+
+ SequenceSet vamsasSet = new SequenceSet();
+ Sequence vamsasSeq;
+ // JalviewModelSequence jms = new JalviewModelSequence();
+
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");
+
+ if (jal.getDataset() != null)
+ {
+ // dataset id is the dataset's hashcode
+ vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ if (storeDS)
+ {
+ // switch jal and the dataset
+ jal = jal.getDataset();
+ rjal = jal;
+ }
+ }
+ if (jal.getProperties() != null)
+ {
+ Enumeration en = jal.getProperties().keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ SequenceSetProperties ssp = new SequenceSetProperties();
+ ssp.setKey(key);
+ ssp.setValue(jal.getProperties().get(key).toString());
+ // vamsasSet.addSequenceSetProperties(ssp);
+ vamsasSet.getSequenceSetProperties().add(ssp);
+ }
+ }
+
+ JSeq jseq;
+ Set<String> calcIdSet = new HashSet<>();
+ // record the set of vamsas sequence XML POJO we create.
+ HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
+ // SAVE SEQUENCES
+ for (final SequenceI jds : rjal.getSequences())
+ {
+ final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
+ : jds.getDatasetSequence();
+ String id = seqHash(jds);
+ if (vamsasSetIds.get(id) == null)
+ {
+ if (seqRefIds.get(id) != null && !storeDS)
+ {
+ // This happens for two reasons: 1. multiple views are being
+ // serialised.
+ // 2. the hashCode has collided with another sequence's code. This
+ // DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+ // vamsasSet.addSequence(vamsasSeq);
+ vamsasSet.getSequence().add(vamsasSeq);
+ vamsasSetIds.put(id, vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
+ }
+ jseq = new JSeq();
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour(av.getSequenceColour(jds).getRGB());
+
+ jseq.setId(id); // jseq id should be a string not a number
+ if (!storeDS)
+ {
+ // Store any sequences this sequence represents
+ if (av.hasHiddenRows())
+ {
+ // use rjal, contains the full height alignment
+ jseq.setHidden(
+ av.getAlignment().getHiddenSequences().isHidden(jds));
+
+ if (av.isHiddenRepSequence(jds))
+ {
+ jalview.datamodel.SequenceI[] reps = av
+ .getRepresentedSequences(jds).getSequencesInOrder(rjal);
+
+ for (int h = 0; h < reps.length; h++)
+ {
+ if (reps[h] != jds)
+ {
+ // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
+ jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
+ }
+ }
+ }
+ }
+ // mark sequence as reference - if it is the reference for this view
+ if (jal.hasSeqrep())
+ {
+ jseq.setViewreference(jds == jal.getSeqrep());
+ }
+ }
+
+ // TODO: omit sequence features from each alignment view's XML dump if we
+ // are storing dataset
+ List<SequenceFeature> sfs = jds.getSequenceFeatures();
+ for (SequenceFeature sf : sfs)
+ {
+ // Features features = new Features();
+ Feature features = new Feature();
+
+ features.setBegin(sf.getBegin());
+ features.setEnd(sf.getEnd());
+ features.setDescription(sf.getDescription());
+ features.setType(sf.getType());
+ features.setFeatureGroup(sf.getFeatureGroup());
+ features.setScore(sf.getScore());
+ if (sf.links != null)
+ {
+ for (int l = 0; l < sf.links.size(); l++)
+ {
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf.links.elementAt(l).toString());
+ // features.addOtherData(keyValue);
+ features.getOtherData().add(keyValue);
+ }
+ }
+ if (sf.otherDetails != null)
+ {
+ /*
+ * save feature attributes, which may be simple strings or
+ * map valued (have sub-attributes)
+ */
+ for (Entry<String, Object> entry : sf.otherDetails.entrySet())
+ {
+ String key = entry.getKey();
+ Object value = entry.getValue();
+ if (value instanceof Map<?, ?>)
+ {
+ for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
+ .entrySet())
+ {
+ OtherData otherData = new OtherData();
+ otherData.setKey(key);
+ otherData.setKey2(subAttribute.getKey());
+ otherData.setValue(subAttribute.getValue().toString());
+ // features.addOtherData(otherData);
+ features.getOtherData().add(otherData);
+ }
+ }
+ else
+ {
+ OtherData otherData = new OtherData();
+ otherData.setKey(key);
+ otherData.setValue(value.toString());
+ // features.addOtherData(otherData);
+ features.getOtherData().add(otherData);
+ }
+ }
+ }
+
+ // jseq.addFeatures(features);
+ jseq.getFeatures().add(features);
+ }
+
+ /*
+ * save PDB entries for sequence
+ */
+ if (jdatasq.getAllPDBEntries() != null)
+ {
+ Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
+ while (en.hasMoreElements())
+ {
+ Pdbids pdb = new Pdbids();
+ jalview.datamodel.PDBEntry entry = en.nextElement();
+
+ String pdbId = entry.getId();
+ pdb.setId(pdbId);
+ pdb.setType(entry.getType());
+
+ /*
+ * Store any structure views associated with this sequence. This
+ * section copes with duplicate entries in the project, so a dataset
+ * only view *should* be coped with sensibly.
+ */
+ // This must have been loaded, is it still visible?
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ String matchedFile = null;
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof StructureViewerBase)
+ {
+ StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
+ 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);
+ File viewerState = viewFrame.saveSession();
+ if (viewerState != null)
+ {
+ copyFileToJar(jout, viewerState.getPath(),
+ getViewerJarEntryName(viewId), viewerType);
+ }
+ else
+ {
+ Console.error(
+ "Failed to save viewer state for " + viewerType);
+ }
+ }
+ }
+ }
+
+ if (matchedFile != null || entry.getFile() != null)
+ {
+ if (entry.getFile() != null)
+ {
+ // use entry's file
+ matchedFile = entry.getFile();
+ }
+ pdb.setFile(matchedFile); // entry.getFile());
+ if (pdbfiles == null)
+ {
+ pdbfiles = new ArrayList<>();
+ }
+
+ if (!pdbfiles.contains(pdbId))
+ {
+ pdbfiles.add(pdbId);
+ copyFileToJar(jout, matchedFile, pdbId, pdbId);
+ }
+ }
+
+ Enumeration<String> props = entry.getProperties();
+ if (props.hasMoreElements())
+ {
+ // PdbentryItem item = new PdbentryItem();
+ while (props.hasMoreElements())
+ {
+ Property prop = new Property();
+ String key = props.nextElement();
+ prop.setName(key);
+ prop.setValue(entry.getProperty(key).toString());
+ // item.addProperty(prop);
+ pdb.getProperty().add(prop);
+ }
+ // pdb.addPdbentryItem(item);
+ }
+
+ // jseq.addPdbids(pdb);
+ jseq.getPdbids().add(pdb);
+ }
+ }
+
+ saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
+
+ if (jds.hasHMMProfile())
+ {
+ saveHmmerProfile(jout, jseq, jds);
+ }
+ // jms.addJSeq(jseq);
+ object.getJSeq().add(jseq);
+ }
+
+ if (!storeDS && av.hasHiddenRows())
+ {
+ jal = av.getAlignment();
+ }
+ // SAVE MAPPINGS
+ // FOR DATASET
+ if (storeDS && jal.getCodonFrames() != null)
+ {
+ List<AlignedCodonFrame> jac = jal.getCodonFrames();
+ for (AlignedCodonFrame acf : jac)
+ {
+ AlcodonFrame alc = new AlcodonFrame();
+ if (acf.getProtMappings() != null
+ && acf.getProtMappings().length > 0)
+ {
+ boolean hasMap = false;
+ SequenceI[] dnas = acf.getdnaSeqs();
+ jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+ for (int m = 0; m < pmaps.length; m++)
+ {
+ AlcodMap alcmap = new AlcodMap();
+ alcmap.setDnasq(seqHash(dnas[m]));
+ alcmap.setMapping(
+ createVamsasMapping(pmaps[m], dnas[m], null, false));
+ // alc.addAlcodMap(alcmap);
+ alc.getAlcodMap().add(alcmap);
+ hasMap = true;
+ }
+ if (hasMap)
+ {
+ // vamsasSet.addAlcodonFrame(alc);
+ vamsasSet.getAlcodonFrame().add(alc);
+ }
+ }
+ // TODO: delete this ? dead code from 2.8.3->2.9 ?
+ // {
+ // AlcodonFrame alc = new AlcodonFrame();
+ // vamsasSet.addAlcodonFrame(alc);
+ // for (int p = 0; p < acf.aaWidth; p++)
+ // {
+ // Alcodon cmap = new Alcodon();
+ // if (acf.codons[p] != null)
+ // {
+ // // Null codons indicate a gapped column in the translated peptide
+ // // alignment.
+ // cmap.setPos1(acf.codons[p][0]);
+ // cmap.setPos2(acf.codons[p][1]);
+ // cmap.setPos3(acf.codons[p][2]);
+ // }
+ // alc.addAlcodon(cmap);
+ // }
+ // if (acf.getProtMappings() != null
+ // && acf.getProtMappings().length > 0)
+ // {
+ // SequenceI[] dnas = acf.getdnaSeqs();
+ // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
+ // for (int m = 0; m < pmaps.length; m++)
+ // {
+ // AlcodMap alcmap = new AlcodMap();
+ // alcmap.setDnasq(seqHash(dnas[m]));
+ // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+ // false));
+ // alc.addAlcodMap(alcmap);
+ // }
+ // }
+ }
+ }
+
+ // SAVE TREES
+ // /////////////////////////////////
+ if (!storeDS && av.getCurrentTree() != null)
+ {
+ // FIND ANY ASSOCIATED TREES
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+ if (Desktop.getDesktopPane() != null)
+ {
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof TreePanel)
+ {
+ TreePanel tp = (TreePanel) frames[t];
+
+ if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
+ {
+ JalviewModel.Tree tree = new JalviewModel.Tree();
+ tree.setTitle(tp.getTitle());
+ tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
+ tree.setNewick(tp.getTree().print());
+ tree.setThreshold(tp.getTreeCanvas().getThreshold());
+
+ tree.setFitToWindow(tp.fitToWindow.getState());
+ tree.setFontName(tp.getTreeFont().getName());
+ tree.setFontSize(tp.getTreeFont().getSize());
+ tree.setFontStyle(tp.getTreeFont().getStyle());
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());
+ tree.setShowDistances(tp.distanceMenu.getState());
+
+ tree.setHeight(tp.getHeight());
+ tree.setWidth(tp.getWidth());
+ tree.setXpos(tp.getX());
+ tree.setYpos(tp.getY());
+ tree.setId(makeHashCode(tp, null));
+ tree.setLinkToAllViews(
+ tp.getTreeCanvas().isApplyToAllViews());
+
+ // jms.addTree(tree);
+ object.getTree().add(tree);
+ }
+ }
+ }
+ }
+ }
+
+ /*
+ * save PCA viewers
+ */
+ if (!storeDS && Desktop.getDesktopPane() != null)
+ {
+ for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
+ {
+ if (frame instanceof PCAPanel)
+ {
+ PCAPanel panel = (PCAPanel) frame;
+ if (panel.getAlignViewport().getAlignment() == jal)
+ {
+ savePCA(panel, object);
+ }
+ }
+ }
+ }
+
+ // SAVE ANNOTATIONS
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
+ if (storeDS)
+ {
+ for (SequenceI sq : jal.getSequences())
+ {
+ // Store annotation on dataset sequences only
+ AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
+ {
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
+ }
+ }
+ }
+ else
+ {
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ // Store the annotation shown on the alignment.
+ AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
+ }
+ }
+ // SAVE GROUPS
+ if (jal.getGroups() != null)
+ {
+ JGroup[] groups = new JGroup[jal.getGroups().size()];
+ int i = -1;
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
+ {
+ JGroup jGroup = new JGroup();
+ groups[++i] = jGroup;
+
+ jGroup.setStart(sg.getStartRes());
+ jGroup.setEnd(sg.getEndRes());
+ jGroup.setName(sg.getName());
+ if (groupRefs.containsKey(sg))
+ {
+ // group has references so set its ID field
+ jGroup.setId(groupRefs.get(sg));
+ }
+ ColourSchemeI colourScheme = sg.getColourScheme();
+ if (colourScheme != null)
+ {
+ ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
+ if (groupColourScheme.conservationApplied())
+ {
+ jGroup.setConsThreshold(groupColourScheme.getConservationInc());
+
+ if (colourScheme instanceof jalview.schemes.UserColourScheme)
+ {
+ jGroup.setColour(
+ setUserColourScheme(colourScheme, userColours,
+ object));
+ }
+ else
+ {
+ jGroup.setColour(colourScheme.getSchemeName());
+ }
+ }
+ else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ jGroup.setColour("AnnotationColourGradient");
+ jGroup.setAnnotationColours(constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) colourScheme,
+ userColours, object));
+ }
+ else if (colourScheme instanceof jalview.schemes.UserColourScheme)
+ {
+ jGroup.setColour(
+ setUserColourScheme(colourScheme, userColours, object));
+ }
+ else
+ {
+ jGroup.setColour(colourScheme.getSchemeName());
+ }
+
+ jGroup.setPidThreshold(groupColourScheme.getThreshold());
+ }
+
+ jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
+ jGroup.setDisplayBoxes(sg.getDisplayBoxes());
+ jGroup.setDisplayText(sg.getDisplayText());
+ jGroup.setColourText(sg.getColourText());
+ jGroup.setTextCol1(sg.textColour.getRGB());
+ jGroup.setTextCol2(sg.textColour2.getRGB());
+ jGroup.setTextColThreshold(sg.thresholdTextColour);
+ jGroup.setShowUnconserved(sg.getShowNonconserved());
+ jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
+ jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
+ jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
+ for (SequenceI seq : sg.getSequences())
+ {
+ // jGroup.addSeq(seqHash(seq));
+ jGroup.getSeq().add(seqHash(seq));
+ }
+ }
+
+ //jms.setJGroup(groups);
+ Object group;
+ for (JGroup grp : groups)
+ {
+ object.getJGroup().add(grp);
+ }
+ }
+ if (!storeDS)
+ {
+ // /////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(
+ makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
+ view.setId(av.getViewId());
+ if (av.getCodingComplement() != null)
+ {
+ view.setComplementId(av.getCodingComplement().getViewId());
+ }
+ view.setViewName(av.getViewName());
+ view.setGatheredViews(av.isGatherViewsHere());
+
+ Rectangle size = ap.av.getExplodedGeometry();
+ Rectangle position = size;
+ if (size == null)
+ {
+ size = ap.alignFrame.getBounds();
+ if (av.getCodingComplement() != null)
+ {
+ position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
+ .getBounds();
+ }
+ else
+ {
+ position = size;
+ }
+ }
+ view.setXpos(position.x);
+ view.setYpos(position.y);
+
+ view.setWidth(size.width);
+ view.setHeight(size.height);
+
+ view.setStartRes(vpRanges.getStartRes());
+ view.setStartSeq(vpRanges.getStartSeq());
+
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
+ userColours, object));
+ }
+ else if (av
+ .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ AnnotationColourScheme ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, object);
+
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
+ else
+ {
+ view.setBgColour(ColourSchemeProperty
+ .getColourName(av.getGlobalColourScheme()));
+ }
+
+ ResidueShaderI vcs = av.getResidueShading();
+ ColourSchemeI cs = av.getGlobalColourScheme();
+
+ if (cs != null)
+ {
+ if (vcs.conservationApplied())
+ {
+ view.setConsThreshold(vcs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(setUserColourScheme(cs, userColours, object));
+ }
+ }
+ view.setPidThreshold(vcs.getThreshold());
+ }
+
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ final Font font = av.getFont();
+ view.setFontName(font.getName());
+ view.setFontSize(font.getSize());
+ view.setFontStyle(font.getStyle());
+ view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
+ view.setRenderGaps(av.isRenderGaps());
+ view.setShowAnnotation(av.isShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.isRightAlignIds());
+ view.setShowSequenceFeatures(av.isShowSequenceFeatures());
+ view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.getTextColour().getRGB());
+ view.setTextCol2(av.getTextColour2().getRGB());
+ view.setTextColThreshold(av.getThresholdTextColour());
+ view.setShowConsensusHistogram(av.isShowConsensusHistogram());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
+ view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
+ view.setShowGroupConsensus(av.isShowGroupConsensus());
+ view.setShowGroupConservation(av.isShowGroupConservation());
+ view.setShowNPfeatureTooltip(av.isShowNPFeats());
+ view.setShowDbRefTooltip(av.isShowDBRefs());
+ 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();
+
+ FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer();
+ String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
+
+ Vector<String> settingsAdded = new Vector<>();
+ if (renderOrder != null)
+ {
+ for (String featureType : renderOrder)
+ {
+ FeatureSettings.Setting setting = new FeatureSettings.Setting();
+ setting.setType(featureType);
+
+ /*
+ * save any filter for the feature type
+ */
+ FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
+ if (filter != null) {
+ Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
+ FeatureMatcherI firstFilter = filters.next();
+ setting.setMatcherSet(Jalview2XML.marshalFilter(
+ firstFilter, filters, filter.isAnded()));
+ }
+
+ /*
+ * save colour scheme for the feature type
+ */
+ FeatureColourI fcol = fr.getFeatureStyle(featureType);
+ if (!fcol.isSimpleColour())
+ {
+ setting.setColour(fcol.getMaxColour().getRGB());
+ setting.setMincolour(fcol.getMinColour().getRGB());
+ setting.setMin(fcol.getMin());
+ setting.setMax(fcol.getMax());
+ setting.setColourByLabel(fcol.isColourByLabel());
+ if (fcol.isColourByAttribute())
+ {
+ String[] attName = fcol.getAttributeName();
+ setting.getAttributeName().add(attName[0]);
+ if (attName.length > 1)
+ {
+ setting.getAttributeName().add(attName[1]);
+ }
+ }
+ setting.setAutoScale(fcol.isAutoScaled());
+ setting.setThreshold(fcol.getThreshold());
+ Color noColour = fcol.getNoColour();
+ if (noColour == null)
+ {
+ setting.setNoValueColour(NoValueColour.NONE);
+ }
+ else if (noColour.equals(fcol.getMaxColour()))
+ {
+ setting.setNoValueColour(NoValueColour.MAX);
+ }
+ else
+ {
+ setting.setNoValueColour(NoValueColour.MIN);
+ }
+ // -1 = No threshold, 0 = Below, 1 = Above
+ setting.setThreshstate(fcol.isAboveThreshold() ? 1
+ : (fcol.isBelowThreshold() ? 0 : -1));
+ }
+ else
+ {
+ setting.setColour(fcol.getColour().getRGB());
+ }
+
+ setting.setDisplay(
+ av.getFeaturesDisplayed().isVisible(featureType));
+ float rorder = fr
+ .getOrder(featureType);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ /// fs.addSetting(setting);
+ fs.getSetting().add(setting);
+ settingsAdded.addElement(featureType);
+ }
+ }
+
+ // is groups actually supposed to be a map here ?
+ Iterator<String> en = fr.getFeatureGroups().iterator();
+ Vector<String> groupsAdded = new Vector<>();
+ while (en.hasNext())
+ {
+ String grp = en.next();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
+ .booleanValue());
+ // fs.addGroup(g);
+ fs.getGroup().add(g);
+ groupsAdded.addElement(grp);
+ }
+ // jms.setFeatureSettings(fs);
+ object.setFeatureSettings(fs);
+ }
+
+ if (av.hasHiddenColumns())
+ {
+ jalview.datamodel.HiddenColumns hidden = av.getAlignment()
+ .getHiddenColumns();
+ if (hidden == null)
+ {
+ Console.warn(
+ "REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ }
+ else
+ {
+ Iterator<int[]> hiddenRegions = hidden.iterator();
+ while (hiddenRegions.hasNext())
+ {
+ int[] region = hiddenRegions.next();
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ // view.addHiddenColumns(hc);
+ view.getHiddenColumns().add(hc);
+ }
+ }
+ }
+ if (calcIdSet.size() > 0)
+ {
+ for (String calcId : calcIdSet)
+ {
+ if (calcId.trim().length() > 0)
+ {
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ // view.addCalcIdParam(cidp);
+ view.getCalcIdParam().add(cidp);
+ }
+ }
+ }
+ }
+
+ // jms.addViewport(view);
+ object.getViewport().add(view);
+ }
+ // object.setJalviewModelSequence(jms);
+ // object.getVamsasModel().addSequenceSet(vamsasSet);
+ object.getVamsasModel().getSequenceSet().add(vamsasSet);
+
+ if (jout != null && fileName != null)
+ {
+ // We may not want to write the object to disk,
+ // eg we can copy the alignViewport to a new view object
+ // using save and then load
+ try
+ {
+ fileName = fileName.replace('\\', '/');
+ System.out.println("Writing jar entry " + fileName);
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
+ PrintWriter pout = new PrintWriter(
+ new OutputStreamWriter(jout, UTF_8));
+ JAXBContext jaxbContext = JAXBContext
+ .newInstance(JalviewModel.class);
+ Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
+
+ // output pretty printed
+ // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
+ jaxbMarshaller.marshal(
+ new ObjectFactory().createJalviewModel(object), pout);
+
+ // jaxbMarshaller.marshal(object, pout);
+ // marshaller.marshal(object);
+ pout.flush();
+ jout.closeEntry();
+ } catch (Exception ex)
+ {
+ // TODO: raise error in GUI if marshalling failed.
+ System.err.println("Error writing Jalview project");
+ ex.printStackTrace();
+ }
+ }
+ return object;
+ }
+ /**
+ * Saves the HMMER profile associated with the sequence as a file in the jar,
+ * in HMMER format, and saves the name of the file as a child element of the
+ * XML sequence element
+ *
+ * @param jout
+ * @param xmlSeq
+ * @param seq
+ */
+ protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
+ SequenceI seq)
+ {
+ HiddenMarkovModel profile = seq.getHMM();
+ if (profile == null)
+ {
+ Console.warn("Want to save HMM profile for " + seq.getName()
+ + " but none found");
+ return;
+ }
+ HMMFile hmmFile = new HMMFile(profile);
+ String hmmAsString = hmmFile.print();
+ String jarEntryName = HMMER_PREFIX + nextCounter();
+ try
+ {
+ writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
+ xmlSeq.setHmmerProfile(jarEntryName);
+ } catch (IOException e)
+ {
+ Console.warn("Error saving HMM profile: " + e.getMessage());
+ }
+ }
- @Override
- boolean resolve()
- {
- SequenceI seq = getSrefDatasetSeq();
- if (seq == null)
- {
- return false;
- }
- jmap.setTo(seq);
- return true;
- }
- };
- return fref;
- }
+
+ /**
+ * Writes PCA viewer attributes and computed values to an XML model object and
+ * adds it to the JalviewModel. Any exceptions are reported by logging.
+ */
+ protected void savePCA(PCAPanel panel, JalviewModel object)
+ {
+ try
+ {
+ PcaViewer viewer = new PcaViewer();
+ viewer.setHeight(panel.getHeight());
+ viewer.setWidth(panel.getWidth());
+ viewer.setXpos(panel.getX());
+ viewer.setYpos(panel.getY());
+ viewer.setTitle(panel.getTitle());
+ PCAModel pcaModel = panel.getPcaModel();
+ viewer.setScoreModelName(pcaModel.getScoreModelName());
+ viewer.setXDim(panel.getSelectedDimensionIndex(X));
+ viewer.setYDim(panel.getSelectedDimensionIndex(Y));
+ viewer.setZDim(panel.getSelectedDimensionIndex(Z));
+ viewer.setBgColour(
+ panel.getRotatableCanvas().getBackgroundColour().getRGB());
+ viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
+ float[] spMin = panel.getRotatableCanvas().getSeqMin();
+ SeqPointMin spmin = new SeqPointMin();
+ spmin.setXPos(spMin[0]);
+ spmin.setYPos(spMin[1]);
+ spmin.setZPos(spMin[2]);
+ viewer.setSeqPointMin(spmin);
+ float[] spMax = panel.getRotatableCanvas().getSeqMax();
+ SeqPointMax spmax = new SeqPointMax();
+ spmax.setXPos(spMax[0]);
+ spmax.setYPos(spMax[1]);
+ spmax.setZPos(spMax[2]);
+ viewer.setSeqPointMax(spmax);
+ viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
+ viewer.setLinkToAllViews(
+ panel.getRotatableCanvas().isApplyToAllViews());
+ SimilarityParamsI sp = pcaModel.getSimilarityParameters();
+ viewer.setIncludeGaps(sp.includeGaps());
+ viewer.setMatchGaps(sp.matchGaps());
+ viewer.setIncludeGappedColumns(sp.includeGappedColumns());
+ viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
+
+ /*
+ * sequence points on display
+ */
+ for (jalview.datamodel.SequencePoint spt : pcaModel
+ .getSequencePoints())
+ {
+ SequencePoint point = new SequencePoint();
+ point.setSequenceRef(seqHash(spt.getSequence()));
+ point.setXPos(spt.coord.x);
+ point.setYPos(spt.coord.y);
+ point.setZPos(spt.coord.z);
+ viewer.getSequencePoint().add(point);
+ }
+
+ /*
+ * (end points of) axes on display
+ */
+ for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
+ {
+
+ Axis axis = new Axis();
+ axis.setXPos(p.x);
+ axis.setYPos(p.y);
+ axis.setZPos(p.z);
+ viewer.getAxis().add(axis);
+ }
+
+ /*
+ * raw PCA data (note we are not restoring PCA inputs here -
+ * alignment view, score model, similarity parameters)
+ */
+ PcaDataType data = new PcaDataType();
+ viewer.setPcaData(data);
+ PCA pca = pcaModel.getPcaData();
+
+ DoubleMatrix pm = new DoubleMatrix();
+ saveDoubleMatrix(pca.getPairwiseScores(), pm);
+ data.setPairwiseMatrix(pm);
+
+ DoubleMatrix tm = new DoubleMatrix();
+ saveDoubleMatrix(pca.getTridiagonal(), tm);
+ data.setTridiagonalMatrix(tm);
+
+ DoubleMatrix eigenMatrix = new DoubleMatrix();
+ data.setEigenMatrix(eigenMatrix);
+ saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
+
+ object.getPcaViewer().add(viewer);
+ } catch (Throwable t)
+ {
+ Console.error("Error saving PCA: " + t.getMessage());
+ }
+ }
- protected SeqFref newAlcodMapRef(final String sref,
- final AlignedCodonFrame _cf,
- final jalview.datamodel.Mapping _jmap)
- {
+ /**
+ * Stores values from a matrix into an XML element, including (if present) the
+ * D or E vectors
+ *
+ * @param m
+ * @param xmlMatrix
+ * @see #loadDoubleMatrix(DoubleMatrix)
+ */
+ protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
+ {
+ xmlMatrix.setRows(m.height());
+ xmlMatrix.setColumns(m.width());
+ for (int i = 0; i < m.height(); i++)
+ {
+ DoubleVector row = new DoubleVector();
+ for (int j = 0; j < m.width(); j++)
+ {
+ row.getV().add(m.getValue(i, j));
+ }
+ xmlMatrix.getRow().add(row);
+ }
+ if (m.getD() != null)
+ {
+ DoubleVector dVector = new DoubleVector();
+ for (double d : m.getD())
+ {
+ dVector.getV().add(d);
+ }
+ xmlMatrix.setD(dVector);
+ }
+ if (m.getE() != null)
+ {
+ DoubleVector eVector = new DoubleVector();
+ for (double e : m.getE())
+ {
+ eVector.getV().add(e);
+ }
+ xmlMatrix.setE(eVector);
+ }
+ }
- SeqFref fref = new SeqFref(sref, "Codon Frame")
- {
- AlignedCodonFrame cf = _cf;
+ /**
+ * Loads XML matrix data into a new Matrix object, including the D and/or E
+ * vectors (if present)
+ *
+ * @param mData
+ * @return
+ * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
+ */
+ protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
+ {
+ int rows = mData.getRows();
+ double[][] vals = new double[rows][];
+
+ for (int i = 0; i < rows; i++)
+ {
+ List<Double> dVector = mData.getRow().get(i).getV();
+ vals[i] = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vals[i][dvi++] = d;
+ }
+ }
+
+ MatrixI m = new Matrix(vals);
+
+ if (mData.getD() != null)
+ {
+ List<Double> dVector = mData.getD().getV();
+ double[] vec = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vec[dvi++] = d;
+ }
+ m.setD(vec);
+ }
+ if (mData.getE() != null)
+ {
+ List<Double> dVector = mData.getE().getV();
+ double[] vec = new double[dVector.size()];
+ int dvi = 0;
+ for (Double d : dVector)
+ {
+ vec[dvi++] = d;
+ }
+ m.setE(vec);
+ }
+
+ return m;
+ }
- public jalview.datamodel.Mapping mp = _jmap;
+ /**
+ * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
+ * for each viewer, with
+ * <ul>
+ * <li>viewer geometry (position, size, split pane divider location)</li>
+ * <li>index of the selected structure in the viewer (currently shows gapped
+ * or ungapped)</li>
+ * <li>the id of the annotation holding RNA secondary structure</li>
+ * <li>(currently only one SS is shown per viewer, may be more in future)</li>
+ * </ul>
+ * Varna viewer state is also written out (in native Varna XML) to separate
+ * project jar entries. A separate entry is written for each RNA structure
+ * displayed, with the naming convention
+ * <ul>
+ * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
+ * </ul>
+ *
+ * @param jout
+ * @param jseq
+ * @param jds
+ * @param viewIds
+ * @param ap
+ * @param storeDataset
+ */
+ protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
+ final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
+ boolean storeDataset)
+ {
+ if (Desktop.getDesktopPane() == null)
+ {
+ return;
+ }
+ JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof AppVarna)
+ {
+ AppVarna varna = (AppVarna) frames[f];
+ /*
+ * link the sequence to every viewer that is showing it and is linked to
+ * its alignment panel
+ */
+ if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
+ {
+ String viewId = varna.getViewId();
+ RnaViewer rna = new RnaViewer();
+ rna.setViewId(viewId);
+ rna.setTitle(varna.getTitle());
+ rna.setXpos(varna.getX());
+ rna.setYpos(varna.getY());
+ rna.setWidth(varna.getWidth());
+ rna.setHeight(varna.getHeight());
+ rna.setDividerLocation(varna.getDividerLocation());
+ rna.setSelectedRna(varna.getSelectedIndex());
+ // jseq.addRnaViewer(rna);
+ jseq.getRnaViewer().add(rna);
+
+ /*
+ * Store each Varna panel's state once in the project per sequence.
+ * First time through only (storeDataset==false)
+ */
+ // boolean storeSessions = false;
+ // String sequenceViewId = viewId + seqsToIds.get(jds);
+ // if (!storeDataset && !viewIds.contains(sequenceViewId))
+ // {
+ // viewIds.add(sequenceViewId);
+ // storeSessions = true;
+ // }
+ for (RnaModel model : varna.getModels())
+ {
+ if (model.seq == jds)
+ {
+ /*
+ * VARNA saves each view (sequence or alignment secondary
+ * structure, gapped or trimmed) as a separate XML file
+ */
+ String jarEntryName = rnaSessions.get(model);
+ if (jarEntryName == null)
+ {
+
+ String varnaStateFile = varna.getStateInfo(model.rna);
+ jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
+ copyFileToJar(jout, varnaStateFile, jarEntryName, "Varna");
+ rnaSessions.put(model, jarEntryName);
+ }
+ SecondaryStructure ss = new SecondaryStructure();
+ String annotationId = varna.getAnnotation(jds).annotationId;
+ ss.setAnnotationId(annotationId);
+ ss.setViewerState(jarEntryName);
+ ss.setGapped(model.gapped);
+ ss.setTitle(model.title);
+ // rna.addSecondaryStructure(ss);
+ rna.getSecondaryStructure().add(ss);
+ }
+ }
+ }
+ }
+ }
+ }
- @Override
- public boolean isResolvable()
- {
- return super.isResolvable() && mp.getTo() != null;
- }
+ /**
+ * Copy the contents of a file to a new entry added to the output jar
+ *
+ * @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 msg)
+ {
+ try (InputStream is = new FileInputStream(infilePath))
+ {
+ File file = new File(infilePath);
+ if (file.exists() && jout != null)
+ {
+ 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();
+ }
+ }
- @Override
- boolean resolve()
- {
- SequenceI seq = getSrefDatasetSeq();
- if (seq == null)
- {
- return false;
- }
- cf.addMap(seq, mp.getTo(), mp.getMap());
- return true;
- }
- };
- return fref;
- }
- protected void resolveFrefedSequences()
- {
- Iterator<SeqFref> nextFref = frefedSequence.iterator();
- int toresolve = frefedSequence.size();
- int unresolved = 0, failedtoresolve = 0;
- while (nextFref.hasNext())
- {
- SeqFref ref = nextFref.next();
- if (ref.isResolvable())
- {
- try
- {
- if (ref.resolve())
- {
- nextFref.remove();
- }
- else
- {
- failedtoresolve++;
- }
- } catch (Exception x)
- {
- System.err.println(
- "IMPLEMENTATION ERROR: Failed to resolve forward reference for sequence "
- + ref.getSref());
- x.printStackTrace();
- failedtoresolve++;
- }
- }
- else
- {
- unresolved++;
- }
- }
- if (unresolved > 0)
- {
- System.err.println("Jalview Project Import: There were " + unresolved
- + " forward references left unresolved on the stack.");
- }
- if (failedtoresolve > 0)
+ /**
+ * Write the data to a new entry of given name in the output jar file
+ *
+ * @param jout
+ * @param jarEntryName
+ * @param data
+ * @throws IOException
+ */
+ protected void writeJarEntry(JarOutputStream jout, String jarEntryName,
+ byte[] data) throws IOException
{
- System.err.println("SERIOUS! " + failedtoresolve
- + " resolvable forward references failed to resolve.");
+ if (jout != null)
+ {
+ jarEntryName = jarEntryName.replace('\\','/');
+ 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();
+ }
}
- if (incompleteSeqs != null && incompleteSeqs.size() > 0)
+
+ /**
+ * 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
{
- System.err.println(
- "Jalview Project Import: There are " + incompleteSeqs.size()
- + " sequences which may have incomplete metadata.");
- if (incompleteSeqs.size() < 10)
- {
- for (SequenceI s : incompleteSeqs.values())
- {
- System.err.println(s.toString());
- }
- }
- else
- {
- System.err.println(
- "Too many to report. Skipping output of incomplete sequences.");
- }
+ byte[] buffer = new byte[4096];
+ int bytesRead = 0;
+ while ((bytesRead = in.read(buffer)) != -1)
+ {
+ out.write(buffer, 0, bytesRead);
+ }
}
- }
- /**
- * This maintains a map of viewports, the key being the seqSetId. Important to
- * set historyItem and redoList for multiple views
- */
- Map<String, AlignViewport> viewportsAdded = new HashMap<>();
-
- Map<String, AlignmentAnnotation> annotationIds = new HashMap<>();
+ /**
+ * Save the state of a structure viewer
+ *
+ * @param ap
+ * @param jds
+ * @param pdb
+ * the archive XML element under which to save the state
+ * @param entry
+ * @param viewIds
+ * @param matchedFile
+ * @param viewFrame
+ * @return
+ */
+ protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
+ Pdbids pdb, PDBEntry entry, List<String> viewIds,
+ String matchedFile, StructureViewerBase viewFrame)
+ {
+ final AAStructureBindingModel bindingModel = viewFrame.getBinding();
+
+ /*
+ * Look for any bindings for this viewer to the PDB file of interest
+ * (including part matches excluding chain id)
+ */
+ for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
+ {
+ final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
+ final String pdbId = pdbentry.getId();
+ if (!pdbId.equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
+ .startsWith(pdbId.toLowerCase(Locale.ROOT))))
+ {
+ /*
+ * not interested in a binding to a different PDB entry here
+ */
+ continue;
+ }
+ if (matchedFile == null)
+ {
+ matchedFile = pdbentry.getFile();
+ }
+ else if (!matchedFile.equals(pdbentry.getFile()))
+ {
+ Console.warn(
+ "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + pdbentry.getFile());
+ }
+ // record the
+ // file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
+
+ for (int smap = 0; smap < viewFrame.getBinding()
+ .getSequence()[peid].length; smap++)
+ {
+ // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ if (jds == viewFrame.getBinding().getSequence()[peid][smap])
+ {
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(viewFrame.getX());
+ state.setYpos(viewFrame.getY());
+ state.setWidth(viewFrame.getWidth());
+ state.setHeight(viewFrame.getHeight());
+ final String viewId = viewFrame.getViewId();
+ state.setViewId(viewId);
+ state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
+ state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
+ state.setColourByJmol(viewFrame.isColouredByViewer());
+ state.setType(viewFrame.getViewerType().toString());
+ // pdb.addStructureState(state);
+ pdb.getStructureState().add(state);
+ }
+ }
+ }
+ return matchedFile;
+ }
- String uniqueSetSuffix = "";
+ /**
+ * Populates the AnnotationColourScheme xml for save. This captures the
+ * settings of the options in the 'Colour by Annotation' dialog.
+ *
+ * @param acg
+ * @param userColours
+ * @param jm
+ * @return
+ */
+ private AnnotationColourScheme constructAnnotationColours(
+ AnnotationColourGradient acg, List<UserColourScheme> userColours,
+ JalviewModel jm)
+ {
+ AnnotationColourScheme ac = new AnnotationColourScheme();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ // 2.10.2 save annotationId (unique) not annotation label
+ ac.setAnnotation(acg.getAnnotation().annotationId);
+ if (acg.getBaseColour() instanceof UserColourScheme)
+ {
+ ac.setColourScheme(
+ setUserColourScheme(acg.getBaseColour(), userColours, jm));
+ }
+ else
+ {
+ ac.setColourScheme(
+ ColourSchemeProperty.getColourName(acg.getBaseColour()));
+ }
+
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ ac.setPerSequence(acg.isSeqAssociated());
+ ac.setPredefinedColours(acg.isPredefinedColours());
+ return ac;
+ }
+
+ private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
+ IdentityHashMap<SequenceGroup, String> groupRefs,
+ AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
+ SequenceSet vamsasSet)
+ {
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
+
+ AlignmentAnnotation annotation = aa[i];
+ if (annotation.annotationId != null)
+ {
+ annotationIds.put(annotation.annotationId, annotation);
+ }
+
+ an.setId(annotation.annotationId);
+
+ an.setVisible(annotation.visible);
+
+ an.setDescription(annotation.description);
+
+ if (annotation.sequenceRef != null)
+ {
+ // 2.9 JAL-1781 xref on sequence id rather than name
+ an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
+ }
+ if (annotation.groupRef != null)
+ {
+ String groupIdr = groupRefs.get(annotation.groupRef);
+ if (groupIdr == null)
+ {
+ // make a locally unique String
+ groupRefs.put(annotation.groupRef,
+ groupIdr = ("" + System.currentTimeMillis()
+ + annotation.groupRef.getName()
+ + groupRefs.size()));
+ }
+ an.setGroupRef(groupIdr.toString());
+ }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(annotation.graphHeight);
+ an.setCentreColLabels(annotation.centreColLabels);
+ an.setScaleColLabels(annotation.scaleColLabel);
+ an.setShowAllColLabels(annotation.showAllColLabels);
+ an.setBelowAlignment(annotation.belowAlignment);
+
+ if (annotation.graph > 0)
+ {
+ an.setGraph(true);
+ an.setGraphType(annotation.graph);
+ an.setGraphGroup(annotation.graphGroup);
+ if (annotation.getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(annotation.getThreshold().label);
+ line.setValue(annotation.getThreshold().value);
+ line.setColour(annotation.getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
+
+ an.setLabel(annotation.label);
+
+ if (annotation == av.getAlignmentQualityAnnot()
+ || annotation == av.getAlignmentConservationAnnotation()
+ || annotation == av.getAlignmentConsensusAnnotation()
+ || annotation.autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(annotation.autoCalculated);
+ }
+ if (annotation.hasScore())
+ {
+ an.setScore(annotation.getScore());
+ }
+
+ if (annotation.getCalcId() != null)
+ {
+ calcIdSet.add(annotation.getCalcId());
+ an.setCalcId(annotation.getCalcId());
+ }
+ if (annotation.hasProperties())
+ {
+ for (String pr : annotation.getProperties())
+ {
+ jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
+ prop.setName(pr);
+ prop.setValue(annotation.getProperty(pr));
+ // an.addProperty(prop);
+ an.getProperty().add(prop);
+ }
+ }
+
+ AnnotationElement ae;
+ if (annotation.annotations != null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < annotation.annotations.length; a++)
+ {
+ if ((annotation == null) || (annotation.annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ if (annotation.annotations[a].description != null)
+ {
+ ae.setDescription(annotation.annotations[a].description);
+ }
+ if (annotation.annotations[a].displayCharacter != null)
+ {
+ ae.setDisplayCharacter(
+ annotation.annotations[a].displayCharacter);
+ }
+
+ if (!Float.isNaN(annotation.annotations[a].value))
+ {
+ ae.setValue(annotation.annotations[a].value);
+ }
+
+ ae.setPosition(a);
+ if (annotation.annotations[a].secondaryStructure > ' ')
+ {
+ ae.setSecondaryStructure(
+ annotation.annotations[a].secondaryStructure + "");
+ }
+
+ if (annotation.annotations[a].colour != null
+ && annotation.annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(annotation.annotations[a].colour.getRGB());
+ }
+
+ // an.addAnnotationElement(ae);
+ an.getAnnotationElement().add(ae);
+ if (annotation.autoCalculated)
+ {
+ // only write one non-null entry into the annotation row -
+ // sufficient to get the visualization attributes necessary to
+ // display data
+ continue;
+ }
+ }
+ }
+ else
+ {
+ an.setScoreOnly(true);
+ }
+ if (!storeDS || (storeDS && !annotation.autoCalculated))
+ {
+ // skip autocalculated annotation - these are only provided for
+ // alignments
+ // vamsasSet.addAnnotation(an);
+ vamsasSet.getAnnotation().add(an);
+ }
+ }
+
+ }
+
+ private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
+ {
+ AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
+ if (settings != null)
+ {
+ CalcIdParam vCalcIdParam = new CalcIdParam();
+ vCalcIdParam.setCalcId(calcId);
+ // vCalcIdParam.addServiceURL(settings.getServiceURI());
+ vCalcIdParam.getServiceURL().add(settings.getServiceURI());
+ // generic URI allowing a third party to resolve another instance of the
+ // service used for this calculation
+ for (String url : settings.getServiceURLs())
+ {
+ // vCalcIdParam.addServiceURL(urls);
+ vCalcIdParam.getServiceURL().add(url);
+ }
+ vCalcIdParam.setVersion("1.0");
+ if (settings.getPreset() != null)
+ {
+ WsParamSetI setting = settings.getPreset();
+ vCalcIdParam.setName(setting.getName());
+ vCalcIdParam.setDescription(setting.getDescription());
+ }
+ else
+ {
+ vCalcIdParam.setName("");
+ vCalcIdParam.setDescription("Last used parameters");
+ }
+ // need to be able to recover 1) settings 2) user-defined presets or
+ // recreate settings from preset 3) predefined settings provided by
+ // service - or settings that can be transferred (or discarded)
+ vCalcIdParam.setParameters(
+ settings.getWsParamFile().replace("\n", "|\\n|"));
+ vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
+ // todo - decide if updateImmediately is needed for any projects.
+
+ return vCalcIdParam;
+ }
+ return null;
+ }
+
+ private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
+ AlignViewport av)
+ {
+ if (calcIdParam.getVersion().equals("1.0"))
+ {
+ final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
+ ServiceWithParameters service = PreferredServiceRegistry.getRegistry()
+ .getPreferredServiceFor(calcIds);
+ if (service != null)
+ {
+ WsParamSetI parmSet = null;
+ try
+ {
+ parmSet = service.getParamStore().parseServiceParameterFile(
+ calcIdParam.getName(), calcIdParam.getDescription(),
+ calcIds,
+ calcIdParam.getParameters().replace("|\\n|", "\n"));
+ } catch (IOException x)
+ {
+ Console.warn("Couldn't parse parameter data for "
+ + calcIdParam.getCalcId(), x);
+ return false;
+ }
+ List<ArgumentI> argList = null;
+ if (calcIdParam.getName().length() > 0)
+ {
+ parmSet = service.getParamStore()
+ .getPreset(calcIdParam.getName());
+ if (parmSet != null)
+ {
+ // TODO : check we have a good match with settings in AACon -
+ // otherwise we'll need to create a new preset
+ }
+ }
+ else
+ {
+ argList = parmSet.getArguments();
+ parmSet = null;
+ }
+ AutoCalcSetting settings = new AAConSettings(
+ calcIdParam.isAutoUpdate(), service, parmSet, argList);
+ av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
+ calcIdParam.isNeedsUpdate());
+ return true;
+ }
+ else
+ {
+ Console.warn(
+ "Cannot resolve a service for the parameters used in this project. Try configuring a JABAWS server.");
+ return false;
+ }
+ }
+ throw new Error(MessageManager.formatMessage(
+ "error.unsupported_version_calcIdparam", new Object[]
+ { calcIdParam.toString() }));
+ }
- /**
- * List of pdbfiles added to Jar
- */
- List<String> pdbfiles = null;
+ /**
+ * External mapping between jalview objects and objects yielding a valid and
+ * unique object ID string. This is null for normal Jalview project IO, but
+ * non-null when a jalview project is being read or written as part of a
+ * vamsas session.
+ */
+ IdentityHashMap jv2vobj = null;
- // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
- public void saveState(File statefile)
- {
- FileOutputStream fos = null;
+ /**
+ * Construct a unique ID for jvobj using either existing bindings or if none
+ * exist, the result of the hashcode call for the object.
+ *
+ * @param jvobj
+ * jalview data object
+ * @return unique ID for referring to jvobj
+ */
+ private String makeHashCode(Object jvobj, String altCode)
+ {
+ if (jv2vobj != null)
+ {
+ Object id = jv2vobj.get(jvobj);
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // check string ID mappings
+ if (jvids2vobj != null && jvobj instanceof String)
+ {
+ id = jvids2vobj.get(jvobj);
+ }
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // give up and warn that something has gone wrong
+ Console.warn(
+ "Cannot find ID for object in external mapping : " + jvobj);
+ }
+ return altCode;
+ }
- try
+ /**
+ * return local jalview object mapped to ID, if it exists
+ *
+ * @param idcode
+ * (may be null)
+ * @return null or object bound to idcode
+ */
+ private Object retrieveExistingObj(String idcode)
{
+ if (idcode != null && vobj2jv != null)
+ {
+ return vobj2jv.get(idcode);
+ }
+ return null;
+ }
- fos = new FileOutputStream(statefile);
+ /**
+ * binding from ID strings from external mapping table to jalview data model
+ * objects.
+ */
+ private Hashtable vobj2jv;
+
+ private Sequence createVamsasSequence(String id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, String id,
+ SequenceI jds, SequenceI parentseq)
+ {
+ Sequence vamsasSeq = new Sequence();
+ vamsasSeq.setId(id);
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+ List<DBRefEntry> dbrefs = null;
+ if (jds.getDatasetSequence() != null)
+ {
+ vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
+ }
+ else
+ {
+ // seqId==dsseqid so we can tell which sequences really are
+ // dataset sequences only
+ vamsasSeq.setDsseqid(id);
+ dbrefs = jds.getDBRefs();
+ if (parentseq == null)
+ {
+ parentseq = jds;
+ }
+ }
+
+ /*
+ * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
+ */
+ if (dbrefs != null)
+ {
+ for (int d = 0, nd = dbrefs.size(); d < nd; d++)
+ {
+ DBRef dbref = new DBRef();
+ DBRefEntry ref = dbrefs.get(d);
+ dbref.setSource(ref.getSource());
+ dbref.setVersion(ref.getVersion());
+ dbref.setAccessionId(ref.getAccessionId());
+ dbref.setCanonical(ref.isCanonical());
+ if (ref instanceof GeneLocus)
+ {
+ dbref.setLocus(true);
+ }
+ if (ref.hasMap())
+ {
+ Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
+ jds, recurse);
+ dbref.setMapping(mp);
+ }
+ vamsasSeq.getDBRef().add(dbref);
+ }
+ }
+ return vamsasSeq;
+ }
+
+ private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+ SequenceI parentseq, SequenceI jds, boolean recurse)
+ {
+ Mapping mp = null;
+ if (jmp.getMap() != null)
+ {
+ mp = new Mapping();
+
+ jalview.util.MapList mlst = jmp.getMap();
+ List<int[]> r = mlst.getFromRanges();
+ for (int[] range : r)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(range[0]);
+ mfrom.setEnd(range[1]);
+ // mp.addMapListFrom(mfrom);
+ mp.getMapListFrom().add(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int[] range : r)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(range[0]);
+ mto.setEnd(range[1]);
+ // mp.addMapListTo(mto);
+ mp.getMapListTo().add(mto);
+ }
+ mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
+ mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
+ if (jmp.getTo() != null)
+ {
+ // MappingChoice mpc = new MappingChoice();
+
+ // check/create ID for the sequence referenced by getTo()
+
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
+ }
+ else
+ {
+ jmpid = seqHash(ps = parentseq);
+ }
+ // mpc.setDseqFor(jmpid);
+ mp.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(jmpid))
+ {
+ Console.debug("creatign new DseqFor ID");
+ seqRefIds.put(jmpid, ps);
+ }
+ else
+ {
+ Console.debug("reusing DseqFor ID");
+ }
+
+ // mp.setMappingChoice(mpc);
+ }
+ }
+ return mp;
+ }
+
+ String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ List<UserColourScheme> userColours, JalviewModel jm)
+ {
+ String id = null;
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+ boolean newucs = false;
+ if (!userColours.contains(ucs))
+ {
+ userColours.add(ucs);
+ newucs = true;
+ }
+ id = "ucs" + userColours.indexOf(ucs);
+ if (newucs)
+ {
+ // actually create the scheme's entry in the XML model
+ java.awt.Color[] colours = ucs.getColours();
+ UserColours uc = new UserColours();
+ // UserColourScheme jbucs = new UserColourScheme();
+ JalviewUserColours jbucs = new JalviewUserColours();
+
+ for (int i = 0; i < colours.length; i++)
+ {
+ Colour col = new Colour();
+ col.setName(ResidueProperties.aa[i]);
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ // jbucs.addColour(col);
+ jbucs.getColour().add(col);
+ }
+ if (ucs.getLowerCaseColours() != null)
+ {
+ colours = ucs.getLowerCaseColours();
+ for (int i = 0; i < colours.length; i++)
+ {
+ Colour col = new Colour();
+ col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ // jbucs.addColour(col);
+ jbucs.getColour().add(col);
+ }
+ }
+
+ uc.setId(id);
+ uc.setUserColourScheme(jbucs);
+ // jm.addUserColours(uc);
+ jm.getUserColours().add(uc);
+ }
+
+ return id;
+ }
+
+ jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
+ String id)
+ {
+ List<UserColours> uc = jm.getUserColours();
+ UserColours colours = null;
+ /*
+ for (int i = 0; i < uc.length; i++)
+ {
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
+ break;
+ }
+ }
+ */
+ for (UserColours c : uc)
+ {
+ if (c.getId().equals(id))
+ {
+ colours = c;
+ break;
+ }
+ }
+
+ java.awt.Color[] newColours = new java.awt.Color[24];
+
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ // colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ colours.getUserColourScheme().getColour().get(i).getRGB(),
+ 16));
+ }
+
+ jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
+ newColours);
+
+ if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
+ {
+ newColours = new java.awt.Color[23];
+ for (int i = 0; i < 23; i++)
+ {
+ newColours[i] = new java.awt.Color(
+ Integer.parseInt(colours.getUserColourScheme().getColour()
+ .get(i + 24).getRGB(), 16));
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
+
+ return ucs;
+ }
- JarOutputStream jout = new JarOutputStream(fos);
- saveState(jout);
- fos.close();
+ /**
+ * Load a jalview project archive from a jar file
+ *
+ * @param file
+ * - HTTP URL or filename
+ */
+ public AlignFrame loadJalviewAlign(final Object file)
+ {
+
+ jalview.gui.AlignFrame af = null;
+
+ try
+ {
+ // create list to store references for any new Jmol viewers created
+ newStructureViewers = new Vector<>();
+ // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ // Workaround is to make sure caller implements the JarInputStreamProvider
+ // interface
+ // so we can re-open the jar input stream for each entry.
+
+ jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
+ af = loadJalviewAlign(jprovider);
+ if (af != null)
+ {
+ af.setMenusForViewport();
+ }
+ } catch (MalformedURLException e)
+ {
+ errorMessage = "Invalid URL format for '" + file + "'";
+ reportErrors();
+ } finally
+ {
+ try
+ {
+ // was invokeAndWait
+
+ // BH 2019 -- can't wait
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ setLoadingFinishedForNewStructureViewers();
+ }
+ });
+ } catch (Exception x)
+ {
+ System.err.println("Error loading alignment: " + x.getMessage());
+ }
+ }
+ this.jarFile = null;
+ return af;
+ }
+
+ @SuppressWarnings("unused")
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final Object ofile) throws MalformedURLException
+ {
+
+ try
+ {
+ String file = (ofile instanceof File
+ ? ((File) ofile).getCanonicalPath()
+ : ofile.toString());
+ byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
+ : null;
+ if (bytes != null)
+ {
+ this.jarFile = (File) ofile;
+ }
+ URL url;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded.clear();
+ frefedSequence = null;
+
+ if (HttpUtils.startsWithHttpOrHttps(file))
+ {
+ url = new URL(file);
+ } else {
+ url = null;
+ }
+ return new jarInputStreamProvider()
+ {
+
+ @Override
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
+ : (url != null ? url.openStream()
+ : new FileInputStream(file));
+ return new JarInputStream(is);
+ }
+
+ @Override
+ public File getFile()
+ {
+ return jarFile;
+ }
+
+ @Override
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ } catch (IOException e)
+ {
+ e.printStackTrace();
+ return null;
+ }
+ }
- } 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 = "Did't write Jalview Archive to output file '"
- + statefile + "' - See console error log for details";
- }
- else
- {
- errorMessage += "(Didn't write Jalview Archive to output file '"
- + statefile + ")";
- }
- e.printStackTrace();
- } finally
- {
- if (fos != null)
- {
- try
- {
- fos.close();
- } catch (IOException e)
- {
- // ignore
- }
- }
+ /**
+ * Recover jalview session from a jalview project archive. Caller may
+ * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
+ * themselves. Any null fields will be initialised with default values,
+ * non-null fields are left alone.
+ *
+ * @param jprovider
+ * @return
+ */
+ public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
+ {
+ errorMessage = null;
+ if (uniqueSetSuffix == null)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+ }
+ if (seqRefIds == null)
+ {
+ initSeqRefs();
+ }
+ AlignFrame af = null, _af = null;
+ IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
+ Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
+ String fileName = jprovider.getFilename();
+ File file = jprovider.getFile();
+ List<AlignFrame> alignFrames = new ArrayList<>();
+ try
+ {
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
+
+ // Look for all the entry names ending with ".xml"
+ // This includes all panels and at least one frame.
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ do
+ {
+ jin = jprovider.getJarInputStream();
+ for (int i = 0; i < entryCount; i++)
+ {
+ jarentry = jin.getNextJarEntry();
+ }
+ String name = (jarentry == null ? null : jarentry.getName());
+
+ // System.out.println("Jalview2XML opening " + name);
+ if (name != null && name.endsWith(".xml"))
+ {
+ // DataSet for.... is read last.
+
+
+ // The question here is what to do with the two
+ // .xml files in the jvp file.
+ // Some number of them, "...Dataset for...", will be the
+ // Only AlignPanels and will have Viewport.
+ // One or more will be the source data, with the DBRefs.
+ //
+ // JVP file writing (above) ensures tha the AlignPanels are written
+ // first, then all relevant datasets (which are
+ // Jalview.datamodel.Alignment).
+ //
+
+ // Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
+ JAXBContext jc = JAXBContext
+ .newInstance("jalview.xml.binding.jalview");
+ XMLStreamReader streamReader = XMLInputFactory.newInstance()
+ .createXMLStreamReader(jin);
+ javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
+ JAXBElement<JalviewModel> jbe = um
+ .unmarshal(streamReader, JalviewModel.class);
+ JalviewModel model = jbe.getValue();
+
+ if (true) // !skipViewport(object))
+ {
+ // Q: Do we have to load from the model, even if it
+ // does not have a viewport, could we discover that early on?
+ // Q: Do we need to load this object?
+ _af = loadFromObject(model, fileName, file, true, jprovider);
+ // Platform.timeCheck("Jalview2XML.loadFromObject",
+ // Platform.TIME_MARK);
+
+ if (_af != null)
+ {
+ alignFrames.add(_af);
+ }
+ if (_af != null && model.getViewport().size() > 0)
+ {
+
+ // That is, this is one of the AlignmentPanel models
+ if (af == null)
+ {
+ // store a reference to the first view
+ af = _af;
+ }
+ if (_af.getViewport().isGatherViewsHere())
+ {
+ // if this is a gathered view, keep its reference since
+ // after gathering views, only this frame will remain
+ af = _af;
+ gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
+ _af);
+ }
+ // Save dataset to register mappings once all resolved
+ importedDatasets.put(
+ af.getViewport().getAlignment().getDataset(),
+ af.getViewport().getAlignment().getDataset());
+ }
+ }
+ entryCount++;
+ }
+ else if (jarentry != null)
+ {
+ // Some other file here.
+ entryCount++;
+ }
+ } while (jarentry != null);
+ jin.close();
+ resolveFrefedSequences();
+ } catch (IOException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + fileName;
+ System.err.println(
+ "Exception whilst loading jalview XML file : " + ex + "\n");
+ } catch (Exception ex)
+ {
+ System.err.println("Parsing as Jalview Version 2 file failed.");
+ ex.printStackTrace(System.err);
+ if (attemptversion1parse)
+ {
+ // used to attempt to parse as V1 castor-generated xml
+ }
+ if (Desktop.getInstance() != null)
+ {
+ Desktop.getInstance().stopLoading();
+ }
+ if (af != null)
+ {
+ System.out.println("Successfully loaded archive file");
+ return af;
+ }
+ ex.printStackTrace();
+
+ System.err.println(
+ "Exception whilst loading jalview XML file : " + ex + "\n");
+ } catch (OutOfMemoryError e)
+ {
+ // Don't use the OOM Window here
+ errorMessage = "Out of memory loading jalview XML file";
+ System.err.println("Out of memory whilst loading jalview XML file");
+ e.printStackTrace();
+ } finally
+ {
+ for (AlignFrame alf : alignFrames)
+ {
+ alf.alignPanel.setHoldRepaint(false);
+ }
+ }
+
+ /*
+ * Regather multiple views (with the same sequence set id) to the frame (if
+ * any) that is flagged as the one to gather to, i.e. convert them to tabbed
+ * views instead of separate frames. Note this doesn't restore a state where
+ * some expanded views in turn have tabbed views - the last "first tab" read
+ * in will play the role of gatherer for all.
+ */
+ for (AlignFrame fr : gatherToThisFrame.values())
+ {
+ Desktop.getInstance().gatherViews(fr);
+ }
+
+ restoreSplitFrames();
+ for (AlignmentI ds : importedDatasets.keySet())
+ {
+ if (ds.getCodonFrames() != null)
+ {
+ Desktop.getStructureSelectionManager()
+ .registerMappings(ds.getCodonFrames());
+ }
+ }
+ if (errorMessage != null)
+ {
+ reportErrors();
+ }
+
+ if (Desktop.getInstance() != null)
+ {
+ Desktop.getInstance().stopLoading();
+ }
+
+ return af;
}
- reportErrors();
- }
-
- /**
- * Writes a jalview project archive to the given Jar output stream.
- *
- * @param jout
- */
- public void saveState(JarOutputStream jout)
- {
- AlignFrame[] frames = Desktop.getAlignFrames();
- if (frames == null)
- {
- return;
+ /**
+ * Try to reconstruct and display SplitFrame windows, where each contains
+ * complementary dna and protein alignments. Done by pairing up AlignFrame
+ * objects (created earlier) which have complementary viewport ids associated.
+ */
+ protected void restoreSplitFrames()
+ {
+ List<SplitFrame> gatherTo = new ArrayList<>();
+ List<AlignFrame> addedToSplitFrames = new ArrayList<>();
+ Map<String, AlignFrame> dna = new HashMap<>();
+
+ /*
+ * Identify the DNA alignments
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (af.getViewport().getAlignment().isNucleotide())
+ {
+ dna.put(candidate.getKey().getId(), af);
+ }
+ }
+
+ /*
+ * Try to match up the protein complements
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!af.getViewport().getAlignment().isNucleotide())
+ {
+ String complementId = candidate.getKey().getComplementId();
+ // only non-null complements should be in the Map
+ if (complementId != null && dna.containsKey(complementId))
+ {
+ final AlignFrame dnaFrame = dna.get(complementId);
+ SplitFrame sf = createSplitFrame(dnaFrame, af);
+ addedToSplitFrames.add(dnaFrame);
+ addedToSplitFrames.add(af);
+ dnaFrame.setMenusForViewport();
+ af.setMenusForViewport();
+ if (af.getViewport().isGatherViewsHere())
+ {
+ gatherTo.add(sf);
+ }
+ }
+ }
+ }
+
+ /*
+ * Open any that we failed to pair up (which shouldn't happen!) as
+ * standalone AlignFrame's.
+ */
+ for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
+ .entrySet())
+ {
+ AlignFrame af = candidate.getValue();
+ if (!addedToSplitFrames.contains(af))
+ {
+ Viewport view = candidate.getKey();
+ Desktop.addInternalFrame(af, view.getTitle(),
+ safeInt(view.getWidth()), safeInt(view.getHeight()));
+ af.setMenusForViewport();
+ System.err.println("Failed to restore view " + view.getTitle()
+ + " to split frame");
+ }
+ }
+
+ /*
+ * Gather back into tabbed views as flagged.
+ */
+ for (SplitFrame sf : gatherTo)
+ {
+ Desktop.getInstance().gatherViews(sf);
+ }
+
+ splitFrameCandidates.clear();
}
- saveAllFrames(Arrays.asList(frames), jout);
- }
-
- /**
- * core method for storing state for a set of AlignFrames.
- *
- * @param frames
- * - frames involving all data to be exported (including those
- * contained in splitframes, though not the split frames themselves)
- * @param jout
- * - project output stream
- */
- private void saveAllFrames(List<AlignFrame> frames, JarOutputStream jout)
- {
- Hashtable<String, AlignFrame> dsses = new Hashtable<>();
- /*
- * ensure cached data is clear before starting
+ /**
+ * Construct and display one SplitFrame holding DNA and protein alignments.
+ *
+ * @param dnaFrame
+ * @param proteinFrame
+ * @return
*/
- // todo tidy up seqRefIds, seqsToIds initialisation / reset
- rnaSessions.clear();
- splitFrameCandidates.clear();
-
- try
+ protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
+ AlignFrame proteinFrame)
{
+ SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
+ String title = MessageManager.getString("label.linked_view_title");
+ int width = (int) dnaFrame.getBounds().getWidth();
+ int height = (int) (dnaFrame.getBounds().getHeight()
+ + proteinFrame.getBounds().getHeight() + 50);
- // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- // //////////////////////////////////////////////////
-
- List<String> shortNames = new ArrayList<>();
- List<String> viewIds = new ArrayList<>();
-
- // REVERSE ORDER
- for (int i = frames.size() - 1; i > -1; i--)
- {
- AlignFrame af = frames.get(i);
- AlignViewport vp = af.getViewport();
- // skip ?
- if (skipList != null && skipList
- .containsKey(vp.getSequenceSetId()))
- {
- continue;
- }
-
- String shortName = makeFilename(af, shortNames);
-
- AlignmentI alignment = vp.getAlignment();
- List<? extends AlignmentViewPanel> panels = af.getAlignPanels();
- int apSize = panels.size();
-
- for (int ap = 0; ap < apSize; ap++)
- {
- AlignmentPanel apanel = (AlignmentPanel) panels.get(ap);
- String fileName = apSize == 1 ? shortName : ap + shortName;
- if (!fileName.endsWith(".xml"))
- {
- fileName = fileName + ".xml";
- }
-
- saveState(apanel, fileName, jout, viewIds);
+ /*
+ * SplitFrame location is saved to both enclosed frames
+ */
+ splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
+ Desktop.addInternalFrame(splitFrame, title, width, height);
- }
- if (apSize > 0)
- {
- // BH moved next bit out of inner loop, not that it really matters.
- // so we are testing to make sure we actually have an alignment,
- // apparently.
- String dssid = getDatasetIdRef(alignment.getDataset());
- if (!dsses.containsKey(dssid))
- {
- // We have not already covered this data by reference from another
- // frame.
- dsses.put(dssid, af);
- }
- }
- }
+ /*
+ * And compute cDNA consensus (couldn't do earlier with consensus as
+ * mappings were not yet present)
+ */
+ proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
- writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
- jout);
-
- try
- {
- jout.flush();
- } catch (Exception foo)
- {
- }
- jout.close();
- } catch (Exception ex)
- {
- // 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 - see error output for details";
- }
- ex.printStackTrace();
+ return splitFrame;
}
- }
-
- /**
- * Generates a distinct file name, based on the title of the AlignFrame, by
- * appending _n for increasing n until an unused name is generated. The new
- * name (without its extension) is added to the list.
- *
- * @param af
- * @param namesUsed
- * @return the generated name, with .xml extension
- */
- protected String makeFilename(AlignFrame af, List<String> namesUsed)
- {
- String shortName = af.getTitle();
- if (shortName.indexOf(File.separatorChar) > -1)
- {
- shortName = shortName
- .substring(shortName.lastIndexOf(File.separatorChar) + 1);
- }
+ /**
+ * check errorMessage for a valid error message and raise an error box in the
+ * GUI or write the current errorMessage to stderr and then clear the error
+ * state.
+ */
+ protected void reportErrors()
+ {
+ reportErrors(false);
+ }
+
+ protected void reportErrors(final boolean saving)
+ {
+ if (errorMessage != null)
+ {
+ final String finalErrorMessage = errorMessage;
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
+ finalErrorMessage,
+ "Error " + (saving ? "saving" : "loading")
+ + " Jalview file",
+ JvOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println("Problem loading Jalview file: " + errorMessage);
+ }
+ }
+ errorMessage = null;
+ }
+
+ Map<String, String> alreadyLoadedPDB = new HashMap<>();
- int count = 1;
+ /**
+ * when set, local views will be updated from view stored in JalviewXML
+ * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
+ * sync if this is set to true.
+ */
+ private final boolean updateLocalViews = false;
- while (namesUsed.contains(shortName))
+ /**
+ * Returns the path to a temporary file holding the PDB file for the given PDB
+ * id. The first time of asking, searches for a file of that name in the
+ * Jalview project jar, and copies it to a new temporary file. Any repeat
+ * requests just return the path to the file previously created.
+ *
+ * @param jprovider
+ * @param pdbId
+ * @return
+ */
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
+ String origFile)
{
- if (shortName.endsWith("_" + (count - 1)))
- {
- shortName = shortName.substring(0, shortName.lastIndexOf("_"));
- }
+ if (alreadyLoadedPDB.containsKey(pdbId))
+ {
+ return alreadyLoadedPDB.get(pdbId).toString();
+ }
- shortName = shortName.concat("_" + count);
- count++;
+ String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
+ origFile);
+ if (tempFile != null)
+ {
+ alreadyLoadedPDB.put(pdbId, tempFile);
+ }
+ return tempFile;
}
- namesUsed.add(shortName);
-
- if (!shortName.endsWith(".xml"))
- {
- shortName = shortName + ".xml";
+ /**
+ * Copies the jar entry of given name to a new temporary file and returns the
+ * path to the file, or null if the entry is not found.
+ *
+ * @param jprovider
+ * @param jarEntryName
+ * @param prefix
+ * a prefix for the temporary file name, must be at least three
+ * characters long
+ * @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 suffixModel)
+ {
+ BufferedReader in = null;
+ PrintWriter out = null;
+ String suffix = ".tmp";
+ if (suffixModel == null)
+ {
+ suffixModel = jarEntryName;
+ }
+ int sfpos = suffixModel.lastIndexOf(".");
+ if (sfpos > -1 && sfpos < (suffixModel.length() - 1))
+ {
+ suffix = "." + suffixModel.substring(sfpos + 1);
+ }
+
+ 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));
+ File outFile = File.createTempFile(prefix, suffix);
+ outFile.deleteOnExit();
+ try (OutputStream os = new FileOutputStream(outFile))
+ {
+ copyAll(jin, os);
+ }
+ String t = outFile.getAbsolutePath();
+ return t;
+ }
+ else
+ {
+ Console.warn(
+ "Couldn't find entry in Jalview Jar for " + jarEntryName);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return null;
+ }
+
+ private class JvAnnotRow
+ {
+ public JvAnnotRow(int i, AlignmentAnnotation jaa)
+ {
+ order = i;
+ template = jaa;
+ }
+
+ /**
+ * persisted version of annotation row from which to take vis properties
+ */
+ public jalview.datamodel.AlignmentAnnotation template;
+
+ /**
+ * original position of the annotation row in the alignment
+ */
+ public int order;
}
- return shortName;
- }
- // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
- public boolean saveAlignment(AlignFrame af, String jarFile,
- String fileName)
- {
- try
+ /**
+ * Load alignment frame from jalview XML DOM object. For a DOM object that
+ * includes one or more Viewport elements (one with a title that does NOT
+ * contain "Dataset for"), create the frame.
+ *
+ * @param jalviewModel
+ * DOM
+ * @param fileName
+ * filename source string
+ * @param file
+ * @param loadTreesAndStructures
+ * when false only create Viewport
+ * @param jprovider
+ * data source provider
+ * @return alignment frame created from view stored in DOM
+ */
+ AlignFrame loadFromObject(JalviewModel jalviewModel, String fileName,
+ File file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
- // 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);
+ SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
+ List<Sequence> vamsasSeqs = vamsasSet.getSequence();
- JarOutputStream jout = new JarOutputStream(fos);
- List<AlignFrame> frames = new ArrayList<>();
+ // JalviewModelSequence jms = object.getJalviewModelSequence();
- // resolve splitframes
- if (af.getViewport().getCodingComplement() != null)
- {
- frames = ((SplitFrame) af.getSplitViewContainer()).getAlignFrames();
- }
- else
- {
- frames.add(af);
- }
- saveAllFrames(frames, jout);
- try
- {
- jout.flush();
- } catch (Exception foo)
- {
- }
- jout.close();
- boolean success = true;
+ // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ // : null;
+ Viewport view = (jalviewModel.getViewport().size() > 0)
+ ? jalviewModel.getViewport().get(0)
+ : null;
- if (doBackup)
- {
- backupfiles.setWriteSuccess(success);
- success = backupfiles.rollBackupsAndRenameTempFile();
- }
+ // ////////////////////////////////
+ // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
+ //
+ //
+ // If we just load in the same jar file again, the sequenceSetId
+ // will be the same, and we end up with multiple references
+ // to the same sequenceSet. We must modify this id on load
+ // so that each load of the file gives a unique id
+
+ /**
+ * used to resolve correct alignment dataset for alignments with multiple
+ * views
+ */
+ String uniqueSeqSetId = null;
+ String viewId = null;
+ if (view != null)
+ {
+ uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+ viewId = (view.getId() == null ? null
+ : view.getId() + uniqueSetSuffix);
+ }
+
+ // ////////////////////////////////
+ // LOAD SEQUENCES
+
+ List<SequenceI> hiddenSeqs = null;
+
+ List<SequenceI> tmpseqs = new ArrayList<>();
+
+ boolean multipleView = false;
+ SequenceI referenceseqForView = null;
+ // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
+ List<JSeq> jseqs = jalviewModel.getJSeq();
+ int vi = 0; // counter in vamsasSeq array
+ for (int i = 0; i < jseqs.size(); i++)
+ {
+ JSeq jseq = jseqs.get(i);
+ String seqId = jseq.getId();
+
+ SequenceI tmpSeq = seqRefIds.get(seqId);
+ if (tmpSeq != null)
+ {
+ if (!incompleteSeqs.containsKey(seqId))
+ {
+ // may not need this check, but keep it for at least 2.9,1 release
+ if (tmpSeq.getStart() != jseq.getStart()
+ || tmpSeq.getEnd() != jseq.getEnd())
+ {
+ Console.warn(
+ 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
+ {
+ incompleteSeqs.remove(seqId);
+ }
+ if (vamsasSeqs.size() > vi
+ && vamsasSeqs.get(vi).getId().equals(seqId))
+ {
+ // most likely we are reading a dataset XML document so
+ // update from vamsasSeq section of XML for this sequence
+ tmpSeq.setName(vamsasSeqs.get(vi).getName());
+ tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
+ tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
+ vi++;
+ }
+ else
+ {
+ // reading multiple views, so vamsasSeq set is a subset of JSeq
+ multipleView = true;
+ }
+ tmpSeq.setStart(jseq.getStart());
+ tmpSeq.setEnd(jseq.getEnd());
+ tmpseqs.add(tmpSeq);
+ }
+ else
+ {
+ Sequence vamsasSeq = vamsasSeqs.get(vi);
+ tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
+ vamsasSeq.getSequence());
+ tmpSeq.setDescription(vamsasSeq.getDescription());
+ tmpSeq.setStart(jseq.getStart());
+ tmpSeq.setEnd(jseq.getEnd());
+ tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq.getId(), tmpSeq);
+ tmpseqs.add(tmpSeq);
+ vi++;
+ }
+
+ if (safeBoolean(jseq.isViewreference()))
+ {
+ referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
+ }
+
+ if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
+ {
+ if (hiddenSeqs == null)
+ {
+ hiddenSeqs = new ArrayList<>();
+ }
+
+ hiddenSeqs.add(tmpSeq);
+ }
+ }
+
+ // /
+ // Create the alignment object from the sequence set
+ // ///////////////////////////////
+ SequenceI[] orderedSeqs = tmpseqs
+ .toArray(new SequenceI[tmpseqs.size()]);
- return success;
- } catch (Exception ex)
- {
- errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
- ex.printStackTrace();
- return false;
+ AlignmentI al = null;
+ // so we must create or recover the dataset alignment before going further
+ // ///////////////////////////////
+ if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+ {
+ // older jalview projects do not have a dataset - so creat alignment and
+ // dataset
+ al = new Alignment(orderedSeqs);
+ al.setDataset(null);
+ }
+ else
+ {
+ boolean isdsal = jalviewModel.getViewport().isEmpty();
+ if (isdsal)
+ {
+ // we are importing a dataset record, so
+ // recover reference to an alignment already materialsed as dataset
+ al = getDatasetFor(vamsasSet.getDatasetId());
+ }
+ if (al == null)
+ {
+ // materialse the alignment
+ al = new Alignment(orderedSeqs);
+ }
+ if (isdsal)
+ {
+ addDatasetRef(vamsasSet.getDatasetId(), al);
+ }
+
+ // finally, verify all data in vamsasSet is actually present in al
+ // passing on flag indicating if it is actually a stored dataset
+ recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
+ }
+
+ if (referenceseqForView != null)
+ {
+ al.setSeqrep(referenceseqForView);
+ }
+ // / Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
+ .get(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
+ // ///////////////////////////////
+
+ Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
+ if (!multipleView)
+ {
+ // load sequence features, database references and any associated PDB
+ // structures for the alignment
+ //
+ // prior to 2.10, this part would only be executed the first time a
+ // sequence was encountered, but not afterwards.
+ // now, for 2.10 projects, this is also done if the xml doc includes
+ // dataset sequences not actually present in any particular view.
+ //
+ for (int i = 0; i < vamsasSeqs.size(); i++)
+ {
+ JSeq jseq = jseqs.get(i);
+ if (jseq.getFeatures().size() > 0)
+ {
+ List<Feature> features = jseq.getFeatures();
+ for (int f = 0; f < features.size(); f++)
+ {
+ Feature feat = features.get(f);
+ SequenceFeature sf = new SequenceFeature(feat.getType(),
+ feat.getDescription(), feat.getBegin(), feat.getEnd(),
+ safeFloat(feat.getScore()), feat.getFeatureGroup());
+ sf.setStatus(feat.getStatus());
+
+ /*
+ * load any feature attributes - include map-valued attributes
+ */
+ Map<String, Map<String, String>> mapAttributes = new HashMap<>();
+ for (int od = 0; od < feat.getOtherData().size(); od++)
+ {
+ OtherData keyValue = feat.getOtherData().get(od);
+ String attributeName = keyValue.getKey();
+ String attributeValue = keyValue.getValue();
+ if (attributeName.startsWith("LINK"))
+ {
+ sf.addLink(attributeValue);
+ }
+ else
+ {
+ String subAttribute = keyValue.getKey2();
+ if (subAttribute == null)
+ {
+ // simple string-valued attribute
+ sf.setValue(attributeName, attributeValue);
+ }
+ else
+ {
+ // attribute 'key' has sub-attribute 'key2'
+ if (!mapAttributes.containsKey(attributeName))
+ {
+ mapAttributes.put(attributeName, new HashMap<>());
+ }
+ mapAttributes.get(attributeName).put(subAttribute,
+ attributeValue);
+ }
+ }
+ }
+ for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
+ .entrySet())
+ {
+ sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
+ }
+
+ // adds feature to datasequence's feature set (since Jalview 2.10)
+ al.getSequenceAt(i).addSequenceFeature(sf);
+ }
+ }
+ if (vamsasSeqs.get(i).getDBRef().size() > 0)
+ {
+ // adds dbrefs to datasequence's set (since Jalview 2.10)
+ addDBRefs(
+ al.getSequenceAt(i).getDatasetSequence() == null
+ ? al.getSequenceAt(i)
+ : al.getSequenceAt(i).getDatasetSequence(),
+ vamsasSeqs.get(i));
+ }
+ if (jseq.getPdbids().size() > 0)
+ {
+ List<Pdbids> ids = jseq.getPdbids();
+ for (int p = 0; p < ids.size(); p++)
+ {
+ Pdbids pdbid = ids.get(p);
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
+ entry.setId(pdbid.getId());
+ if (pdbid.getType() != null)
+ {
+ if (PDBEntry.Type.getType(pdbid.getType()) != null)
+ {
+ entry.setType(PDBEntry.Type.getType(pdbid.getType()));
+ }
+ else
+ {
+ entry.setType(PDBEntry.Type.FILE);
+ }
+ }
+ // jprovider is null when executing 'New View'
+ if (pdbid.getFile() != null && jprovider != null)
+ {
+ if (!pdbloaded.containsKey(pdbid.getFile()))
+ {
+ entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
+ pdbid.getFile()));
+ }
+ else
+ {
+ entry.setFile(pdbloaded.get(pdbid.getId()).toString());
+ }
+ }
+ /*
+ if (pdbid.getPdbentryItem() != null)
+ {
+ for (PdbentryItem item : pdbid.getPdbentryItem())
+ {
+ for (Property pr : item.getProperty())
+ {
+ entry.setProperty(pr.getName(), pr.getValue());
+ }
+ }
+ }
+ */
+ for (Property prop : pdbid.getProperty())
+ {
+ entry.setProperty(prop.getName(), prop.getValue());
+ }
+ Desktop.getStructureSelectionManager()
+ .registerPDBEntry(entry);
+ // adds PDBEntry to datasequence's set (since Jalview 2.10)
+ if (al.getSequenceAt(i).getDatasetSequence() != null)
+ {
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ else
+ {
+ al.getSequenceAt(i).addPDBId(entry);
+ }
+ }
+ }
+ /*
+ * load any HMMER profile
+ */
+ // TODO fix this
+
+ String hmmJarFile = jseqs.get(i).getHmmerProfile();
+ if (hmmJarFile != null && jprovider != null)
+ {
+ loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i));
+ }
+ }
+ } // end !multipleview
+
+ // ///////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+
+ if (vamsasSet.getAlcodonFrame().size() > 0)
+ {
+ // TODO Potentially this should only be done once for all views of an
+ // alignment
+ List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
+ for (int i = 0; i < alc.size(); i++)
+ {
+ AlignedCodonFrame cf = new AlignedCodonFrame();
+ if (alc.get(i).getAlcodMap().size() > 0)
+ {
+ List<AlcodMap> maps = alc.get(i).getAlcodMap();
+ for (int m = 0; m < maps.size(); m++)
+ {
+ AlcodMap map = maps.get(m);
+ SequenceI dnaseq = seqRefIds.get(map.getDnasq());
+ // Load Mapping
+ jalview.datamodel.Mapping mapping = null;
+ // attach to dna sequence reference.
+ if (map.getMapping() != null)
+ {
+ mapping = addMapping(map.getMapping());
+ if (dnaseq != null && mapping.getTo() != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(
+ newAlcodMapRef(map.getDnasq(), cf, mapping));
+ }
+ }
+ }
+ al.addCodonFrame(cf);
+ }
+ }
+ }
+
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
+ List<JvAnnotRow> autoAlan = new ArrayList<>();
+
+ /*
+ * store any annotations which forward reference a group's ID
+ */
+ Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
+
+ if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
+ {
+ List<Annotation> an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.size(); i++)
+ {
+ Annotation annotation = an.get(i);
+
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (annotation.getLabel().equals("Quality")
+ || annotation.getLabel().equals("Conservation")
+ || annotation.getLabel().equals("Consensus"))
+ {
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ // JAXB has no has() test; schema defaults value to false
+ // if (!annotation.hasAutoCalculated())
+ // {
+ // annotation.setAutoCalculated(true);
+ // }
+ }
+ if (autoForView || annotation.isAutoCalculated())
+ {
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ annotation.setId(null);
+ }
+
+ // set visibility for other annotation in this view
+ String annotationId = annotation.getId();
+ if (annotationId != null && annotationIds.containsKey(annotationId))
+ {
+ AlignmentAnnotation jda = annotationIds.get(annotationId);
+ // in principle Visible should always be true for annotation displayed
+ // in multiple views
+ if (annotation.isVisible() != null)
+ {
+ jda.visible = annotation.isVisible();
+ }
+
+ al.addAnnotation(jda);
+
+ continue;
+ }
+ // Construct new annotation from model.
+ List<AnnotationElement> ae = annotation.getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = null;
+ java.awt.Color firstColour = null;
+ int anpos;
+ if (!annotation.isScoreOnly())
+ {
+ anot = new jalview.datamodel.Annotation[al.getWidth()];
+ for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
+ {
+ AnnotationElement annElement = ae.get(aa);
+ anpos = annElement.getPosition();
+
+ if (anpos >= anot.length)
+ {
+ continue;
+ }
+
+ float value = safeFloat(annElement.getValue());
+ anot[anpos] = new jalview.datamodel.Annotation(
+ annElement.getDisplayCharacter(),
+ annElement.getDescription(),
+ (annElement.getSecondaryStructure() == null
+ || annElement.getSecondaryStructure()
+ .length() == 0)
+ ? ' '
+ : annElement
+ .getSecondaryStructure()
+ .charAt(0),
+ value);
+ anot[anpos].colour = new Color(safeInt(annElement.getColour()));
+ if (firstColour == null)
+ {
+ firstColour = anot[anpos].colour;
+ }
+ }
+ }
+ // create the new AlignmentAnnotation
+ jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ if (annotation.isGraph())
+ {
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
+ jaa = new jalview.datamodel.AlignmentAnnotation(
+ annotation.getLabel(), annotation.getDescription(), anot,
+ llim, hlim, safeInt(annotation.getGraphType()));
+
+ jaa.graphGroup = safeInt(annotation.getGraphGroup());
+ jaa._linecolour = firstColour;
+ if (annotation.getThresholdLine() != null)
+ {
+ jaa.setThreshold(new jalview.datamodel.GraphLine(
+ safeFloat(annotation.getThresholdLine().getValue()),
+ annotation.getThresholdLine().getLabel(),
+ new java.awt.Color(safeInt(
+ annotation.getThresholdLine().getColour()))));
+ }
+ if (autoForView || annotation.isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
+ }
+ }
+ else
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(
+ annotation.getLabel(), annotation.getDescription(), anot);
+ jaa._linecolour = firstColour;
+ }
+ // register new annotation
+ // Annotation graphs such as Conservation will not have id.
+ if (annotation.getId() != null)
+ {
+ annotationIds.put(annotation.getId(), jaa);
+ jaa.annotationId = annotation.getId();
+ }
+ // recover sequence association
+ String sequenceRef = annotation.getSequenceRef();
+ if (sequenceRef != null)
+ {
+ // from 2.9 sequenceRef is to sequence id (JAL-1781)
+ SequenceI sequence = seqRefIds.get(sequenceRef);
+ if (sequence == null)
+ {
+ // in pre-2.9 projects sequence ref is to sequence name
+ sequence = al.findName(sequenceRef);
+ }
+ if (sequence != null)
+ {
+ jaa.createSequenceMapping(sequence, 1, true);
+ sequence.addAlignmentAnnotation(jaa);
+ }
+ }
+ // and make a note of any group association
+ if (annotation.getGroupRef() != null
+ && annotation.getGroupRef().length() > 0)
+ {
+ List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+ .get(annotation.getGroupRef());
+ if (aal == null)
+ {
+ aal = new ArrayList<>();
+ groupAnnotRefs.put(annotation.getGroupRef(), aal);
+ }
+ aal.add(jaa);
+ }
+
+ if (annotation.getScore() != null)
+ {
+ jaa.setScore(annotation.getScore().doubleValue());
+ }
+ if (annotation.isVisible() != null)
+ {
+ jaa.visible = annotation.isVisible().booleanValue();
+ }
+
+ if (annotation.isCentreColLabels() != null)
+ {
+ jaa.centreColLabels = annotation.isCentreColLabels()
+ .booleanValue();
+ }
+
+ if (annotation.isScaleColLabels() != null)
+ {
+ jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
+ }
+ if (annotation.isAutoCalculated())
+ {
+ // newer files have an 'autoCalculated' flag and store calculation
+ // state in viewport properties
+ jaa.autoCalculated = true; // means annotation will be marked for
+ // update at end of load.
+ }
+ if (annotation.getGraphHeight() != null)
+ {
+ jaa.graphHeight = annotation.getGraphHeight().intValue();
+ }
+ jaa.belowAlignment = annotation.isBelowAlignment();
+ jaa.setCalcId(annotation.getCalcId());
+ if (annotation.getProperty().size() > 0)
+ {
+ for (Annotation.Property prop : annotation
+ .getProperty())
+ {
+ jaa.setProperty(prop.getName(), prop.getValue());
+ }
+ }
+ if (jaa.autoCalculated)
+ {
+ autoAlan.add(new JvAnnotRow(i, jaa));
+ }
+ else
+ // if (!autoForView)
+ {
+ // add autocalculated group annotation and any user created annotation
+ // for the view
+ al.addAnnotation(jaa);
+ }
+ }
+ }
+ // ///////////////////////
+ // LOAD GROUPS
+ // Create alignment markup and styles for this view
+ if (jalviewModel.getJGroup().size() > 0)
+ {
+ List<JGroup> groups = jalviewModel.getJGroup();
+ boolean addAnnotSchemeGroup = false;
+ for (int i = 0; i < groups.size(); i++)
+ {
+ JGroup jGroup = groups.get(i);
+ ColourSchemeI cs = null;
+ if (jGroup.getColour() != null)
+ {
+ if (jGroup.getColour().startsWith("ucs"))
+ {
+ cs = getUserColourScheme(jalviewModel, jGroup.getColour());
+ }
+ else if (jGroup.getColour().equals("AnnotationColourGradient")
+ && jGroup.getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColourScheme(null, al,
+ jGroup.getColour());
+ }
+ }
+ int pidThreshold = safeInt(jGroup.getPidThreshold());
+
+ Vector<SequenceI> seqs = new Vector<>();
+
+ for (int s = 0; s < jGroup.getSeq().size(); s++)
+ {
+ String seqId = jGroup.getSeq().get(s);
+ SequenceI ts = seqRefIds.get(seqId);
+
+ if (ts != null)
+ {
+ seqs.addElement(ts);
+ }
+ }
+
+ if (seqs.size() < 1)
+ {
+ continue;
+ }
+
+ SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
+ safeBoolean(jGroup.isDisplayBoxes()),
+ safeBoolean(jGroup.isDisplayText()),
+ safeBoolean(jGroup.isColourText()),
+ safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
+ sg.getGroupColourScheme().setThreshold(pidThreshold, true);
+ sg.getGroupColourScheme()
+ .setConservationInc(safeInt(jGroup.getConsThreshold()));
+ sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
+
+ sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
+ sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
+ sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
+ sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
+ // attributes with a default in the schema are never null
+ sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
+ sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
+ sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
+ sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
+ if (jGroup.getConsThreshold() != null
+ && jGroup.getConsThreshold().intValue() != 0)
+ {
+ Conservation c = new Conservation("All", sg.getSequences(null), 0,
+ sg.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, 25);
+ sg.cs.setConservation(c);
+ }
+
+ if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
+ {
+ // re-instate unique group/annotation row reference
+ List<AlignmentAnnotation> jaal = groupAnnotRefs
+ .get(jGroup.getId());
+ if (jaal != null)
+ {
+ for (AlignmentAnnotation jaa : jaal)
+ {
+ jaa.groupRef = sg;
+ if (jaa.autoCalculated)
+ {
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Consensus for "))
+ {
+ sg.setConsensus(jaa);
+ }
+ // match up and try to set group autocalc alignment row for this
+ // annotation
+ if (jaa.label.startsWith("Conservation for "))
+ {
+ sg.setConservationRow(jaa);
+ }
+ }
+ }
+ }
+ }
+ al.addGroup(sg);
+ if (addAnnotSchemeGroup)
+ {
+ // reconstruct the annotation colourscheme
+ sg.setColourScheme(
+ constructAnnotationColour(jGroup.getAnnotationColours(),
+ null, al, jalviewModel, false));
+ }
+ }
+ }
+ if (view == null)
+ {
+ // only dataset in this model, so just return.
+ return null;
+ }
+ // ///////////////////////////////
+ // LOAD VIEWPORT
+
+ // now check to see if we really need to create a new viewport.
+ if (multipleView && viewportsAdded.size() == 0)
+ {
+ // We recovered an alignment for which a viewport already exists.
+ // TODO: fix up any settings necessary for overlaying stored state onto
+ // state recovered from another document. (may not be necessary).
+ // we may need a binding from a viewport in memory to one recovered from
+ // XML.
+ // and then recover its containing af to allow the settings to be applied.
+ // TODO: fix for vamsas demo
+ System.err.println(
+ "About to recover a viewport for existing alignment: Sequence set ID is "
+ + uniqueSeqSetId);
+ Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
+ if (seqsetobj != null)
+ {
+ if (seqsetobj instanceof String)
+ {
+ uniqueSeqSetId = (String) seqsetobj;
+ System.err.println(
+ "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ + uniqueSeqSetId);
+ }
+ else
+ {
+ System.err.println(
+ "Warning : Collision between sequence set ID string and existing jalview object mapping.");
+ }
+
+ }
+ }
+ /**
+ * indicate that annotation colours are applied across all groups (pre
+ * Jalview 2.8.1 behaviour)
+ */
+ boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
+ jalviewModel.getVersion());
+
+ AlignFrame af = null;
+ AlignmentPanel ap = null;
+ AlignViewport av = null;
+ if (viewId != null)
+ {
+ // Check to see if this alignment already has a view id == viewId
+ jalview.gui.AlignmentPanel views[] = Desktop
+ .getAlignmentPanels(uniqueSeqSetId);
+ if (views != null && views.length > 0)
+ {
+ for (int v = 0; v < views.length; v++)
+ {
+ ap = views[v];
+ av = ap.av;
+ if (av.getViewId().equalsIgnoreCase(viewId))
+ {
+ // recover the existing alignpanel, alignframe, viewport
+ af = ap.alignFrame;
+ break;
+ // TODO: could even skip resetting view settings if we don't want to
+ // change the local settings from other jalview processes
+ }
+ }
+ }
+ }
+
+ if (af == null)
+ {
+ af = loadViewport(fileName, file, jseqs, hiddenSeqs, al, jalviewModel, view,
+ uniqueSeqSetId, viewId, autoAlan);
+ av = af.getViewport();
+ // note that this only retrieves the most recently accessed
+ // tab of an AlignFrame.
+ ap = af.alignPanel;
+ }
+
+ /*
+ * Load any trees, PDB structures and viewers
+ *
+ * Not done if flag is false (when this method is used for New View)
+ */
+ final AlignFrame af0 = af;
+ final AlignViewport av0 = av;
+ final AlignmentPanel ap0 = ap;
+ // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
+ // Platform.TIME_MARK);
+ if (loadTreesAndStructures)
+ {
+ if (!jalviewModel.getTree().isEmpty())
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ loadTrees(jalviewModel, view, af0, av0, ap0);
+ // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
+ }
+ });
+ }
+ if (!jalviewModel.getPcaViewer().isEmpty())
+ {
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ loadPCAViewers(jalviewModel, ap0);
+ // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
+ }
+ });
+ }
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ // Platform.timeCheck(null, Platform.TIME_MARK);
+ loadPDBStructures(jprovider, jseqs, af0, ap0);
+ // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
+ }
+ });
+ SwingUtilities.invokeLater(new Runnable()
+ {
+ @Override
+ public void run()
+ {
+ loadRnaViewers(jprovider, jseqs, ap0);
+ }
+ });
+ }
+ // and finally return.
+ // but do not set holdRepaint true just yet, because this could be the
+ // initial frame with just its dataset.
+ return af;
}
- }
- /**
- * Each AlignFrame has a single data set associated with it. Note that none of
- * these frames are split frames, because Desktop.getAlignFrames() collects
- * top and bottom separately here.
- *
- * @param dsses
- * @param fileName
- * @param jout
- */
- private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
- String fileName, JarOutputStream jout)
- {
-
- // Note that in saveAllFrames we have associated each specific dataset to
- // ONE of its associated frames.
- for (String dssids : dsses.keySet())
- {
- AlignFrame _af = dsses.get(dssids);
- String jfileName = fileName + " Dataset for " + _af.getTitle();
- if (!jfileName.endsWith(".xml"))
- {
- jfileName = jfileName + ".xml";
- }
- saveState(_af.alignPanel, jfileName, true, jout, null);
+ /**
+ * Loads a HMMER profile from a file stored in the project, and associates it
+ * with the specified sequence
+ *
+ * @param jprovider
+ * @param hmmJarFile
+ * @param seq
+ */
+ protected void loadHmmerProfile(jarInputStreamProvider jprovider,
+ String hmmJarFile, SequenceI seq)
+ {
+ try
+ {
+ String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
+ HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
+ HiddenMarkovModel hmmModel = parser.getHMM();
+ hmmModel = new HiddenMarkovModel(hmmModel, seq);
+ seq.setHMM(hmmModel);
+ } catch (IOException e)
+ {
+ Console.warn("Error loading HMM profile for " + seq.getName() + ": "
+ + e.getMessage());
+ }
}
- }
-
- /**
- * create a JalviewModel from an alignment view and marshall it to a
- * JarOutputStream
- *
- * @param ap
- * panel to create jalview model for
- * @param fileName
- * name of alignment panel written to output stream
- * @param jout
- * jar output stream
- * @param viewIds
- * @param out
- * jar entry name
- */
- protected JalviewModel saveState(AlignmentPanel ap, String fileName,
- JarOutputStream jout, List<String> viewIds)
- {
- return saveState(ap, fileName, false, jout, viewIds);
- }
- /**
- * create a JalviewModel from an alignment view and marshall it to a
- * JarOutputStream
- *
- * @param ap
- * panel to create jalview model for
- * @param fileName
- * name of alignment panel written to output stream
- * @param storeDS
- * when true, only write the dataset for the alignment, not the data
- * associated with the view.
- * @param jout
- * jar output stream
- * @param out
- * jar entry name
- */
- protected JalviewModel saveState(AlignmentPanel ap, String fileName,
- boolean storeDS, JarOutputStream jout, List<String> viewIds)
- {
- if (viewIds == null)
- {
- viewIds = new ArrayList<>();
+ /**
+ * 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.
+ *
+ * Currently each viewer shows just one sequence and structure (gapped and
+ * trimmed), however this method is designed to support multiple sequences or
+ * structures in viewers if wanted in future.
+ *
+ * @param jprovider
+ * @param jseqs
+ * @param ap
+ */
+ protected void loadRnaViewers(jarInputStreamProvider jprovider,
+ List<JSeq> jseqs, AlignmentPanel ap)
+ {
+ /*
+ * scan the sequences for references to viewers; create each one the first
+ * time it is referenced, add Rna models to existing viewers
+ */
+ for (JSeq jseq : jseqs)
+ {
+ for (int i = 0; i < jseq.getRnaViewer().size(); i++)
+ {
+ RnaViewer viewer = jseq.getRnaViewer().get(i);
+ AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
+ ap);
+
+ for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
+ {
+ SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
+ SequenceI seq = seqRefIds.get(jseq.getId());
+ AlignmentAnnotation ann = this.annotationIds
+ .get(ss.getAnnotationId());
+
+ /*
+ * add the structure to the Varna display (with session state copied
+ * from the jar to a temporary file)
+ */
+ boolean gapped = safeBoolean(ss.isGapped());
+ String rnaTitle = ss.getTitle();
+ String sessionState = ss.getViewerState();
+ String tempStateFile = copyJarEntry(jprovider, sessionState,
+ "varna", null);
+ RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
+ appVarna.addModelSession(rna, rnaTitle, tempStateFile);
+ }
+ appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
+ }
+ }
}
- initSeqRefs();
-
- List<UserColourScheme> userColours = new ArrayList<>();
-
- AlignViewport av = ap.av;
- ViewportRanges vpRanges = av.getRanges();
-
- final ObjectFactory objectFactory = new ObjectFactory();
- JalviewModel object = objectFactory.createJalviewModel();
- object.setVamsasModel(new VAMSAS());
-
- // object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- try
- {
- GregorianCalendar c = new GregorianCalendar();
- DatatypeFactory datatypeFactory = DatatypeFactory.newInstance();
- XMLGregorianCalendar now = datatypeFactory.newXMLGregorianCalendar(c);// gregorianCalendar);
- object.setCreationDate(now);
- } catch (DatatypeConfigurationException e)
- {
- System.err.println("error writing date: " + e.toString());
+ /**
+ * Locate and return an already instantiated matching AppVarna, or create one
+ * if not found
+ *
+ * @param viewer
+ * @param viewIdSuffix
+ * @param ap
+ * @return
+ */
+ protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
+ String viewIdSuffix, AlignmentPanel ap)
+ {
+ /*
+ * on each load a suffix is appended to the saved viewId, to avoid conflicts
+ * if load is repeated
+ */
+ String postLoadId = viewer.getViewId() + viewIdSuffix;
+ for (JInternalFrame frame : getAllFrames())
+ {
+ if (frame instanceof AppVarna)
+ {
+ AppVarna varna = (AppVarna) frame;
+ if (postLoadId.equals(varna.getViewId()))
+ {
+ // this viewer is already instantiated
+ // could in future here add ap as another 'parent' of the
+ // AppVarna window; currently just 1-to-many
+ return varna;
+ }
+ }
+ }
+
+ /*
+ * viewer not found - make it
+ */
+ RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
+ safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
+ safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
+ safeInt(viewer.getDividerLocation()));
+ AppVarna varna = new AppVarna(model, ap);
+
+ return varna;
}
- object.setVersion(
- jalview.bin.Cache.getDefault("VERSION", "Development Build"));
/**
- * rjal is full height alignment, jal is actual alignment with full metadata
- * but excludes hidden sequences.
+ * Load any saved trees
+ *
+ * @param jm
+ * @param view
+ * @param af
+ * @param av
+ * @param ap
*/
- jalview.datamodel.AlignmentI rjal = av.getAlignment(), jal = rjal;
-
- if (av.hasHiddenRows())
- {
- rjal = jal.getHiddenSequences().getFullAlignment();
+ protected void loadTrees(JalviewModel jm, Viewport view,
+ AlignFrame af, AlignViewport av, AlignmentPanel ap)
+ {
+ // TODO result of automated refactoring - are all these parameters needed?
+ try
+ {
+ for (int t = 0; t < jm.getTree().size(); t++)
+ {
+
+ Tree tree = jm.getTree().get(t);
+
+ TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
+ if (tp == null)
+ {
+ tp = af.showNewickTree(new NewickFile(tree.getNewick()),
+ tree.getTitle(), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight()), safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()));
+ if (tp == null)
+ {
+ Console.warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
+ if (tree.getId() != null)
+ {
+ // perhaps bind the tree id to something ?
+ }
+ }
+ else
+ {
+ // update local tree attributes ?
+ // TODO: should check if tp has been manipulated by user - if so its
+ // settings shouldn't be modified
+ tp.setTitle(tree.getTitle());
+ tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
+ safeInt(tree.getYpos()), safeInt(tree.getWidth()),
+ safeInt(tree.getHeight())));
+ tp.setViewport(av); // af.viewport;
+ // TODO: verify 'associate with all views' works still
+ tp.getTreeCanvas().setViewport(av); // af.viewport;
+ tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
+ }
+ tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
+
+ tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
+ tp.fitToWindow_actionPerformed(null);
+
+ if (tree.getFontName() != null)
+ {
+ tp.setTreeFont(
+ new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
+ safeInt(tree.getFontSize())));
+ }
+ else
+ {
+ tp.setTreeFont(
+ new Font(view.getFontName(), safeInt(view.getFontStyle()),
+ safeInt(view.getFontSize())));
+ }
+
+ tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
+ tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
+ tp.showDistances(safeBoolean(tree.isShowDistances()));
+
+ tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
+
+ if (safeBoolean(tree.isCurrentTree()))
+ {
+ af.getViewport().setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
}
- SequenceSet vamsasSet = new SequenceSet();
- Sequence vamsasSeq;
- // JalviewModelSequence jms = new JalviewModelSequence();
-
- vamsasSet.setGapChar(jal.getGapCharacter() + "");
-
- if (jal.getDataset() != null)
- {
- // dataset id is the dataset's hashcode
- vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
- if (storeDS)
- {
- // switch jal and the dataset
- jal = jal.getDataset();
- rjal = jal;
- }
- }
- if (jal.getProperties() != null)
- {
- Enumeration en = jal.getProperties().keys();
- while (en.hasMoreElements())
- {
- String key = en.nextElement().toString();
- SequenceSetProperties ssp = new SequenceSetProperties();
- ssp.setKey(key);
- ssp.setValue(jal.getProperties().get(key).toString());
- // vamsasSet.addSequenceSetProperties(ssp);
- vamsasSet.getSequenceSetProperties().add(ssp);
- }
+ /**
+ * Load and link any saved structure viewers.
+ *
+ * @param jprovider
+ * @param jseqs
+ * @param af
+ * @param ap
+ */
+ protected void loadPDBStructures(jarInputStreamProvider jprovider,
+ List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
+ {
+ /*
+ * Run through all PDB ids on the alignment, and collect mappings between
+ * distinct view ids and all sequences referring to that view.
+ */
+ Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
+
+ for (int i = 0; i < jseqs.size(); i++)
+ {
+ JSeq jseq = jseqs.get(i);
+ if (jseq.getPdbids().size() > 0)
+ {
+ List<Pdbids> ids = jseq.getPdbids();
+ for (int p = 0; p < ids.size(); p++)
+ {
+ Pdbids pdbid = ids.get(p);
+ final int structureStateCount = pdbid.getStructureState().size();
+ for (int s = 0; s < structureStateCount; s++)
+ {
+ // check to see if we haven't already created this structure view
+ final StructureState structureState = pdbid
+ .getStructureState().get(s);
+ String sviewid = (structureState.getViewId() == null) ? null
+ : structureState.getViewId() + uniqueSetSuffix;
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+ // Originally : pdbid.getFile()
+ // : TODO: verify external PDB file recovery still works in normal
+ // jalview project load
+ jpdb.setFile(
+ loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
+ jpdb.setId(pdbid.getId());
+
+ int x = safeInt(structureState.getXpos());
+ int y = safeInt(structureState.getYpos());
+ int width = safeInt(structureState.getWidth());
+ int height = safeInt(structureState.getHeight());
+
+ // Probably don't need to do this anymore...
+ // Desktop.getDesktop().getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
+ pdbid.getFile());
+ jalview.datamodel.SequenceI seq = seqRefIds
+ .get(jseq.getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
+ + height;
+ }
+ 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(),
+ viewerType));
+ // Legacy pre-2.7 conversion JAL-823 :
+ // do not assume any view has to be linked for colour by
+ // sequence
+ }
+
+ // assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}, boolean[] {
+ // linkAlignPanel,superposeWithAlignpanel}} from hash
+ StructureViewerModel jmoldat = structureViewers.get(sviewid);
+ jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
+ || structureState.isAlignwithAlignPanel());
+
+ /*
+ * Default colour by linked panel to false if not specified (e.g.
+ * for pre-2.7 projects)
+ */
+ boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
+ colourWithAlignPanel |= structureState.isColourwithAlignPanel();
+ jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
+
+ /*
+ * Default colour by viewer to true if not specified (e.g. for
+ * pre-2.7 projects)
+ */
+ boolean colourByViewer = jmoldat.isColourByViewer();
+ colourByViewer &= structureState.isColourByJmol();
+ jmoldat.setColourByViewer(colourByViewer);
+
+ if (jmoldat.getStateData().length() < structureState
+ .getValue()/*Content()*/.length())
+ {
+ jmoldat.setStateData(structureState.getValue());// Content());
+ }
+ if (pdbid.getFile() != null)
+ {
+ File mapkey = new File(pdbid.getFile());
+ StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
+ if (seqstrmaps == null)
+ {
+ jmoldat.getFileData().put(mapkey,
+ seqstrmaps = jmoldat.new StructureData(pdbFile,
+ pdbid.getId()));
+ }
+ if (!seqstrmaps.getSeqList().contains(seq))
+ {
+ seqstrmaps.getSeqList().add(seq);
+ // TODO and chains?
+ }
+ }
+ else
+ {
+ errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
+ Console.warn(errorMessage);
+ }
+ }
+ }
+ }
+ }
+ // Instantiate the associated structure views
+ for (Entry<String, StructureViewerModel> entry : structureViewers
+ .entrySet())
+ {
+ try
+ {
+ createOrLinkStructureViewer(entry, af, ap, jprovider);
+ } catch (Exception e)
+ {
+ System.err.println(
+ "Error loading structure viewer: " + e.getMessage());
+ // failed - try the next one
+ }
+ }
}
- JSeq jseq;
- Set<String> calcIdSet = new HashSet<>();
- // record the set of vamsas sequence XML POJO we create.
- HashMap<String, Sequence> vamsasSetIds = new HashMap<>();
- // SAVE SEQUENCES
- for (final SequenceI jds : rjal.getSequences())
- {
- final SequenceI jdatasq = jds.getDatasetSequence() == null ? jds
- : jds.getDatasetSequence();
- String id = seqHash(jds);
- if (vamsasSetIds.get(id) == null)
- {
- if (seqRefIds.get(id) != null && !storeDS)
- {
- // This happens for two reasons: 1. multiple views are being
- // serialised.
- // 2. the hashCode has collided with another sequence's code. This
- // DOES
- // HAPPEN! (PF00072.15.stk does this)
- // JBPNote: Uncomment to debug writing out of files that do not read
- // back in due to ArrayOutOfBoundExceptions.
- // System.err.println("vamsasSeq backref: "+id+"");
- // System.err.println(jds.getName()+"
- // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(jds));
- // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- // System.err.println(rsq.getName()+"
- // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- // System.err.println("Hashcode: "+seqHash(rsq));
- }
- else
- {
- vamsasSeq = createVamsasSequence(id, jds);
-// vamsasSet.addSequence(vamsasSeq);
- vamsasSet.getSequence().add(vamsasSeq);
- vamsasSetIds.put(id, vamsasSeq);
- seqRefIds.put(id, jds);
- }
- }
- jseq = new JSeq();
- jseq.setStart(jds.getStart());
- jseq.setEnd(jds.getEnd());
- jseq.setColour(av.getSequenceColour(jds).getRGB());
-
- jseq.setId(id); // jseq id should be a string not a number
- if (!storeDS)
- {
- // Store any sequences this sequence represents
- if (av.hasHiddenRows())
- {
- // use rjal, contains the full height alignment
- jseq.setHidden(
- av.getAlignment().getHiddenSequences().isHidden(jds));
-
- if (av.isHiddenRepSequence(jds))
- {
- jalview.datamodel.SequenceI[] reps = av
- .getRepresentedSequences(jds).getSequencesInOrder(rjal);
-
- for (int h = 0; h < reps.length; h++)
- {
- if (reps[h] != jds)
- {
- // jseq.addHiddenSequences(rjal.findIndex(reps[h]));
- jseq.getHiddenSequences().add(rjal.findIndex(reps[h]));
- }
- }
- }
- }
- // mark sequence as reference - if it is the reference for this view
- if (jal.hasSeqrep())
- {
- jseq.setViewreference(jds == jal.getSeqrep());
- }
- }
-
- // TODO: omit sequence features from each alignment view's XML dump if we
- // are storing dataset
- List<SequenceFeature> sfs = jds.getSequenceFeatures();
- for (SequenceFeature sf : sfs)
- {
- // Features features = new Features();
- Feature features = new Feature();
-
- features.setBegin(sf.getBegin());
- features.setEnd(sf.getEnd());
- features.setDescription(sf.getDescription());
- features.setType(sf.getType());
- features.setFeatureGroup(sf.getFeatureGroup());
- features.setScore(sf.getScore());
- if (sf.links != null)
- {
- for (int l = 0; l < sf.links.size(); l++)
- {
- OtherData keyValue = new OtherData();
- keyValue.setKey("LINK_" + l);
- keyValue.setValue(sf.links.elementAt(l).toString());
- // features.addOtherData(keyValue);
- features.getOtherData().add(keyValue);
- }
- }
- if (sf.otherDetails != null)
- {
- /*
- * save feature attributes, which may be simple strings or
- * map valued (have sub-attributes)
- */
- for (Entry<String, Object> entry : sf.otherDetails.entrySet())
- {
- String key = entry.getKey();
- Object value = entry.getValue();
- if (value instanceof Map<?, ?>)
- {
- for (Entry<String, Object> subAttribute : ((Map<String, Object>) value)
- .entrySet())
- {
- OtherData otherData = new OtherData();
- otherData.setKey(key);
- otherData.setKey2(subAttribute.getKey());
- otherData.setValue(subAttribute.getValue().toString());
- // features.addOtherData(otherData);
- features.getOtherData().add(otherData);
- }
- }
- else
- {
- OtherData otherData = new OtherData();
- otherData.setKey(key);
- otherData.setValue(value.toString());
- // features.addOtherData(otherData);
- features.getOtherData().add(otherData);
- }
- }
- }
-
- // jseq.addFeatures(features);
- jseq.getFeatures().add(features);
- }
-
- /*
- * save PDB entries for sequence
- */
- if (jdatasq.getAllPDBEntries() != null)
- {
- Enumeration<PDBEntry> en = jdatasq.getAllPDBEntries().elements();
- while (en.hasMoreElements())
- {
- Pdbids pdb = new Pdbids();
- jalview.datamodel.PDBEntry entry = en.nextElement();
-
- String pdbId = entry.getId();
- pdb.setId(pdbId);
- pdb.setType(entry.getType());
-
- /*
- * Store any structure views associated with this sequence. This
- * section copes with duplicate entries in the project, so a dataset
- * only view *should* be coped with sensibly.
- */
- // This must have been loaded, is it still visible?
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
- String matchedFile = null;
- for (int f = frames.length - 1; f > -1; f--)
- {
- if (frames[f] instanceof StructureViewerBase)
- {
- StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
- 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);
- File viewerState = viewFrame.saveSession();
- if (viewerState != null)
- {
- copyFileToJar(jout, viewerState.getPath(),
- getViewerJarEntryName(viewId), viewerType);
- }
- else
- {
- Cache.log.error(
- "Failed to save viewer state for " + viewerType);
- }
- }
- }
- }
-
- if (matchedFile != null || entry.getFile() != null)
- {
- if (entry.getFile() != null)
- {
- // use entry's file
- matchedFile = entry.getFile();
- }
- pdb.setFile(matchedFile); // entry.getFile());
- if (pdbfiles == null)
- {
- pdbfiles = new ArrayList<>();
- }
-
- if (!pdbfiles.contains(pdbId))
- {
- pdbfiles.add(pdbId);
- copyFileToJar(jout, matchedFile, pdbId, pdbId);
- }
- }
-
- Enumeration<String> props = entry.getProperties();
- if (props.hasMoreElements())
- {
- // PdbentryItem item = new PdbentryItem();
- while (props.hasMoreElements())
- {
- Property prop = new Property();
- String key = props.nextElement();
- prop.setName(key);
- prop.setValue(entry.getProperty(key).toString());
- // item.addProperty(prop);
- pdb.getProperty().add(prop);
- }
- // pdb.addPdbentryItem(item);
- }
-
- // jseq.addPdbids(pdb);
- jseq.getPdbids().add(pdb);
- }
- }
-
- saveRnaViewers(jout, jseq, jds, viewIds, ap, storeDS);
-
- if (jds.hasHMMProfile())
- {
- saveHmmerProfile(jout, jseq, jds);
- }
- // jms.addJSeq(jseq);
- object.getJSeq().add(jseq);
+ /**
+ *
+ * @param viewerData
+ * @param af
+ * @param ap
+ * @param jprovider
+ */
+ protected void createOrLinkStructureViewer(
+ Entry<String, StructureViewerModel> viewerData, AlignFrame af,
+ AlignmentPanel ap, jarInputStreamProvider jprovider)
+ {
+ final StructureViewerModel stateData = viewerData.getValue();
+
+ /*
+ * Search for any viewer windows already open from other alignment views
+ * that exactly match the stored structure state
+ */
+ StructureViewerBase comp = findMatchingViewer(viewerData);
+
+ if (comp != null)
+ {
+ linkStructureViewer(ap, comp, stateData);
+ return;
+ }
+
+ String type = stateData.getType();
+ try
+ {
+ ViewerType viewerType = ViewerType.valueOf(type);
+ createStructureViewer(viewerType, viewerData, af, jprovider);
+ } catch (IllegalArgumentException | NullPointerException e)
+ {
+ // TODO JAL-3619 show error dialog / offer an alternative viewer
+ Console.error("Invalid structure viewer type: " + type);
+ }
}
-
- if (!storeDS && av.hasHiddenRows())
- {
- jal = av.getAlignment();
- }
- // SAVE MAPPINGS
- // FOR DATASET
- if (storeDS && jal.getCodonFrames() != null)
- {
- List<AlignedCodonFrame> jac = jal.getCodonFrames();
- for (AlignedCodonFrame acf : jac)
- {
- AlcodonFrame alc = new AlcodonFrame();
- if (acf.getProtMappings() != null
- && acf.getProtMappings().length > 0)
- {
- boolean hasMap = false;
- SequenceI[] dnas = acf.getdnaSeqs();
- jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
- for (int m = 0; m < pmaps.length; m++)
- {
- AlcodMap alcmap = new AlcodMap();
- alcmap.setDnasq(seqHash(dnas[m]));
- alcmap.setMapping(
- createVamsasMapping(pmaps[m], dnas[m], null, false));
- // alc.addAlcodMap(alcmap);
- alc.getAlcodMap().add(alcmap);
- hasMap = true;
- }
- if (hasMap)
- {
- // vamsasSet.addAlcodonFrame(alc);
- vamsasSet.getAlcodonFrame().add(alc);
- }
- }
- // TODO: delete this ? dead code from 2.8.3->2.9 ?
- // {
- // AlcodonFrame alc = new AlcodonFrame();
- // vamsasSet.addAlcodonFrame(alc);
- // for (int p = 0; p < acf.aaWidth; p++)
- // {
- // Alcodon cmap = new Alcodon();
- // if (acf.codons[p] != null)
- // {
- // // Null codons indicate a gapped column in the translated peptide
- // // alignment.
- // cmap.setPos1(acf.codons[p][0]);
- // cmap.setPos2(acf.codons[p][1]);
- // cmap.setPos3(acf.codons[p][2]);
- // }
- // alc.addAlcodon(cmap);
- // }
- // if (acf.getProtMappings() != null
- // && acf.getProtMappings().length > 0)
- // {
- // SequenceI[] dnas = acf.getdnaSeqs();
- // jalview.datamodel.Mapping[] pmaps = acf.getProtMappings();
- // for (int m = 0; m < pmaps.length; m++)
- // {
- // AlcodMap alcmap = new AlcodMap();
- // alcmap.setDnasq(seqHash(dnas[m]));
- // alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
- // false));
- // alc.addAlcodMap(alcmap);
- // }
- // }
- }
- }
-
- // SAVE TREES
- // /////////////////////////////////
- if (!storeDS && av.getCurrentTree() != null)
- {
- // FIND ANY ASSOCIATED TREES
- // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
- if (Desktop.getDesktopPane() != null)
- {
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
-
- for (int t = 0; t < frames.length; t++)
- {
- if (frames[t] instanceof TreePanel)
- {
- TreePanel tp = (TreePanel) frames[t];
-
- if (tp.getTreeCanvas().getViewport().getAlignment() == jal)
- {
- JalviewModel.Tree tree = new JalviewModel.Tree();
- tree.setTitle(tp.getTitle());
- tree.setCurrentTree((av.getCurrentTree() == tp.getTree()));
- tree.setNewick(tp.getTree().print());
- tree.setThreshold(tp.getTreeCanvas().getThreshold());
-
- tree.setFitToWindow(tp.fitToWindow.getState());
- tree.setFontName(tp.getTreeFont().getName());
- tree.setFontSize(tp.getTreeFont().getSize());
- tree.setFontStyle(tp.getTreeFont().getStyle());
- tree.setMarkUnlinked(tp.placeholdersMenu.getState());
-
- tree.setShowBootstrap(tp.bootstrapMenu.getState());
- tree.setShowDistances(tp.distanceMenu.getState());
-
- tree.setHeight(tp.getHeight());
- tree.setWidth(tp.getWidth());
- tree.setXpos(tp.getX());
- tree.setYpos(tp.getY());
- tree.setId(makeHashCode(tp, null));
- tree.setLinkToAllViews(
- tp.getTreeCanvas().isApplyToAllViews());
-
- // jms.addTree(tree);
- object.getTree().add(tree);
- }
- }
- }
- }
- }
-
- /*
- * save PCA viewers
- */
- if (!storeDS && Desktop.getDesktopPane() != null)
- {
- for (JInternalFrame frame : Desktop.getDesktopPane().getAllFrames())
- {
- if (frame instanceof PCAPanel)
- {
- PCAPanel panel = (PCAPanel) frame;
- if (panel.getAlignViewport().getAlignment() == jal)
- {
- savePCA(panel, object);
- }
- }
- }
- }
-
- // SAVE ANNOTATIONS
/**
- * store forward refs from an annotationRow to any groups
- */
- IdentityHashMap<SequenceGroup, String> groupRefs = new IdentityHashMap<>();
- if (storeDS)
- {
- for (SequenceI sq : jal.getSequences())
- {
- // Store annotation on dataset sequences only
- AlignmentAnnotation[] aa = sq.getAnnotation();
- if (aa != null && aa.length > 0)
- {
- storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
- vamsasSet);
- }
- }
- }
- else
- {
- if (jal.getAlignmentAnnotation() != null)
- {
- // Store the annotation shown on the alignment.
- AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
- storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
- vamsasSet);
- }
- }
- // SAVE GROUPS
- if (jal.getGroups() != null)
- {
- JGroup[] groups = new JGroup[jal.getGroups().size()];
- int i = -1;
- for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
- {
- JGroup jGroup = new JGroup();
- groups[++i] = jGroup;
-
- jGroup.setStart(sg.getStartRes());
- jGroup.setEnd(sg.getEndRes());
- jGroup.setName(sg.getName());
- if (groupRefs.containsKey(sg))
- {
- // group has references so set its ID field
- jGroup.setId(groupRefs.get(sg));
- }
- ColourSchemeI colourScheme = sg.getColourScheme();
- if (colourScheme != null)
- {
- ResidueShaderI groupColourScheme = sg.getGroupColourScheme();
- if (groupColourScheme.conservationApplied())
- {
- jGroup.setConsThreshold(groupColourScheme.getConservationInc());
-
- if (colourScheme instanceof jalview.schemes.UserColourScheme)
- {
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours,
- object));
- }
- else
- {
- jGroup.setColour(colourScheme.getSchemeName());
- }
- }
- else if (colourScheme instanceof jalview.schemes.AnnotationColourGradient)
- {
- jGroup.setColour("AnnotationColourGradient");
- jGroup.setAnnotationColours(constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) colourScheme,
- userColours, object));
- }
- else if (colourScheme instanceof jalview.schemes.UserColourScheme)
- {
- jGroup.setColour(
- setUserColourScheme(colourScheme, userColours, object));
- }
- else
- {
- jGroup.setColour(colourScheme.getSchemeName());
- }
-
- jGroup.setPidThreshold(groupColourScheme.getThreshold());
- }
-
- jGroup.setOutlineColour(sg.getOutlineColour().getRGB());
- jGroup.setDisplayBoxes(sg.getDisplayBoxes());
- jGroup.setDisplayText(sg.getDisplayText());
- jGroup.setColourText(sg.getColourText());
- jGroup.setTextCol1(sg.textColour.getRGB());
- jGroup.setTextCol2(sg.textColour2.getRGB());
- jGroup.setTextColThreshold(sg.thresholdTextColour);
- jGroup.setShowUnconserved(sg.getShowNonconserved());
- jGroup.setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
- jGroup.setShowConsensusHistogram(sg.isShowConsensusHistogram());
- jGroup.setShowSequenceLogo(sg.isShowSequenceLogo());
- jGroup.setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
- for (SequenceI seq : sg.getSequences())
- {
- // jGroup.addSeq(seqHash(seq));
- jGroup.getSeq().add(seqHash(seq));
- }
- }
-
- //jms.setJGroup(groups);
- Object group;
- for (JGroup grp : groups)
- {
- object.getJGroup().add(grp);
- }
- }
- if (!storeDS)
- {
- // /////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(
- makeHashCode(av.getSequenceSetId(), av.getSequenceSetId()));
- view.setId(av.getViewId());
- if (av.getCodingComplement() != null)
- {
- view.setComplementId(av.getCodingComplement().getViewId());
- }
- view.setViewName(av.getViewName());
- view.setGatheredViews(av.isGatherViewsHere());
-
- Rectangle size = ap.av.getExplodedGeometry();
- Rectangle position = size;
- if (size == null)
- {
- size = ap.alignFrame.getBounds();
- if (av.getCodingComplement() != null)
- {
- position = ((SplitFrame) ap.alignFrame.getSplitViewContainer())
- .getBounds();
- }
- else
- {
- position = size;
- }
- }
- view.setXpos(position.x);
- view.setYpos(position.y);
-
- view.setWidth(size.width);
- view.setHeight(size.height);
-
- view.setStartRes(vpRanges.getStartRes());
- view.setStartSeq(vpRanges.getStartSeq());
-
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
- userColours, object));
- }
- else if (av
- .getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
- {
- AnnotationColourScheme ac = constructAnnotationColours(
- (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme(),
- userColours, object);
-
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
- {
- view.setBgColour(ColourSchemeProperty
- .getColourName(av.getGlobalColourScheme()));
- }
-
- ResidueShaderI vcs = av.getResidueShading();
- ColourSchemeI cs = av.getGlobalColourScheme();
-
- if (cs != null)
- {
- if (vcs.conservationApplied())
- {
- view.setConsThreshold(vcs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(setUserColourScheme(cs, userColours, object));
- }
- }
- view.setPidThreshold(vcs.getThreshold());
- }
-
- view.setConservationSelected(av.getConservationSelected());
- view.setPidSelected(av.getAbovePIDThreshold());
- final Font font = av.getFont();
- view.setFontName(font.getName());
- view.setFontSize(font.getSize());
- view.setFontStyle(font.getStyle());
- view.setScaleProteinAsCdna(av.getViewStyle().isScaleProteinAsCdna());
- view.setRenderGaps(av.isRenderGaps());
- view.setShowAnnotation(av.isShowAnnotation());
- view.setShowBoxes(av.getShowBoxes());
- view.setShowColourText(av.getColourText());
- view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.isRightAlignIds());
- view.setShowSequenceFeatures(av.isShowSequenceFeatures());
- view.setShowText(av.getShowText());
- view.setShowUnconserved(av.getShowUnconserved());
- view.setWrapAlignment(av.getWrapAlignment());
- view.setTextCol1(av.getTextColour().getRGB());
- view.setTextCol2(av.getTextColour2().getRGB());
- view.setTextColThreshold(av.getThresholdTextColour());
- view.setShowConsensusHistogram(av.isShowConsensusHistogram());
- view.setShowSequenceLogo(av.isShowSequenceLogo());
- view.setNormaliseSequenceLogo(av.isNormaliseSequenceLogo());
- view.setShowGroupConsensus(av.isShowGroupConsensus());
- view.setShowGroupConservation(av.isShowGroupConservation());
- view.setShowNPfeatureTooltip(av.isShowNPFeats());
- view.setShowDbRefTooltip(av.isShowDBRefs());
- 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();
-
- FeatureRendererModel fr = ap.getSeqPanel().seqCanvas
- .getFeatureRenderer();
- String[] renderOrder = fr.getRenderOrder().toArray(new String[0]);
-
- Vector<String> settingsAdded = new Vector<>();
- if (renderOrder != null)
- {
- for (String featureType : renderOrder)
- {
- FeatureSettings.Setting setting = new FeatureSettings.Setting();
- setting.setType(featureType);
-
- /*
- * save any filter for the feature type
- */
- FeatureMatcherSetI filter = fr.getFeatureFilter(featureType);
- if (filter != null) {
- Iterator<FeatureMatcherI> filters = filter.getMatchers().iterator();
- FeatureMatcherI firstFilter = filters.next();
- setting.setMatcherSet(Jalview2XML.marshalFilter(
- firstFilter, filters, filter.isAnded()));
- }
-
- /*
- * save colour scheme for the feature type
- */
- FeatureColourI fcol = fr.getFeatureStyle(featureType);
- if (!fcol.isSimpleColour())
- {
- setting.setColour(fcol.getMaxColour().getRGB());
- setting.setMincolour(fcol.getMinColour().getRGB());
- setting.setMin(fcol.getMin());
- setting.setMax(fcol.getMax());
- setting.setColourByLabel(fcol.isColourByLabel());
- if (fcol.isColourByAttribute())
- {
- String[] attName = fcol.getAttributeName();
- setting.getAttributeName().add(attName[0]);
- if (attName.length > 1)
- {
- setting.getAttributeName().add(attName[1]);
- }
- }
- setting.setAutoScale(fcol.isAutoScaled());
- setting.setThreshold(fcol.getThreshold());
- Color noColour = fcol.getNoColour();
- if (noColour == null)
- {
- setting.setNoValueColour(NoValueColour.NONE);
- }
- else if (noColour.equals(fcol.getMaxColour()))
- {
- setting.setNoValueColour(NoValueColour.MAX);
- }
- else
- {
- setting.setNoValueColour(NoValueColour.MIN);
- }
- // -1 = No threshold, 0 = Below, 1 = Above
- setting.setThreshstate(fcol.isAboveThreshold() ? 1
- : (fcol.isBelowThreshold() ? 0 : -1));
- }
- else
- {
- setting.setColour(fcol.getColour().getRGB());
- }
-
- setting.setDisplay(
- av.getFeaturesDisplayed().isVisible(featureType));
- float rorder = fr
- .getOrder(featureType);
- if (rorder > -1)
- {
- setting.setOrder(rorder);
- }
- /// fs.addSetting(setting);
- fs.getSetting().add(setting);
- settingsAdded.addElement(featureType);
- }
- }
-
- // is groups actually supposed to be a map here ?
- Iterator<String> en = fr.getFeatureGroups().iterator();
- Vector<String> groupsAdded = new Vector<>();
- while (en.hasNext())
- {
- String grp = en.next();
- if (groupsAdded.contains(grp))
- {
- continue;
- }
- Group g = new Group();
- g.setName(grp);
- g.setDisplay(((Boolean) fr.checkGroupVisibility(grp, false))
- .booleanValue());
- // fs.addGroup(g);
- fs.getGroup().add(g);
- groupsAdded.addElement(grp);
- }
- // jms.setFeatureSettings(fs);
- object.setFeatureSettings(fs);
- }
-
- if (av.hasHiddenColumns())
- {
- jalview.datamodel.HiddenColumns hidden = av.getAlignment()
- .getHiddenColumns();
- if (hidden == null)
- {
- warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
- }
- else
- {
- Iterator<int[]> hiddenRegions = hidden.iterator();
- while (hiddenRegions.hasNext())
- {
- int[] region = hiddenRegions.next();
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- // view.addHiddenColumns(hc);
- view.getHiddenColumns().add(hc);
- }
- }
- }
- if (calcIdSet.size() > 0)
- {
- for (String calcId : calcIdSet)
- {
- if (calcId.trim().length() > 0)
- {
- CalcIdParam cidp = createCalcIdParam(calcId, av);
- // Some calcIds have no parameters.
- if (cidp != null)
- {
- // view.addCalcIdParam(cidp);
- view.getCalcIdParam().add(cidp);
- }
- }
- }
- }
-
- // jms.addViewport(view);
- object.getViewport().add(view);
- }
- // object.setJalviewModelSequence(jms);
- // object.getVamsasModel().addSequenceSet(vamsasSet);
- object.getVamsasModel().getSequenceSet().add(vamsasSet);
-
- if (jout != null && fileName != null)
- {
- // We may not want to write the object to disk,
- // eg we can copy the alignViewport to a new view object
- // using save and then load
- try
- {
- fileName = fileName.replace('\\', '/');
- System.out.println("Writing jar entry " + fileName);
- JarEntry entry = new JarEntry(fileName);
- jout.putNextEntry(entry);
- PrintWriter pout = new PrintWriter(
- new OutputStreamWriter(jout, UTF_8));
- JAXBContext jaxbContext = JAXBContext
- .newInstance(JalviewModel.class);
- Marshaller jaxbMarshaller = jaxbContext.createMarshaller();
-
- // output pretty printed
- // jaxbMarshaller.setProperty(Marshaller.JAXB_FORMATTED_OUTPUT, true);
- jaxbMarshaller.marshal(
- new ObjectFactory().createJalviewModel(object), pout);
-
- // jaxbMarshaller.marshal(object, pout);
- // marshaller.marshal(object);
- pout.flush();
- jout.closeEntry();
- } catch (Exception ex)
- {
- // TODO: raise error in GUI if marshalling failed.
- System.err.println("Error writing Jalview project");
- ex.printStackTrace();
- }
- }
- return object;
- }
- /**
- * Saves the HMMER profile associated with the sequence as a file in the jar,
- * in HMMER format, and saves the name of the file as a child element of the
- * XML sequence element
- *
- * @param jout
- * @param xmlSeq
- * @param seq
- */
- protected void saveHmmerProfile(JarOutputStream jout, JSeq xmlSeq,
- SequenceI seq)
- {
- HiddenMarkovModel profile = seq.getHMM();
- if (profile == null)
- {
- warn("Want to save HMM profile for " + seq.getName()
- + " but none found");
- return;
- }
- HMMFile hmmFile = new HMMFile(profile);
- String hmmAsString = hmmFile.print();
- String jarEntryName = HMMER_PREFIX + nextCounter();
- try
- {
- writeJarEntry(jout, jarEntryName, hmmAsString.getBytes());
- xmlSeq.setHmmerProfile(jarEntryName);
- } catch (IOException e)
- {
- warn("Error saving HMM profile: " + e.getMessage());
- }
- }
-
-
- /**
- * Writes PCA viewer attributes and computed values to an XML model object and
- * adds it to the JalviewModel. Any exceptions are reported by logging.
- */
- protected void savePCA(PCAPanel panel, JalviewModel object)
- {
- try
- {
- PcaViewer viewer = new PcaViewer();
- viewer.setHeight(panel.getHeight());
- viewer.setWidth(panel.getWidth());
- viewer.setXpos(panel.getX());
- viewer.setYpos(panel.getY());
- viewer.setTitle(panel.getTitle());
- PCAModel pcaModel = panel.getPcaModel();
- viewer.setScoreModelName(pcaModel.getScoreModelName());
- viewer.setXDim(panel.getSelectedDimensionIndex(X));
- viewer.setYDim(panel.getSelectedDimensionIndex(Y));
- viewer.setZDim(panel.getSelectedDimensionIndex(Z));
- viewer.setBgColour(
- panel.getRotatableCanvas().getBackgroundColour().getRGB());
- viewer.setScaleFactor(panel.getRotatableCanvas().getScaleFactor());
- float[] spMin = panel.getRotatableCanvas().getSeqMin();
- SeqPointMin spmin = new SeqPointMin();
- spmin.setXPos(spMin[0]);
- spmin.setYPos(spMin[1]);
- spmin.setZPos(spMin[2]);
- viewer.setSeqPointMin(spmin);
- float[] spMax = panel.getRotatableCanvas().getSeqMax();
- SeqPointMax spmax = new SeqPointMax();
- spmax.setXPos(spMax[0]);
- spmax.setYPos(spMax[1]);
- spmax.setZPos(spMax[2]);
- viewer.setSeqPointMax(spmax);
- viewer.setShowLabels(panel.getRotatableCanvas().isShowLabels());
- viewer.setLinkToAllViews(
- panel.getRotatableCanvas().isApplyToAllViews());
- SimilarityParamsI sp = pcaModel.getSimilarityParameters();
- viewer.setIncludeGaps(sp.includeGaps());
- viewer.setMatchGaps(sp.matchGaps());
- viewer.setIncludeGappedColumns(sp.includeGappedColumns());
- viewer.setDenominateByShortestLength(sp.denominateByShortestLength());
-
- /*
- * sequence points on display
- */
- for (jalview.datamodel.SequencePoint spt : pcaModel
- .getSequencePoints())
- {
- SequencePoint point = new SequencePoint();
- point.setSequenceRef(seqHash(spt.getSequence()));
- point.setXPos(spt.coord.x);
- point.setYPos(spt.coord.y);
- point.setZPos(spt.coord.z);
- viewer.getSequencePoint().add(point);
- }
-
- /*
- * (end points of) axes on display
- */
- for (Point p : panel.getRotatableCanvas().getAxisEndPoints())
- {
-
- Axis axis = new Axis();
- axis.setXPos(p.x);
- axis.setYPos(p.y);
- axis.setZPos(p.z);
- viewer.getAxis().add(axis);
- }
-
- /*
- * raw PCA data (note we are not restoring PCA inputs here -
- * alignment view, score model, similarity parameters)
- */
- PcaDataType data = new PcaDataType();
- viewer.setPcaData(data);
- PCA pca = pcaModel.getPcaData();
-
- DoubleMatrix pm = new DoubleMatrix();
- saveDoubleMatrix(pca.getPairwiseScores(), pm);
- data.setPairwiseMatrix(pm);
-
- DoubleMatrix tm = new DoubleMatrix();
- saveDoubleMatrix(pca.getTridiagonal(), tm);
- data.setTridiagonalMatrix(tm);
-
- DoubleMatrix eigenMatrix = new DoubleMatrix();
- data.setEigenMatrix(eigenMatrix);
- saveDoubleMatrix(pca.getEigenmatrix(), eigenMatrix);
-
- object.getPcaViewer().add(viewer);
- } catch (Throwable t)
- {
- Cache.log.error("Error saving PCA: " + t.getMessage());
- }
- }
-
- /**
- * Stores values from a matrix into an XML element, including (if present) the
- * D or E vectors
- *
- * @param m
- * @param xmlMatrix
- * @see #loadDoubleMatrix(DoubleMatrix)
- */
- protected void saveDoubleMatrix(MatrixI m, DoubleMatrix xmlMatrix)
- {
- xmlMatrix.setRows(m.height());
- xmlMatrix.setColumns(m.width());
- for (int i = 0; i < m.height(); i++)
- {
- DoubleVector row = new DoubleVector();
- for (int j = 0; j < m.width(); j++)
- {
- row.getV().add(m.getValue(i, j));
- }
- xmlMatrix.getRow().add(row);
- }
- if (m.getD() != null)
- {
- DoubleVector dVector = new DoubleVector();
- for (double d : m.getD())
- {
- dVector.getV().add(d);
- }
- xmlMatrix.setD(dVector);
- }
- if (m.getE() != null)
- {
- DoubleVector eVector = new DoubleVector();
- for (double e : m.getE())
- {
- eVector.getV().add(e);
- }
- xmlMatrix.setE(eVector);
- }
- }
-
- /**
- * Loads XML matrix data into a new Matrix object, including the D and/or E
- * vectors (if present)
- *
- * @param mData
- * @return
- * @see Jalview2XML#saveDoubleMatrix(MatrixI, DoubleMatrix)
- */
- protected MatrixI loadDoubleMatrix(DoubleMatrix mData)
- {
- int rows = mData.getRows();
- double[][] vals = new double[rows][];
-
- for (int i = 0; i < rows; i++)
- {
- List<Double> dVector = mData.getRow().get(i).getV();
- vals[i] = new double[dVector.size()];
- int dvi = 0;
- for (Double d : dVector)
- {
- vals[i][dvi++] = d;
- }
- }
-
- MatrixI m = new Matrix(vals);
-
- if (mData.getD() != null)
- {
- List<Double> dVector = mData.getD().getV();
- double[] vec = new double[dVector.size()];
- int dvi = 0;
- for (Double d : dVector)
- {
- vec[dvi++] = d;
- }
- m.setD(vec);
- }
- if (mData.getE() != null)
- {
- List<Double> dVector = mData.getE().getV();
- double[] vec = new double[dVector.size()];
- int dvi = 0;
- for (Double d : dVector)
- {
- vec[dvi++] = d;
- }
- m.setE(vec);
- }
-
- return m;
- }
-
- /**
- * Save any Varna viewers linked to this sequence. Writes an rnaViewer element
- * for each viewer, with
- * <ul>
- * <li>viewer geometry (position, size, split pane divider location)</li>
- * <li>index of the selected structure in the viewer (currently shows gapped
- * or ungapped)</li>
- * <li>the id of the annotation holding RNA secondary structure</li>
- * <li>(currently only one SS is shown per viewer, may be more in future)</li>
- * </ul>
- * Varna viewer state is also written out (in native Varna XML) to separate
- * project jar entries. A separate entry is written for each RNA structure
- * displayed, with the naming convention
- * <ul>
- * <li>rna_viewId_sequenceId_annotationId_[gapped|trimmed]</li>
- * </ul>
- *
- * @param jout
- * @param jseq
- * @param jds
- * @param viewIds
- * @param ap
- * @param storeDataset
- */
- protected void saveRnaViewers(JarOutputStream jout, JSeq jseq,
- final SequenceI jds, List<String> viewIds, AlignmentPanel ap,
- boolean storeDataset)
- {
- if (Desktop.getDesktopPane() == null)
- {
- return;
- }
- JInternalFrame[] frames = Desktop.getDesktopPane().getAllFrames();
- for (int f = frames.length - 1; f > -1; f--)
- {
- if (frames[f] instanceof AppVarna)
- {
- AppVarna varna = (AppVarna) frames[f];
- /*
- * link the sequence to every viewer that is showing it and is linked to
- * its alignment panel
- */
- if (varna.isListeningFor(jds) && ap == varna.getAlignmentPanel())
- {
- String viewId = varna.getViewId();
- RnaViewer rna = new RnaViewer();
- rna.setViewId(viewId);
- rna.setTitle(varna.getTitle());
- rna.setXpos(varna.getX());
- rna.setYpos(varna.getY());
- rna.setWidth(varna.getWidth());
- rna.setHeight(varna.getHeight());
- rna.setDividerLocation(varna.getDividerLocation());
- rna.setSelectedRna(varna.getSelectedIndex());
- // jseq.addRnaViewer(rna);
- jseq.getRnaViewer().add(rna);
-
- /*
- * Store each Varna panel's state once in the project per sequence.
- * First time through only (storeDataset==false)
- */
- // boolean storeSessions = false;
- // String sequenceViewId = viewId + seqsToIds.get(jds);
- // if (!storeDataset && !viewIds.contains(sequenceViewId))
- // {
- // viewIds.add(sequenceViewId);
- // storeSessions = true;
- // }
- for (RnaModel model : varna.getModels())
- {
- if (model.seq == jds)
- {
- /*
- * VARNA saves each view (sequence or alignment secondary
- * structure, gapped or trimmed) as a separate XML file
- */
- String jarEntryName = rnaSessions.get(model);
- if (jarEntryName == null)
- {
-
- String varnaStateFile = varna.getStateInfo(model.rna);
- jarEntryName = RNA_PREFIX + viewId + "_" + nextCounter();
- copyFileToJar(jout, varnaStateFile, jarEntryName, "Varna");
- rnaSessions.put(model, jarEntryName);
- }
- SecondaryStructure ss = new SecondaryStructure();
- String annotationId = varna.getAnnotation(jds).annotationId;
- ss.setAnnotationId(annotationId);
- ss.setViewerState(jarEntryName);
- ss.setGapped(model.gapped);
- ss.setTitle(model.title);
- // rna.addSecondaryStructure(ss);
- rna.getSecondaryStructure().add(ss);
- }
- }
- }
- }
- }
- }
-
- /**
- * Copy the contents of a file to a new entry added to the output jar
- *
- * @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 msg)
- {
- try (InputStream is = new FileInputStream(infilePath))
- {
- File file = new File(infilePath);
- if (file.exists() && jout != null)
- {
- 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();
- }
- }
-
- /**
- * 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
- * @param jds
- * @param pdb
- * the archive XML element under which to save the state
- * @param entry
- * @param viewIds
- * @param matchedFile
- * @param viewFrame
- * @return
- */
- protected String saveStructureViewer(AlignmentPanel ap, SequenceI jds,
- Pdbids pdb, PDBEntry entry, List<String> viewIds,
- String matchedFile, StructureViewerBase viewFrame)
- {
- final AAStructureBindingModel bindingModel = viewFrame.getBinding();
-
- /*
- * Look for any bindings for this viewer to the PDB file of interest
- * (including part matches excluding chain id)
- */
- for (int peid = 0; peid < bindingModel.getPdbCount(); peid++)
- {
- final PDBEntry pdbentry = bindingModel.getPdbEntry(peid);
- final String pdbId = pdbentry.getId();
- if (!pdbId.equals(entry.getId())
- && !(entry.getId().length() > 4 && entry.getId().toLowerCase(Locale.ROOT)
- .startsWith(pdbId.toLowerCase(Locale.ROOT))))
- {
- /*
- * not interested in a binding to a different PDB entry here
- */
- continue;
- }
- if (matchedFile == null)
- {
- matchedFile = pdbentry.getFile();
- }
- else if (!matchedFile.equals(pdbentry.getFile()))
- {
- Cache.log.warn(
- "Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
- + pdbentry.getFile());
- }
- // record the
- // file so we
- // can get at it if the ID
- // match is ambiguous (e.g.
- // 1QIP==1qipA)
-
- for (int smap = 0; smap < viewFrame.getBinding()
- .getSequence()[peid].length; smap++)
- {
- // if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
- if (jds == viewFrame.getBinding().getSequence()[peid][smap])
- {
- StructureState state = new StructureState();
- state.setVisible(true);
- state.setXpos(viewFrame.getX());
- state.setYpos(viewFrame.getY());
- state.setWidth(viewFrame.getWidth());
- state.setHeight(viewFrame.getHeight());
- final String viewId = viewFrame.getViewId();
- state.setViewId(viewId);
- state.setAlignwithAlignPanel(viewFrame.isUsedforaligment(ap));
- state.setColourwithAlignPanel(viewFrame.isUsedForColourBy(ap));
- state.setColourByJmol(viewFrame.isColouredByViewer());
- state.setType(viewFrame.getViewerType().toString());
- // pdb.addStructureState(state);
- pdb.getStructureState().add(state);
- }
- }
- }
- return matchedFile;
- }
-
- /**
- * Populates the AnnotationColourScheme xml for save. This captures the
- * settings of the options in the 'Colour by Annotation' dialog.
- *
- * @param acg
- * @param userColours
- * @param jm
- * @return
- */
- private AnnotationColourScheme constructAnnotationColours(
- AnnotationColourGradient acg, List<UserColourScheme> userColours,
- JalviewModel jm)
- {
- AnnotationColourScheme ac = new AnnotationColourScheme();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- // 2.10.2 save annotationId (unique) not annotation label
- ac.setAnnotation(acg.getAnnotation().annotationId);
- if (acg.getBaseColour() instanceof UserColourScheme)
- {
- ac.setColourScheme(
- setUserColourScheme(acg.getBaseColour(), userColours, jm));
- }
- else
- {
- ac.setColourScheme(
- ColourSchemeProperty.getColourName(acg.getBaseColour()));
- }
-
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- ac.setPerSequence(acg.isSeqAssociated());
- ac.setPredefinedColours(acg.isPredefinedColours());
- return ac;
- }
-
- private void storeAlignmentAnnotation(AlignmentAnnotation[] aa,
- IdentityHashMap<SequenceGroup, String> groupRefs,
- AlignmentViewport av, Set<String> calcIdSet, boolean storeDS,
- SequenceSet vamsasSet)
- {
-
- for (int i = 0; i < aa.length; i++)
- {
- Annotation an = new Annotation();
-
- AlignmentAnnotation annotation = aa[i];
- if (annotation.annotationId != null)
- {
- annotationIds.put(annotation.annotationId, annotation);
- }
-
- an.setId(annotation.annotationId);
-
- an.setVisible(annotation.visible);
-
- an.setDescription(annotation.description);
-
- if (annotation.sequenceRef != null)
- {
- // 2.9 JAL-1781 xref on sequence id rather than name
- an.setSequenceRef(seqsToIds.get(annotation.sequenceRef));
- }
- if (annotation.groupRef != null)
- {
- String groupIdr = groupRefs.get(annotation.groupRef);
- if (groupIdr == null)
- {
- // make a locally unique String
- groupRefs.put(annotation.groupRef,
- groupIdr = ("" + System.currentTimeMillis()
- + annotation.groupRef.getName()
- + groupRefs.size()));
- }
- an.setGroupRef(groupIdr.toString());
- }
-
- // store all visualization attributes for annotation
- an.setGraphHeight(annotation.graphHeight);
- an.setCentreColLabels(annotation.centreColLabels);
- an.setScaleColLabels(annotation.scaleColLabel);
- an.setShowAllColLabels(annotation.showAllColLabels);
- an.setBelowAlignment(annotation.belowAlignment);
-
- if (annotation.graph > 0)
- {
- an.setGraph(true);
- an.setGraphType(annotation.graph);
- an.setGraphGroup(annotation.graphGroup);
- if (annotation.getThreshold() != null)
- {
- ThresholdLine line = new ThresholdLine();
- line.setLabel(annotation.getThreshold().label);
- line.setValue(annotation.getThreshold().value);
- line.setColour(annotation.getThreshold().colour.getRGB());
- an.setThresholdLine(line);
- }
- }
- else
- {
- an.setGraph(false);
- }
-
- an.setLabel(annotation.label);
-
- if (annotation == av.getAlignmentQualityAnnot()
- || annotation == av.getAlignmentConservationAnnotation()
- || annotation == av.getAlignmentConsensusAnnotation()
- || annotation.autoCalculated)
- {
- // new way of indicating autocalculated annotation -
- an.setAutoCalculated(annotation.autoCalculated);
- }
- if (annotation.hasScore())
- {
- an.setScore(annotation.getScore());
- }
-
- if (annotation.getCalcId() != null)
- {
- calcIdSet.add(annotation.getCalcId());
- an.setCalcId(annotation.getCalcId());
- }
- if (annotation.hasProperties())
- {
- for (String pr : annotation.getProperties())
- {
- jalview.xml.binding.jalview.Annotation.Property prop = new jalview.xml.binding.jalview.Annotation.Property();
- prop.setName(pr);
- prop.setValue(annotation.getProperty(pr));
- // an.addProperty(prop);
- an.getProperty().add(prop);
- }
- }
-
- AnnotationElement ae;
- if (annotation.annotations != null)
- {
- an.setScoreOnly(false);
- for (int a = 0; a < annotation.annotations.length; a++)
- {
- if ((annotation == null) || (annotation.annotations[a] == null))
- {
- continue;
- }
-
- ae = new AnnotationElement();
- if (annotation.annotations[a].description != null)
- {
- ae.setDescription(annotation.annotations[a].description);
- }
- if (annotation.annotations[a].displayCharacter != null)
- {
- ae.setDisplayCharacter(
- annotation.annotations[a].displayCharacter);
- }
-
- if (!Float.isNaN(annotation.annotations[a].value))
- {
- ae.setValue(annotation.annotations[a].value);
- }
-
- ae.setPosition(a);
- if (annotation.annotations[a].secondaryStructure > ' ')
- {
- ae.setSecondaryStructure(
- annotation.annotations[a].secondaryStructure + "");
- }
-
- if (annotation.annotations[a].colour != null
- && annotation.annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(annotation.annotations[a].colour.getRGB());
- }
-
- // an.addAnnotationElement(ae);
- an.getAnnotationElement().add(ae);
- if (annotation.autoCalculated)
- {
- // only write one non-null entry into the annotation row -
- // sufficient to get the visualization attributes necessary to
- // display data
- continue;
- }
- }
- }
- else
- {
- an.setScoreOnly(true);
- }
- if (!storeDS || (storeDS && !annotation.autoCalculated))
- {
- // skip autocalculated annotation - these are only provided for
- // alignments
- // vamsasSet.addAnnotation(an);
- vamsasSet.getAnnotation().add(an);
- }
- }
-
- }
-
- private CalcIdParam createCalcIdParam(String calcId, AlignViewport av)
- {
- AutoCalcSetting settings = av.getCalcIdSettingsFor(calcId);
- if (settings != null)
- {
- CalcIdParam vCalcIdParam = new CalcIdParam();
- vCalcIdParam.setCalcId(calcId);
- // vCalcIdParam.addServiceURL(settings.getServiceURI());
- vCalcIdParam.getServiceURL().add(settings.getServiceURI());
- // generic URI allowing a third party to resolve another instance of the
- // service used for this calculation
- for (String url : settings.getServiceURLs())
- {
- // vCalcIdParam.addServiceURL(urls);
- vCalcIdParam.getServiceURL().add(url);
- }
- vCalcIdParam.setVersion("1.0");
- if (settings.getPreset() != null)
- {
- WsParamSetI setting = settings.getPreset();
- vCalcIdParam.setName(setting.getName());
- vCalcIdParam.setDescription(setting.getDescription());
- }
- else
- {
- vCalcIdParam.setName("");
- vCalcIdParam.setDescription("Last used parameters");
- }
- // need to be able to recover 1) settings 2) user-defined presets or
- // recreate settings from preset 3) predefined settings provided by
- // service - or settings that can be transferred (or discarded)
- vCalcIdParam.setParameters(
- settings.getWsParamFile().replace("\n", "|\\n|"));
- vCalcIdParam.setAutoUpdate(settings.isAutoUpdate());
- // todo - decide if updateImmediately is needed for any projects.
-
- return vCalcIdParam;
- }
- return null;
- }
-
- private boolean recoverCalcIdParam(CalcIdParam calcIdParam,
- AlignViewport av)
- {
- if (calcIdParam.getVersion().equals("1.0"))
- {
- final String[] calcIds = calcIdParam.getServiceURL().toArray(new String[0]);
- ServiceWithParameters service = PreferredServiceRegistry.getRegistry()
- .getPreferredServiceFor(calcIds);
- if (service != null)
- {
- WsParamSetI parmSet = null;
- try
- {
- parmSet = service.getParamStore().parseServiceParameterFile(
- calcIdParam.getName(), calcIdParam.getDescription(),
- calcIds,
- calcIdParam.getParameters().replace("|\\n|", "\n"));
- } catch (IOException x)
- {
- warn("Couldn't parse parameter data for "
- + calcIdParam.getCalcId(), x);
- return false;
- }
- List<ArgumentI> argList = null;
- if (calcIdParam.getName().length() > 0)
- {
- parmSet = service.getParamStore()
- .getPreset(calcIdParam.getName());
- if (parmSet != null)
- {
- // TODO : check we have a good match with settings in AACon -
- // otherwise we'll need to create a new preset
- }
- }
- else
- {
- argList = parmSet.getArguments();
- parmSet = null;
- }
- AutoCalcSetting settings = new AAConSettings(
- calcIdParam.isAutoUpdate(), service, parmSet, argList);
- av.setCalcIdSettingsFor(calcIdParam.getCalcId(), settings,
- calcIdParam.isNeedsUpdate());
- return true;
- }
- else
- {
- warn("Cannot resolve a service for the parameters used in this project. Try configuring a server in the Web Services preferences tab.");
- return false;
- }
- }
- throw new Error(MessageManager.formatMessage(
- "error.unsupported_version_calcIdparam", new Object[]
- { calcIdParam.toString() }));
- }
-
- /**
- * External mapping between jalview objects and objects yielding a valid and
- * unique object ID string. This is null for normal Jalview project IO, but
- * non-null when a jalview project is being read or written as part of a
- * vamsas session.
- */
- IdentityHashMap jv2vobj = null;
-
- /**
- * Construct a unique ID for jvobj using either existing bindings or if none
- * exist, the result of the hashcode call for the object.
- *
- * @param jvobj
- * jalview data object
- * @return unique ID for referring to jvobj
- */
- private String makeHashCode(Object jvobj, String altCode)
- {
- if (jv2vobj != null)
- {
- Object id = jv2vobj.get(jvobj);
- if (id != null)
- {
- return id.toString();
- }
- // check string ID mappings
- if (jvids2vobj != null && jvobj instanceof String)
- {
- id = jvids2vobj.get(jvobj);
- }
- if (id != null)
- {
- return id.toString();
- }
- // give up and warn that something has gone wrong
- warn("Cannot find ID for object in external mapping : " + jvobj);
- }
- return altCode;
- }
-
- /**
- * return local jalview object mapped to ID, if it exists
- *
- * @param idcode
- * (may be null)
- * @return null or object bound to idcode
- */
- private Object retrieveExistingObj(String idcode)
- {
- if (idcode != null && vobj2jv != null)
- {
- return vobj2jv.get(idcode);
- }
- return null;
- }
-
- /**
- * binding from ID strings from external mapping table to jalview data model
- * objects.
- */
- private Hashtable vobj2jv;
-
- private Sequence createVamsasSequence(String id, SequenceI jds)
- {
- return createVamsasSequence(true, id, jds, null);
- }
-
- private Sequence createVamsasSequence(boolean recurse, String id,
- SequenceI jds, SequenceI parentseq)
- {
- Sequence vamsasSeq = new Sequence();
- vamsasSeq.setId(id);
- vamsasSeq.setName(jds.getName());
- vamsasSeq.setSequence(jds.getSequenceAsString());
- vamsasSeq.setDescription(jds.getDescription());
- List<DBRefEntry> dbrefs = null;
- if (jds.getDatasetSequence() != null)
- {
- vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
- }
- else
- {
- // seqId==dsseqid so we can tell which sequences really are
- // dataset sequences only
- vamsasSeq.setDsseqid(id);
- dbrefs = jds.getDBRefs();
- if (parentseq == null)
- {
- parentseq = jds;
- }
- }
-
- /*
- * save any dbrefs; special subclass GeneLocus is flagged as 'locus'
- */
- if (dbrefs != null)
- {
- for (int d = 0, nd = dbrefs.size(); d < nd; d++)
- {
- DBRef dbref = new DBRef();
- DBRefEntry ref = dbrefs.get(d);
- dbref.setSource(ref.getSource());
- dbref.setVersion(ref.getVersion());
- dbref.setAccessionId(ref.getAccessionId());
- dbref.setCanonical(ref.isCanonical());
- if (ref instanceof GeneLocus)
- {
- dbref.setLocus(true);
- }
- if (ref.hasMap())
- {
- Mapping mp = createVamsasMapping(ref.getMap(), parentseq,
- jds, recurse);
- dbref.setMapping(mp);
- }
- vamsasSeq.getDBRef().add(dbref);
- }
- }
- return vamsasSeq;
- }
-
- private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
- SequenceI parentseq, SequenceI jds, boolean recurse)
- {
- Mapping mp = null;
- if (jmp.getMap() != null)
- {
- mp = new Mapping();
-
- jalview.util.MapList mlst = jmp.getMap();
- List<int[]> r = mlst.getFromRanges();
- for (int[] range : r)
- {
- MapListFrom mfrom = new MapListFrom();
- mfrom.setStart(range[0]);
- mfrom.setEnd(range[1]);
- // mp.addMapListFrom(mfrom);
- mp.getMapListFrom().add(mfrom);
- }
- r = mlst.getToRanges();
- for (int[] range : r)
- {
- MapListTo mto = new MapListTo();
- mto.setStart(range[0]);
- mto.setEnd(range[1]);
- // mp.addMapListTo(mto);
- mp.getMapListTo().add(mto);
- }
- mp.setMapFromUnit(BigInteger.valueOf(mlst.getFromRatio()));
- mp.setMapToUnit(BigInteger.valueOf(mlst.getToRatio()));
- if (jmp.getTo() != null)
- {
- // MappingChoice mpc = new MappingChoice();
-
- // check/create ID for the sequence referenced by getTo()
-
- String jmpid = "";
- SequenceI ps = null;
- if (parentseq != jmp.getTo()
- && parentseq.getDatasetSequence() != jmp.getTo())
- {
- // chaining dbref rather than a handshaking one
- jmpid = seqHash(ps = jmp.getTo());
- }
- else
- {
- jmpid = seqHash(ps = parentseq);
- }
- // mpc.setDseqFor(jmpid);
- mp.setDseqFor(jmpid);
- if (!seqRefIds.containsKey(jmpid))
- {
- jalview.bin.Cache.log.debug("creatign new DseqFor ID");
- seqRefIds.put(jmpid, ps);
- }
- else
- {
- jalview.bin.Cache.log.debug("reusing DseqFor ID");
- }
-
- // mp.setMappingChoice(mpc);
- }
- }
- return mp;
- }
-
- String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
- List<UserColourScheme> userColours, JalviewModel jm)
- {
- String id = null;
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
- boolean newucs = false;
- if (!userColours.contains(ucs))
- {
- userColours.add(ucs);
- newucs = true;
- }
- id = "ucs" + userColours.indexOf(ucs);
- if (newucs)
- {
- // actually create the scheme's entry in the XML model
- java.awt.Color[] colours = ucs.getColours();
- UserColours uc = new UserColours();
- // UserColourScheme jbucs = new UserColourScheme();
- JalviewUserColours jbucs = new JalviewUserColours();
-
- for (int i = 0; i < colours.length; i++)
- {
- Colour col = new Colour();
- col.setName(ResidueProperties.aa[i]);
- col.setRGB(jalview.util.Format.getHexString(colours[i]));
- // jbucs.addColour(col);
- jbucs.getColour().add(col);
- }
- if (ucs.getLowerCaseColours() != null)
- {
- colours = ucs.getLowerCaseColours();
- for (int i = 0; i < colours.length; i++)
- {
- Colour col = new Colour();
- col.setName(ResidueProperties.aa[i].toLowerCase(Locale.ROOT));
- col.setRGB(jalview.util.Format.getHexString(colours[i]));
- // jbucs.addColour(col);
- jbucs.getColour().add(col);
- }
- }
-
- uc.setId(id);
- uc.setUserColourScheme(jbucs);
- // jm.addUserColours(uc);
- jm.getUserColours().add(uc);
- }
-
- return id;
- }
-
- jalview.schemes.UserColourScheme getUserColourScheme(JalviewModel jm,
- String id)
- {
- List<UserColours> uc = jm.getUserColours();
- UserColours colours = null;
- /*
- for (int i = 0; i < uc.length; i++)
- {
- if (uc[i].getId().equals(id))
- {
- colours = uc[i];
- break;
- }
- }
- */
- for (UserColours c : uc)
- {
- if (c.getId().equals(id))
- {
- colours = c;
- break;
- }
- }
-
- java.awt.Color[] newColours = new java.awt.Color[24];
-
- for (int i = 0; i < 24; i++)
- {
- newColours[i] = new java.awt.Color(Integer.parseInt(
- // colours.getUserColourScheme().getColour(i).getRGB(), 16));
- colours.getUserColourScheme().getColour().get(i).getRGB(),
- 16));
- }
-
- jalview.schemes.UserColourScheme ucs = new jalview.schemes.UserColourScheme(
- newColours);
-
- if (colours.getUserColourScheme().getColour().size()/*Count()*/ > 24)
- {
- newColours = new java.awt.Color[23];
- for (int i = 0; i < 23; i++)
- {
- newColours[i] = new java.awt.Color(
- Integer.parseInt(colours.getUserColourScheme().getColour()
- .get(i + 24).getRGB(), 16));
- }
- ucs.setLowerCaseColours(newColours);
- }
-
- return ucs;
- }
- /**
- * contains last error message (if any) encountered by XML loader.
- */
- String errorMessage = null;
-
- /**
- * flag to control whether the Jalview2XML_V1 parser should be deferred to if
- * exceptions are raised during project XML parsing
- */
- public boolean attemptversion1parse = false;
-
- /**
- * Load a jalview project archive from a jar file
- *
- * @param file
- * - HTTP URL or filename
- */
- public AlignFrame loadJalviewAlign(final Object file)
- {
-
- jalview.gui.AlignFrame af = null;
-
- try
- {
- // create list to store references for any new Jmol viewers created
- newStructureViewers = new Vector<>();
- // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- // Workaround is to make sure caller implements the JarInputStreamProvider
- // interface
- // so we can re-open the jar input stream for each entry.
-
- jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
- af = loadJalviewAlign(jprovider);
- if (af != null)
- {
- af.setMenusForViewport();
- }
- } catch (MalformedURLException e)
- {
- errorMessage = "Invalid URL format for '" + file + "'";
- reportErrors();
- } finally
- {
- try
- {
-// was invokeAndWait
-
- // BH 2019 -- can't wait
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- setLoadingFinishedForNewStructureViewers();
- }
- });
- } catch (Exception x)
- {
- System.err.println("Error loading alignment: " + x.getMessage());
- }
- }
- this.jarFile = null;
- return af;
- }
-
- @SuppressWarnings("unused")
- private jarInputStreamProvider createjarInputStreamProvider(
- final Object ofile) throws MalformedURLException
- {
- try
- {
- String file = (ofile instanceof File
- ? ((File) ofile).getCanonicalPath()
- : ofile.toString());
- byte[] bytes = Platform.isJS() ? Platform.getFileBytes((File) ofile)
- : null;
- if (bytes != null)
- {
- this.jarFile = (File) ofile;
- }
- URL url = null;
- errorMessage = null;
- uniqueSetSuffix = null;
- seqRefIds = null;
- viewportsAdded.clear();
- frefedSequence = null;
-
- if (HttpUtils.startsWithHttpOrHttps(file))
- {
- url = new URL(file);
- }
- return new jarInputStreamProvider()
- {
- @Override
- public JarInputStream getJarInputStream() throws IOException
- {
- InputStream is = bytes != null ? new ByteArrayInputStream(bytes)
- : (url != null ? url.openStream()
- : new FileInputStream(file));
- return new JarInputStream(is);
- }
-
- @Override
- public File getFile()
- {
- return jarFile;
- }
-
- @Override
- public String getFilename()
- {
- return file;
- }
- };
- } catch (IOException e)
- {
- e.printStackTrace();
- return null;
- }
- }
-
- /**
- * Recover jalview session from a jalview project archive. Caller may
- * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
- * themselves. Any null fields will be initialised with default values,
- * non-null fields are left alone.
- *
- * @param jprovider
- * @return
- */
- public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
- {
- errorMessage = null;
- if (uniqueSetSuffix == null)
- {
- uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
- }
- if (seqRefIds == null)
- {
- initSeqRefs();
- }
- AlignFrame af = null, _af = null;
- IdentityHashMap<AlignmentI, AlignmentI> importedDatasets = new IdentityHashMap<>();
- Map<String, AlignFrame> gatherToThisFrame = new HashMap<>();
- String fileName = jprovider.getFilename();
- File file = jprovider.getFile();
- List<AlignFrame> alignFrames = new ArrayList<>();
- try
- {
- JarInputStream jin = null;
- JarEntry jarentry = null;
- int entryCount = 1;
-
- // Look for all the entry names ending with ".xml"
- // This includes all panels and at least one frame.
-// Platform.timeCheck(null, Platform.TIME_MARK);
- do
- {
- jin = jprovider.getJarInputStream();
- for (int i = 0; i < entryCount; i++)
- {
- jarentry = jin.getNextJarEntry();
- }
- String name = (jarentry == null ? null : jarentry.getName());
-
-// System.out.println("Jalview2XML opening " + name);
- if (name != null && name.endsWith(".xml"))
- {
- // DataSet for.... is read last.
-
-
- // The question here is what to do with the two
- // .xml files in the jvp file.
- // Some number of them, "...Dataset for...", will be the
- // Only AlignPanels and will have Viewport.
- // One or more will be the source data, with the DBRefs.
- //
- // JVP file writing (above) ensures tha the AlignPanels are written
- // first, then all relevant datasets (which are
- // Jalview.datamodel.Alignment).
- //
-
-// Platform.timeCheck("Jalview2XML JAXB " + name, Platform.TIME_MARK);
- JAXBContext jc = JAXBContext
- .newInstance("jalview.xml.binding.jalview");
- XMLStreamReader streamReader = XMLInputFactory.newInstance()
- .createXMLStreamReader(jin);
- javax.xml.bind.Unmarshaller um = jc.createUnmarshaller();
- JAXBElement<JalviewModel> jbe = um
- .unmarshal(streamReader, JalviewModel.class);
- JalviewModel model = jbe.getValue();
-
- if (true) // !skipViewport(object))
- {
- // Q: Do we have to load from the model, even if it
- // does not have a viewport, could we discover that early on?
- // Q: Do we need to load this object?
- _af = loadFromObject(model, fileName, file, true, jprovider);
-// Platform.timeCheck("Jalview2XML.loadFromObject",
- // Platform.TIME_MARK);
-
- if (_af != null)
- {
- alignFrames.add(_af);
- }
- if (_af != null && model.getViewport().size() > 0)
- {
-
- // That is, this is one of the AlignmentPanel models
- if (af == null)
- {
- // store a reference to the first view
- af = _af;
- }
- if (_af.getViewport().isGatherViewsHere())
- {
- // if this is a gathered view, keep its reference since
- // after gathering views, only this frame will remain
- af = _af;
- gatherToThisFrame.put(_af.getViewport().getSequenceSetId(),
- _af);
- }
- // Save dataset to register mappings once all resolved
- importedDatasets.put(
- af.getViewport().getAlignment().getDataset(),
- af.getViewport().getAlignment().getDataset());
- }
- }
- entryCount++;
- }
- else if (jarentry != null)
- {
- // Some other file here.
- entryCount++;
- }
- } while (jarentry != null);
- resolveFrefedSequences();
- } catch (IOException ex)
- {
- ex.printStackTrace();
- errorMessage = "Couldn't locate Jalview XML file : " + fileName;
- System.err.println(
- "Exception whilst loading jalview XML file : " + ex + "\n");
- } catch (Exception ex)
- {
- System.err.println("Parsing as Jalview Version 2 file failed.");
- ex.printStackTrace(System.err);
- if (attemptversion1parse)
- {
- // used to attempt to parse as V1 castor-generated xml
- }
- if (Desktop.getInstance() != null)
- {
- Desktop.getInstance().stopLoading();
- }
- if (af != null)
- {
- System.out.println("Successfully loaded archive file");
- return af;
- }
- ex.printStackTrace();
-
- System.err.println(
- "Exception whilst loading jalview XML file : " + ex + "\n");
- } catch (OutOfMemoryError e)
- {
- // Don't use the OOM Window here
- errorMessage = "Out of memory loading jalview XML file";
- System.err.println("Out of memory whilst loading jalview XML file");
- e.printStackTrace();
- } finally
- {
- for (AlignFrame alf : alignFrames)
- {
- alf.alignPanel.setHoldRepaint(false);
- }
- }
-
- /*
- * Regather multiple views (with the same sequence set id) to the frame (if
- * any) that is flagged as the one to gather to, i.e. convert them to tabbed
- * views instead of separate frames. Note this doesn't restore a state where
- * some expanded views in turn have tabbed views - the last "first tab" read
- * in will play the role of gatherer for all.
- */
- for (AlignFrame fr : gatherToThisFrame.values())
- {
- Desktop.getInstance().gatherViews(fr);
- }
-
- restoreSplitFrames();
- for (AlignmentI ds : importedDatasets.keySet())
- {
- if (ds.getCodonFrames() != null)
- {
- Desktop.getStructureSelectionManager()
- .registerMappings(ds.getCodonFrames());
- }
- }
- if (errorMessage != null)
- {
- reportErrors();
- }
-
- if (Desktop.getInstance() != null)
- {
- Desktop.getInstance().stopLoading();
- }
-
- return af;
- }
-
- /**
- * Try to reconstruct and display SplitFrame windows, where each contains
- * complementary dna and protein alignments. Done by pairing up AlignFrame
- * objects (created earlier) which have complementary viewport ids associated.
- */
- protected void restoreSplitFrames()
- {
- List<SplitFrame> gatherTo = new ArrayList<>();
- List<AlignFrame> addedToSplitFrames = new ArrayList<>();
- Map<String, AlignFrame> dna = new HashMap<>();
-
- /*
- * Identify the DNA alignments
- */
- for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
- .entrySet())
- {
- AlignFrame af = candidate.getValue();
- if (af.getViewport().getAlignment().isNucleotide())
- {
- dna.put(candidate.getKey().getId(), af);
- }
- }
-
- /*
- * Try to match up the protein complements
- */
- for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
- .entrySet())
- {
- AlignFrame af = candidate.getValue();
- if (!af.getViewport().getAlignment().isNucleotide())
- {
- String complementId = candidate.getKey().getComplementId();
- // only non-null complements should be in the Map
- if (complementId != null && dna.containsKey(complementId))
- {
- final AlignFrame dnaFrame = dna.get(complementId);
- SplitFrame sf = createSplitFrame(dnaFrame, af);
- addedToSplitFrames.add(dnaFrame);
- addedToSplitFrames.add(af);
- dnaFrame.setMenusForViewport();
- af.setMenusForViewport();
- if (af.getViewport().isGatherViewsHere())
- {
- gatherTo.add(sf);
- }
- }
- }
- }
-
- /*
- * Open any that we failed to pair up (which shouldn't happen!) as
- * standalone AlignFrame's.
- */
- for (Entry<Viewport, AlignFrame> candidate : splitFrameCandidates
- .entrySet())
- {
- AlignFrame af = candidate.getValue();
- if (!addedToSplitFrames.contains(af))
- {
- Viewport view = candidate.getKey();
- Desktop.addInternalFrame(af, view.getTitle(),
- safeInt(view.getWidth()), safeInt(view.getHeight()));
- af.setMenusForViewport();
- System.err.println("Failed to restore view " + view.getTitle()
- + " to split frame");
- }
- }
-
- /*
- * Gather back into tabbed views as flagged.
- */
- for (SplitFrame sf : gatherTo)
- {
- Desktop.getInstance().gatherViews(sf);
- }
-
- splitFrameCandidates.clear();
- }
-
- /**
- * Construct and display one SplitFrame holding DNA and protein alignments.
- *
- * @param dnaFrame
- * @param proteinFrame
- * @return
- */
- protected SplitFrame createSplitFrame(AlignFrame dnaFrame,
- AlignFrame proteinFrame)
- {
- SplitFrame splitFrame = new SplitFrame(dnaFrame, proteinFrame);
- String title = MessageManager.getString("label.linked_view_title");
- int width = (int) dnaFrame.getBounds().getWidth();
- int height = (int) (dnaFrame.getBounds().getHeight()
- + proteinFrame.getBounds().getHeight() + 50);
-
- /*
- * SplitFrame location is saved to both enclosed frames
- */
- splitFrame.setLocation(dnaFrame.getX(), dnaFrame.getY());
- Desktop.addInternalFrame(splitFrame, title, width, height);
-
- /*
- * And compute cDNA consensus (couldn't do earlier with consensus as
- * mappings were not yet present)
- */
- proteinFrame.getViewport().alignmentChanged(proteinFrame.alignPanel);
-
- return splitFrame;
- }
-
- /**
- * check errorMessage for a valid error message and raise an error box in the
- * GUI or write the current errorMessage to stderr and then clear the error
- * state.
- */
- protected void reportErrors()
- {
- reportErrors(false);
- }
-
- protected void reportErrors(final boolean saving)
- {
- if (errorMessage != null)
- {
- final String finalErrorMessage = errorMessage;
- if (raiseGUI)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- JvOptionPane.showInternalMessageDialog(Desktop.getDesktopPane(),
- finalErrorMessage,
- "Error " + (saving ? "saving" : "loading")
- + " Jalview file",
- JvOptionPane.WARNING_MESSAGE);
- }
- });
- }
- else
- {
- System.err.println("Problem loading Jalview file: " + errorMessage);
- }
- }
- errorMessage = null;
- }
-
- Map<String, String> alreadyLoadedPDB = new HashMap<>();
-
- /**
- * when set, local views will be updated from view stored in JalviewXML
- * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
- * sync if this is set to true.
- */
- private final boolean updateLocalViews = false;
-
- /**
- * Returns the path to a temporary file holding the PDB file for the given PDB
- * id. The first time of asking, searches for a file of that name in the
- * Jalview project jar, and copies it to a new temporary file. Any repeat
- * requests just return the path to the file previously created.
- *
- * @param jprovider
- * @param pdbId
- * @return
- */
- String loadPDBFile(jarInputStreamProvider jprovider, String pdbId,
- String origFile)
- {
- if (alreadyLoadedPDB.containsKey(pdbId))
- {
- return alreadyLoadedPDB.get(pdbId).toString();
- }
-
- String tempFile = copyJarEntry(jprovider, pdbId, "jalview_pdb",
- origFile);
- if (tempFile != null)
- {
- alreadyLoadedPDB.put(pdbId, tempFile);
- }
- return tempFile;
- }
-
- /**
- * Copies the jar entry of given name to a new temporary file and returns the
- * path to the file, or null if the entry is not found.
- *
- * @param jprovider
- * @param jarEntryName
- * @param prefix
- * a prefix for the temporary file name, must be at least three
- * characters long
- * @param origFile
- * 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)
- {
- BufferedReader in = null;
- PrintWriter out = null;
- String suffix = ".tmp";
- if (origFile == null)
- {
- origFile = jarEntryName;
- }
- int sfpos = origFile.lastIndexOf(".");
- if (sfpos > -1 && sfpos < (origFile.length() - 3))
- {
- suffix = "." + origFile.substring(sfpos + 1);
- }
- 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));
- File outFile = File.createTempFile(prefix, suffix);
- outFile.deleteOnExit();
- try (OutputStream os = new FileOutputStream(outFile))
- {
- copyAll(jin, os);
- }
- String t = outFile.getAbsolutePath();
- return t;
- }
- else
- {
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
- }
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
-
- return null;
- }
-
- private class JvAnnotRow
- {
- public JvAnnotRow(int i, AlignmentAnnotation jaa)
- {
- order = i;
- template = jaa;
- }
-
- /**
- * persisted version of annotation row from which to take vis properties
- */
- public jalview.datamodel.AlignmentAnnotation template;
-
- /**
- * original position of the annotation row in the alignment
- */
- public int order;
- }
-
- /**
- * Load alignment frame from jalview XML DOM object. For a DOM object that
- * includes one or more Viewport elements (one with a title that does NOT
- * contain "Dataset for"), create the frame.
- *
- * @param jalviewModel
- * DOM
- * @param fileName
- * filename source string
- * @param file
- * @param loadTreesAndStructures
- * when false only create Viewport
- * @param jprovider
- * data source provider
- * @return alignment frame created from view stored in DOM
- */
- AlignFrame loadFromObject(JalviewModel jalviewModel, String fileName,
- File file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
- {
- SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0);
- List<Sequence> vamsasSeqs = vamsasSet.getSequence();
-
- // JalviewModelSequence jms = object.getJalviewModelSequence();
-
- // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
- // : null;
- Viewport view = (jalviewModel.getViewport().size() > 0)
- ? jalviewModel.getViewport().get(0)
- : null;
-
- // ////////////////////////////////
- // INITIALISE ALIGNMENT SEQUENCESETID AND VIEWID
- //
- //
- // If we just load in the same jar file again, the sequenceSetId
- // will be the same, and we end up with multiple references
- // to the same sequenceSet. We must modify this id on load
- // so that each load of the file gives a unique id
-
- /**
- * used to resolve correct alignment dataset for alignments with multiple
- * views
- */
- String uniqueSeqSetId = null;
- String viewId = null;
- if (view != null)
- {
- uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
- viewId = (view.getId() == null ? null
- : view.getId() + uniqueSetSuffix);
- }
-
- // ////////////////////////////////
- // LOAD SEQUENCES
-
- List<SequenceI> hiddenSeqs = null;
-
- List<SequenceI> tmpseqs = new ArrayList<>();
-
- boolean multipleView = false;
- SequenceI referenceseqForView = null;
- // JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
- List<JSeq> jseqs = jalviewModel.getJSeq();
- int vi = 0; // counter in vamsasSeq array
- for (int i = 0; i < jseqs.size(); i++)
- {
- JSeq jseq = jseqs.get(i);
- String seqId = jseq.getId();
-
- SequenceI tmpSeq = seqRefIds.get(seqId);
- if (tmpSeq != null)
- {
- if (!incompleteSeqs.containsKey(seqId))
- {
- // may not need this check, but keep it for at least 2.9,1 release
- if (tmpSeq.getStart() != jseq.getStart()
- || tmpSeq.getEnd() != jseq.getEnd())
- {
- System.err.println(
- 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
- {
- incompleteSeqs.remove(seqId);
- }
- if (vamsasSeqs.size() > vi
- && vamsasSeqs.get(vi).getId().equals(seqId))
- {
- // most likely we are reading a dataset XML document so
- // update from vamsasSeq section of XML for this sequence
- tmpSeq.setName(vamsasSeqs.get(vi).getName());
- tmpSeq.setDescription(vamsasSeqs.get(vi).getDescription());
- tmpSeq.setSequence(vamsasSeqs.get(vi).getSequence());
- vi++;
- }
- else
- {
- // reading multiple views, so vamsasSeq set is a subset of JSeq
- multipleView = true;
- }
- tmpSeq.setStart(jseq.getStart());
- tmpSeq.setEnd(jseq.getEnd());
- tmpseqs.add(tmpSeq);
- }
- else
- {
- Sequence vamsasSeq = vamsasSeqs.get(vi);
- tmpSeq = new jalview.datamodel.Sequence(vamsasSeq.getName(),
- vamsasSeq.getSequence());
- tmpSeq.setDescription(vamsasSeq.getDescription());
- tmpSeq.setStart(jseq.getStart());
- tmpSeq.setEnd(jseq.getEnd());
- tmpSeq.setVamsasId(uniqueSetSuffix + seqId);
- seqRefIds.put(vamsasSeq.getId(), tmpSeq);
- tmpseqs.add(tmpSeq);
- vi++;
- }
-
- if (safeBoolean(jseq.isViewreference()))
- {
- referenceseqForView = tmpseqs.get(tmpseqs.size() - 1);
- }
-
- if (jseq.isHidden() != null && jseq.isHidden().booleanValue())
- {
- if (hiddenSeqs == null)
- {
- hiddenSeqs = new ArrayList<>();
- }
-
- hiddenSeqs.add(tmpSeq);
- }
- }
-
- // /
- // Create the alignment object from the sequence set
- // ///////////////////////////////
- SequenceI[] orderedSeqs = tmpseqs
- .toArray(new SequenceI[tmpseqs.size()]);
-
- AlignmentI al = null;
- // so we must create or recover the dataset alignment before going further
- // ///////////////////////////////
- if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
- {
- // older jalview projects do not have a dataset - so creat alignment and
- // dataset
- al = new Alignment(orderedSeqs);
- al.setDataset(null);
- }
- else
- {
- boolean isdsal = jalviewModel.getViewport().isEmpty();
- if (isdsal)
- {
- // we are importing a dataset record, so
- // recover reference to an alignment already materialsed as dataset
- al = getDatasetFor(vamsasSet.getDatasetId());
- }
- if (al == null)
- {
- // materialse the alignment
- al = new Alignment(orderedSeqs);
- }
- if (isdsal)
- {
- addDatasetRef(vamsasSet.getDatasetId(), al);
- }
-
- // finally, verify all data in vamsasSet is actually present in al
- // passing on flag indicating if it is actually a stored dataset
- recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId);
- }
-
- if (referenceseqForView != null)
- {
- al.setSeqrep(referenceseqForView);
- }
- // / Add the alignment properties
- for (int i = 0; i < vamsasSet.getSequenceSetProperties().size(); i++)
- {
- SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties()
- .get(i);
- al.setProperty(ssp.getKey(), ssp.getValue());
- }
-
- // ///////////////////////////////
-
- Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this??
- if (!multipleView)
- {
- // load sequence features, database references and any associated PDB
- // structures for the alignment
- //
- // prior to 2.10, this part would only be executed the first time a
- // sequence was encountered, but not afterwards.
- // now, for 2.10 projects, this is also done if the xml doc includes
- // dataset sequences not actually present in any particular view.
- //
- for (int i = 0; i < vamsasSeqs.size(); i++)
- {
- JSeq jseq = jseqs.get(i);
- if (jseq.getFeatures().size() > 0)
- {
- List<Feature> features = jseq.getFeatures();
- for (int f = 0; f < features.size(); f++)
- {
- Feature feat = features.get(f);
- SequenceFeature sf = new SequenceFeature(feat.getType(),
- feat.getDescription(), feat.getBegin(), feat.getEnd(),
- safeFloat(feat.getScore()), feat.getFeatureGroup());
- sf.setStatus(feat.getStatus());
-
- /*
- * load any feature attributes - include map-valued attributes
- */
- Map<String, Map<String, String>> mapAttributes = new HashMap<>();
- for (int od = 0; od < feat.getOtherData().size(); od++)
- {
- OtherData keyValue = feat.getOtherData().get(od);
- String attributeName = keyValue.getKey();
- String attributeValue = keyValue.getValue();
- if (attributeName.startsWith("LINK"))
- {
- sf.addLink(attributeValue);
- }
- else
- {
- String subAttribute = keyValue.getKey2();
- if (subAttribute == null)
- {
- // simple string-valued attribute
- sf.setValue(attributeName, attributeValue);
- }
- else
- {
- // attribute 'key' has sub-attribute 'key2'
- if (!mapAttributes.containsKey(attributeName))
- {
- mapAttributes.put(attributeName, new HashMap<>());
- }
- mapAttributes.get(attributeName).put(subAttribute,
- attributeValue);
- }
- }
- }
- for (Entry<String, Map<String, String>> mapAttribute : mapAttributes
- .entrySet())
- {
- sf.setValue(mapAttribute.getKey(), mapAttribute.getValue());
- }
-
- // adds feature to datasequence's feature set (since Jalview 2.10)
- al.getSequenceAt(i).addSequenceFeature(sf);
- }
- }
- if (vamsasSeqs.get(i).getDBRef().size() > 0)
- {
- // adds dbrefs to datasequence's set (since Jalview 2.10)
- addDBRefs(
- al.getSequenceAt(i).getDatasetSequence() == null
- ? al.getSequenceAt(i)
- : al.getSequenceAt(i).getDatasetSequence(),
- vamsasSeqs.get(i));
- }
- if (jseq.getPdbids().size() > 0)
- {
- List<Pdbids> ids = jseq.getPdbids();
- for (int p = 0; p < ids.size(); p++)
- {
- Pdbids pdbid = ids.get(p);
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
- entry.setId(pdbid.getId());
- if (pdbid.getType() != null)
- {
- if (PDBEntry.Type.getType(pdbid.getType()) != null)
- {
- entry.setType(PDBEntry.Type.getType(pdbid.getType()));
- }
- else
- {
- entry.setType(PDBEntry.Type.FILE);
- }
- }
- // jprovider is null when executing 'New View'
- if (pdbid.getFile() != null && jprovider != null)
- {
- if (!pdbloaded.containsKey(pdbid.getFile()))
- {
- entry.setFile(loadPDBFile(jprovider, pdbid.getId(),
- pdbid.getFile()));
- }
- else
- {
- entry.setFile(pdbloaded.get(pdbid.getId()).toString());
- }
- }
- /*
- if (pdbid.getPdbentryItem() != null)
- {
- for (PdbentryItem item : pdbid.getPdbentryItem())
- {
- for (Property pr : item.getProperty())
- {
- entry.setProperty(pr.getName(), pr.getValue());
- }
- }
- }
- */
- for (Property prop : pdbid.getProperty())
- {
- entry.setProperty(prop.getName(), prop.getValue());
- }
- Desktop.getStructureSelectionManager()
- .registerPDBEntry(entry);
- // adds PDBEntry to datasequence's set (since Jalview 2.10)
- if (al.getSequenceAt(i).getDatasetSequence() != null)
- {
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
- }
- else
- {
- al.getSequenceAt(i).addPDBId(entry);
- }
- }
- }
- /*
- * load any HMMER profile
- */
- // TODO fix this
-
- String hmmJarFile = jseqs.get(i).getHmmerProfile();
- if (hmmJarFile != null && jprovider != null)
- {
- loadHmmerProfile(jprovider, hmmJarFile, al.getSequenceAt(i));
- }
- }
- } // end !multipleview
-
- // ///////////////////////////////
- // LOAD SEQUENCE MAPPINGS
-
- if (vamsasSet.getAlcodonFrame().size() > 0)
- {
- // TODO Potentially this should only be done once for all views of an
- // alignment
- List<AlcodonFrame> alc = vamsasSet.getAlcodonFrame();
- for (int i = 0; i < alc.size(); i++)
- {
- AlignedCodonFrame cf = new AlignedCodonFrame();
- if (alc.get(i).getAlcodMap().size() > 0)
- {
- List<AlcodMap> maps = alc.get(i).getAlcodMap();
- for (int m = 0; m < maps.size(); m++)
- {
- AlcodMap map = maps.get(m);
- SequenceI dnaseq = seqRefIds.get(map.getDnasq());
- // Load Mapping
- jalview.datamodel.Mapping mapping = null;
- // attach to dna sequence reference.
- if (map.getMapping() != null)
- {
- mapping = addMapping(map.getMapping());
- if (dnaseq != null && mapping.getTo() != null)
- {
- cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
- }
- else
- {
- // defer to later
- frefedSequence.add(
- newAlcodMapRef(map.getDnasq(), cf, mapping));
- }
- }
- }
- al.addCodonFrame(cf);
- }
- }
- }
-
- // ////////////////////////////////
- // LOAD ANNOTATIONS
- List<JvAnnotRow> autoAlan = new ArrayList<>();
-
- /*
- * store any annotations which forward reference a group's ID
- */
- Map<String, List<AlignmentAnnotation>> groupAnnotRefs = new Hashtable<>();
-
- if (vamsasSet.getAnnotation().size()/*Count()*/ > 0)
- {
- List<Annotation> an = vamsasSet.getAnnotation();
-
- for (int i = 0; i < an.size(); i++)
- {
- Annotation annotation = an.get(i);
-
- /**
- * test if annotation is automatically calculated for this view only
- */
- boolean autoForView = false;
- if (annotation.getLabel().equals("Quality")
- || annotation.getLabel().equals("Conservation")
- || annotation.getLabel().equals("Consensus"))
- {
- // Kludge for pre 2.5 projects which lacked the autocalculated flag
- autoForView = true;
- // JAXB has no has() test; schema defaults value to false
- // if (!annotation.hasAutoCalculated())
- // {
- // annotation.setAutoCalculated(true);
- // }
- }
- if (autoForView || annotation.isAutoCalculated())
- {
- // remove ID - we don't recover annotation from other views for
- // view-specific annotation
- annotation.setId(null);
- }
-
- // set visibility for other annotation in this view
- String annotationId = annotation.getId();
- if (annotationId != null && annotationIds.containsKey(annotationId))
- {
- AlignmentAnnotation jda = annotationIds.get(annotationId);
- // in principle Visible should always be true for annotation displayed
- // in multiple views
- if (annotation.isVisible() != null)
- {
- jda.visible = annotation.isVisible();
- }
-
- al.addAnnotation(jda);
-
- continue;
- }
- // Construct new annotation from model.
- List<AnnotationElement> ae = annotation.getAnnotationElement();
- jalview.datamodel.Annotation[] anot = null;
- java.awt.Color firstColour = null;
- int anpos;
- if (!annotation.isScoreOnly())
- {
- anot = new jalview.datamodel.Annotation[al.getWidth()];
- for (int aa = 0; aa < ae.size() && aa < anot.length; aa++)
- {
- AnnotationElement annElement = ae.get(aa);
- anpos = annElement.getPosition();
-
- if (anpos >= anot.length)
- {
- continue;
- }
-
- float value = safeFloat(annElement.getValue());
- anot[anpos] = new jalview.datamodel.Annotation(
- annElement.getDisplayCharacter(),
- annElement.getDescription(),
- (annElement.getSecondaryStructure() == null
- || annElement.getSecondaryStructure()
- .length() == 0)
- ? ' '
- : annElement
- .getSecondaryStructure()
- .charAt(0),
- value);
- anot[anpos].colour = new Color(safeInt(annElement.getColour()));
- if (firstColour == null)
- {
- firstColour = anot[anpos].colour;
- }
- }
- }
- // create the new AlignmentAnnotation
- jalview.datamodel.AlignmentAnnotation jaa = null;
-
- if (annotation.isGraph())
- {
- float llim = 0, hlim = 0;
- // if (autoForView || an[i].isAutoCalculated()) {
- // hlim=11f;
- // }
- jaa = new jalview.datamodel.AlignmentAnnotation(
- annotation.getLabel(), annotation.getDescription(), anot,
- llim, hlim, safeInt(annotation.getGraphType()));
-
- jaa.graphGroup = safeInt(annotation.getGraphGroup());
- jaa._linecolour = firstColour;
- if (annotation.getThresholdLine() != null)
- {
- jaa.setThreshold(new jalview.datamodel.GraphLine(
- safeFloat(annotation.getThresholdLine().getValue()),
- annotation.getThresholdLine().getLabel(),
- new java.awt.Color(safeInt(
- annotation.getThresholdLine().getColour()))));
- }
- if (autoForView || annotation.isAutoCalculated())
- {
- // Hardwire the symbol display line to ensure that labels for
- // histograms are displayed
- jaa.hasText = true;
- }
- }
- else
- {
- jaa = new jalview.datamodel.AlignmentAnnotation(
- annotation.getLabel(), annotation.getDescription(), anot);
- jaa._linecolour = firstColour;
- }
- // register new annotation
- // Annotation graphs such as Conservation will not have id.
- if (annotation.getId() != null)
- {
- annotationIds.put(annotation.getId(), jaa);
- jaa.annotationId = annotation.getId();
- }
- // recover sequence association
- String sequenceRef = annotation.getSequenceRef();
- if (sequenceRef != null)
- {
- // from 2.9 sequenceRef is to sequence id (JAL-1781)
- SequenceI sequence = seqRefIds.get(sequenceRef);
- if (sequence == null)
- {
- // in pre-2.9 projects sequence ref is to sequence name
- sequence = al.findName(sequenceRef);
- }
- if (sequence != null)
- {
- jaa.createSequenceMapping(sequence, 1, true);
- sequence.addAlignmentAnnotation(jaa);
- }
- }
- // and make a note of any group association
- if (annotation.getGroupRef() != null
- && annotation.getGroupRef().length() > 0)
- {
- List<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
- .get(annotation.getGroupRef());
- if (aal == null)
- {
- aal = new ArrayList<>();
- groupAnnotRefs.put(annotation.getGroupRef(), aal);
- }
- aal.add(jaa);
- }
-
- if (annotation.getScore() != null)
- {
- jaa.setScore(annotation.getScore().doubleValue());
- }
- if (annotation.isVisible() != null)
- {
- jaa.visible = annotation.isVisible().booleanValue();
- }
-
- if (annotation.isCentreColLabels() != null)
- {
- jaa.centreColLabels = annotation.isCentreColLabels()
- .booleanValue();
- }
-
- if (annotation.isScaleColLabels() != null)
- {
- jaa.scaleColLabel = annotation.isScaleColLabels().booleanValue();
- }
- if (annotation.isAutoCalculated())
- {
- // newer files have an 'autoCalculated' flag and store calculation
- // state in viewport properties
- jaa.autoCalculated = true; // means annotation will be marked for
- // update at end of load.
- }
- if (annotation.getGraphHeight() != null)
- {
- jaa.graphHeight = annotation.getGraphHeight().intValue();
- }
- jaa.belowAlignment = annotation.isBelowAlignment();
- jaa.setCalcId(annotation.getCalcId());
- if (annotation.getProperty().size() > 0)
- {
- for (Annotation.Property prop : annotation
- .getProperty())
- {
- jaa.setProperty(prop.getName(), prop.getValue());
- }
- }
- if (jaa.autoCalculated)
- {
- autoAlan.add(new JvAnnotRow(i, jaa));
- }
- else
- // if (!autoForView)
- {
- // add autocalculated group annotation and any user created annotation
- // for the view
- al.addAnnotation(jaa);
- }
- }
- }
- // ///////////////////////
- // LOAD GROUPS
- // Create alignment markup and styles for this view
- if (jalviewModel.getJGroup().size() > 0)
- {
- List<JGroup> groups = jalviewModel.getJGroup();
- boolean addAnnotSchemeGroup = false;
- for (int i = 0; i < groups.size(); i++)
- {
- JGroup jGroup = groups.get(i);
- ColourSchemeI cs = null;
- if (jGroup.getColour() != null)
- {
- if (jGroup.getColour().startsWith("ucs"))
- {
- cs = getUserColourScheme(jalviewModel, jGroup.getColour());
- }
- else if (jGroup.getColour().equals("AnnotationColourGradient")
- && jGroup.getAnnotationColours() != null)
- {
- addAnnotSchemeGroup = true;
- }
- else
- {
- cs = ColourSchemeProperty.getColourScheme(null, al,
- jGroup.getColour());
- }
- }
- int pidThreshold = safeInt(jGroup.getPidThreshold());
-
- Vector<SequenceI> seqs = new Vector<>();
-
- for (int s = 0; s < jGroup.getSeq().size(); s++)
- {
- String seqId = jGroup.getSeq().get(s);
- SequenceI ts = seqRefIds.get(seqId);
-
- if (ts != null)
- {
- seqs.addElement(ts);
- }
- }
-
- if (seqs.size() < 1)
- {
- continue;
- }
-
- SequenceGroup sg = new SequenceGroup(seqs, jGroup.getName(), cs,
- safeBoolean(jGroup.isDisplayBoxes()),
- safeBoolean(jGroup.isDisplayText()),
- safeBoolean(jGroup.isColourText()),
- safeInt(jGroup.getStart()), safeInt(jGroup.getEnd()));
- sg.getGroupColourScheme().setThreshold(pidThreshold, true);
- sg.getGroupColourScheme()
- .setConservationInc(safeInt(jGroup.getConsThreshold()));
- sg.setOutlineColour(new Color(safeInt(jGroup.getOutlineColour())));
-
- sg.textColour = new Color(safeInt(jGroup.getTextCol1()));
- sg.textColour2 = new Color(safeInt(jGroup.getTextCol2()));
- sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved()));
- sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold());
- // attributes with a default in the schema are never null
- sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram());
- sg.setshowSequenceLogo(jGroup.isShowSequenceLogo());
- sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo());
- sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus());
- if (jGroup.getConsThreshold() != null
- && jGroup.getConsThreshold().intValue() != 0)
- {
- Conservation c = new Conservation("All", sg.getSequences(null), 0,
- sg.getWidth() - 1);
- c.calculate();
- c.verdict(false, 25);
- sg.cs.setConservation(c);
- }
-
- if (jGroup.getId() != null && groupAnnotRefs.size() > 0)
- {
- // re-instate unique group/annotation row reference
- List<AlignmentAnnotation> jaal = groupAnnotRefs
- .get(jGroup.getId());
- if (jaal != null)
- {
- for (AlignmentAnnotation jaa : jaal)
- {
- jaa.groupRef = sg;
- if (jaa.autoCalculated)
- {
- // match up and try to set group autocalc alignment row for this
- // annotation
- if (jaa.label.startsWith("Consensus for "))
- {
- sg.setConsensus(jaa);
- }
- // match up and try to set group autocalc alignment row for this
- // annotation
- if (jaa.label.startsWith("Conservation for "))
- {
- sg.setConservationRow(jaa);
- }
- }
- }
- }
- }
- al.addGroup(sg);
- if (addAnnotSchemeGroup)
- {
- // reconstruct the annotation colourscheme
- sg.setColourScheme(
- constructAnnotationColour(jGroup.getAnnotationColours(),
- null, al, jalviewModel, false));
- }
- }
- }
- if (view == null)
- {
- // only dataset in this model, so just return.
- return null;
- }
- // ///////////////////////////////
- // LOAD VIEWPORT
-
- // now check to see if we really need to create a new viewport.
- if (multipleView && viewportsAdded.size() == 0)
- {
- // We recovered an alignment for which a viewport already exists.
- // TODO: fix up any settings necessary for overlaying stored state onto
- // state recovered from another document. (may not be necessary).
- // we may need a binding from a viewport in memory to one recovered from
- // XML.
- // and then recover its containing af to allow the settings to be applied.
- // TODO: fix for vamsas demo
- System.err.println(
- "About to recover a viewport for existing alignment: Sequence set ID is "
- + uniqueSeqSetId);
- Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
- if (seqsetobj != null)
- {
- if (seqsetobj instanceof String)
- {
- uniqueSeqSetId = (String) seqsetobj;
- System.err.println(
- "Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
- + uniqueSeqSetId);
- }
- else
- {
- System.err.println(
- "Warning : Collision between sequence set ID string and existing jalview object mapping.");
- }
-
- }
- }
- /**
- * indicate that annotation colours are applied across all groups (pre
- * Jalview 2.8.1 behaviour)
- */
- boolean doGroupAnnColour = Jalview2XML.isVersionStringLaterThan("2.8.1",
- jalviewModel.getVersion());
-
- AlignFrame af = null;
- AlignmentPanel ap = null;
- AlignViewport av = null;
- if (viewId != null)
- {
- // Check to see if this alignment already has a view id == viewId
- jalview.gui.AlignmentPanel views[] = Desktop
- .getAlignmentPanels(uniqueSeqSetId);
- if (views != null && views.length > 0)
- {
- for (int v = 0; v < views.length; v++)
- {
- ap = views[v];
- av = ap.av;
- if (av.getViewId().equalsIgnoreCase(viewId))
- {
- // recover the existing alignpanel, alignframe, viewport
- af = ap.alignFrame;
- break;
- // TODO: could even skip resetting view settings if we don't want to
- // change the local settings from other jalview processes
- }
- }
- }
- }
-
- if (af == null)
- {
- af = loadViewport(fileName, file, jseqs, hiddenSeqs, al, jalviewModel, view,
- uniqueSeqSetId, viewId, autoAlan);
- av = af.getViewport();
- // note that this only retrieves the most recently accessed
- // tab of an AlignFrame.
- ap = af.alignPanel;
- }
-
- /*
- * Load any trees, PDB structures and viewers
- *
- * Not done if flag is false (when this method is used for New View)
- */
- final AlignFrame af0 = af;
- final AlignViewport av0 = av;
- final AlignmentPanel ap0 = ap;
-// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree",
-// Platform.TIME_MARK);
- if (loadTreesAndStructures)
- {
- if (!jalviewModel.getTree().isEmpty())
- {
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
-// Platform.timeCheck(null, Platform.TIME_MARK);
- loadTrees(jalviewModel, view, af0, av0, ap0);
-// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK);
- }
- });
- }
- if (!jalviewModel.getPcaViewer().isEmpty())
- {
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
-// Platform.timeCheck(null, Platform.TIME_MARK);
- loadPCAViewers(jalviewModel, ap0);
-// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK);
- }
- });
- }
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
-// Platform.timeCheck(null, Platform.TIME_MARK);
- loadPDBStructures(jprovider, jseqs, af0, ap0);
-// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK);
- }
- });
- SwingUtilities.invokeLater(new Runnable()
- {
- @Override
- public void run()
- {
- loadRnaViewers(jprovider, jseqs, ap0);
- }
- });
- }
- // and finally return.
- // but do not set holdRepaint true just yet, because this could be the
- // initial frame with just its dataset.
- return af;
- }
-
- /**
- * Loads a HMMER profile from a file stored in the project, and associates it
- * with the specified sequence
- *
- * @param jprovider
- * @param hmmJarFile
- * @param seq
- */
- protected void loadHmmerProfile(jarInputStreamProvider jprovider,
- String hmmJarFile, SequenceI seq)
- {
- try
- {
- String hmmFile = copyJarEntry(jprovider, hmmJarFile, "hmm", null);
- HMMFile parser = new HMMFile(hmmFile, DataSourceType.FILE);
- HiddenMarkovModel hmmModel = parser.getHMM();
- hmmModel = new HiddenMarkovModel(hmmModel, seq);
- seq.setHMM(hmmModel);
- } catch (IOException e)
- {
- warn("Error loading HMM profile for " + seq.getName() + ": "
- + e.getMessage());
- }
- }
-
- /**
- * 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.
- *
- * Currently each viewer shows just one sequence and structure (gapped and
- * trimmed), however this method is designed to support multiple sequences or
- * structures in viewers if wanted in future.
- *
- * @param jprovider
- * @param jseqs
- * @param ap
- */
- protected void loadRnaViewers(jarInputStreamProvider jprovider,
- List<JSeq> jseqs, AlignmentPanel ap)
- {
- /*
- * scan the sequences for references to viewers; create each one the first
- * time it is referenced, add Rna models to existing viewers
- */
- for (JSeq jseq : jseqs)
- {
- for (int i = 0; i < jseq.getRnaViewer().size(); i++)
- {
- RnaViewer viewer = jseq.getRnaViewer().get(i);
- AppVarna appVarna = findOrCreateVarnaViewer(viewer, uniqueSetSuffix,
- ap);
-
- for (int j = 0; j < viewer.getSecondaryStructure().size(); j++)
- {
- SecondaryStructure ss = viewer.getSecondaryStructure().get(j);
- SequenceI seq = seqRefIds.get(jseq.getId());
- AlignmentAnnotation ann = this.annotationIds
- .get(ss.getAnnotationId());
-
- /*
- * add the structure to the Varna display (with session state copied
- * from the jar to a temporary file)
- */
- boolean gapped = safeBoolean(ss.isGapped());
- String rnaTitle = ss.getTitle();
- String sessionState = ss.getViewerState();
- String tempStateFile = copyJarEntry(jprovider, sessionState,
- "varna", null);
- RnaModel rna = new RnaModel(rnaTitle, ann, seq, null, gapped);
- appVarna.addModelSession(rna, rnaTitle, tempStateFile);
- }
- appVarna.setInitialSelection(safeInt(viewer.getSelectedRna()));
- }
- }
- }
-
- /**
- * Locate and return an already instantiated matching AppVarna, or create one
- * if not found
- *
- * @param viewer
- * @param viewIdSuffix
- * @param ap
- * @return
- */
- protected AppVarna findOrCreateVarnaViewer(RnaViewer viewer,
- String viewIdSuffix, AlignmentPanel ap)
- {
- /*
- * on each load a suffix is appended to the saved viewId, to avoid conflicts
- * if load is repeated
- */
- String postLoadId = viewer.getViewId() + viewIdSuffix;
- for (JInternalFrame frame : getAllFrames())
- {
- if (frame instanceof AppVarna)
- {
- AppVarna varna = (AppVarna) frame;
- if (postLoadId.equals(varna.getViewId()))
- {
- // this viewer is already instantiated
- // could in future here add ap as another 'parent' of the
- // AppVarna window; currently just 1-to-many
- return varna;
- }
- }
- }
-
- /*
- * viewer not found - make it
- */
- RnaViewerModel model = new RnaViewerModel(postLoadId, viewer.getTitle(),
- safeInt(viewer.getXpos()), safeInt(viewer.getYpos()),
- safeInt(viewer.getWidth()), safeInt(viewer.getHeight()),
- safeInt(viewer.getDividerLocation()));
- AppVarna varna = new AppVarna(model, ap);
-
- return varna;
- }
-
- /**
- * Load any saved trees
- *
- * @param jm
- * @param view
- * @param af
- * @param av
- * @param ap
- */
- protected void loadTrees(JalviewModel jm, Viewport view,
- AlignFrame af, AlignViewport av, AlignmentPanel ap)
- {
- // TODO result of automated refactoring - are all these parameters needed?
- try
- {
- for (int t = 0; t < jm.getTree().size(); t++)
- {
-
- Tree tree = jm.getTree().get(t);
-
- TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
- if (tp == null)
- {
- tp = af.showNewickTree(new NewickFile(tree.getNewick()),
- tree.getTitle(), safeInt(tree.getWidth()),
- safeInt(tree.getHeight()), safeInt(tree.getXpos()),
- safeInt(tree.getYpos()));
- if (tp == null)
- {
- warn("There was a problem recovering stored Newick tree: \n"
- + tree.getNewick());
- continue;
- }
- if (tree.getId() != null)
- {
- // perhaps bind the tree id to something ?
- }
- }
- else
- {
- // update local tree attributes ?
- // TODO: should check if tp has been manipulated by user - if so its
- // settings shouldn't be modified
- tp.setTitle(tree.getTitle());
- tp.setBounds(new Rectangle(safeInt(tree.getXpos()),
- safeInt(tree.getYpos()), safeInt(tree.getWidth()),
- safeInt(tree.getHeight())));
- tp.setViewport(av); // af.viewport;
- // TODO: verify 'associate with all views' works still
- tp.getTreeCanvas().setViewport(av); // af.viewport;
- tp.getTreeCanvas().setAssociatedPanel(ap); // af.alignPanel;
- }
- tp.getTreeCanvas().setApplyToAllViews(tree.isLinkToAllViews());
-
- tp.fitToWindow.setState(safeBoolean(tree.isFitToWindow()));
- tp.fitToWindow_actionPerformed(null);
-
- if (tree.getFontName() != null)
- {
- tp.setTreeFont(
- new Font(tree.getFontName(), safeInt(tree.getFontStyle()),
- safeInt(tree.getFontSize())));
- }
- else
- {
- tp.setTreeFont(
- new Font(view.getFontName(), safeInt(view.getFontStyle()),
- safeInt(view.getFontSize())));
- }
-
- tp.showPlaceholders(safeBoolean(tree.isMarkUnlinked()));
- tp.showBootstrap(safeBoolean(tree.isShowBootstrap()));
- tp.showDistances(safeBoolean(tree.isShowDistances()));
-
- tp.getTreeCanvas().setThreshold(safeFloat(tree.getThreshold()));
-
- if (safeBoolean(tree.isCurrentTree()))
- {
- af.getViewport().setCurrentTree(tp.getTree());
- }
- }
-
- } catch (Exception ex)
- {
- ex.printStackTrace();
- }
- }
-
- /**
- * Load and link any saved structure viewers.
- *
- * @param jprovider
- * @param jseqs
- * @param af
- * @param ap
- */
- protected void loadPDBStructures(jarInputStreamProvider jprovider,
- List<JSeq> jseqs, AlignFrame af, AlignmentPanel ap)
- {
- /*
- * Run through all PDB ids on the alignment, and collect mappings between
- * distinct view ids and all sequences referring to that view.
- */
- Map<String, StructureViewerModel> structureViewers = new LinkedHashMap<>();
-
- for (int i = 0; i < jseqs.size(); i++)
- {
- JSeq jseq = jseqs.get(i);
- if (jseq.getPdbids().size() > 0)
- {
- List<Pdbids> ids = jseq.getPdbids();
- for (int p = 0; p < ids.size(); p++)
- {
- Pdbids pdbid = ids.get(p);
- final int structureStateCount = pdbid.getStructureState().size();
- for (int s = 0; s < structureStateCount; s++)
- {
- // check to see if we haven't already created this structure view
- final StructureState structureState = pdbid
- .getStructureState().get(s);
- String sviewid = (structureState.getViewId() == null) ? null
- : structureState.getViewId() + uniqueSetSuffix;
- jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
- // Originally : pdbid.getFile()
- // : TODO: verify external PDB file recovery still works in normal
- // jalview project load
- jpdb.setFile(
- loadPDBFile(jprovider, pdbid.getId(), pdbid.getFile()));
- jpdb.setId(pdbid.getId());
-
- int x = safeInt(structureState.getXpos());
- int y = safeInt(structureState.getYpos());
- int width = safeInt(structureState.getWidth());
- int height = safeInt(structureState.getHeight());
-
- // Probably don't need to do this anymore...
- // Desktop.getDesktop().getComponentAt(x, y);
- // TODO: NOW: check that this recovers the PDB file correctly.
- String pdbFile = loadPDBFile(jprovider, pdbid.getId(),
- pdbid.getFile());
- jalview.datamodel.SequenceI seq = seqRefIds
- .get(jseq.getId() + "");
- if (sviewid == null)
- {
- sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width + ","
- + height;
- }
- 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(),
- viewerType));
- // Legacy pre-2.7 conversion JAL-823 :
- // do not assume any view has to be linked for colour by
- // sequence
- }
-
- // assemble String[] { pdb files }, String[] { id for each
- // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
- // seqs_file 2}, boolean[] {
- // linkAlignPanel,superposeWithAlignpanel}} from hash
- StructureViewerModel jmoldat = structureViewers.get(sviewid);
- jmoldat.setAlignWithPanel(jmoldat.isAlignWithPanel()
- || structureState.isAlignwithAlignPanel());
-
- /*
- * Default colour by linked panel to false if not specified (e.g.
- * for pre-2.7 projects)
- */
- boolean colourWithAlignPanel = jmoldat.isColourWithAlignPanel();
- colourWithAlignPanel |= structureState.isColourwithAlignPanel();
- jmoldat.setColourWithAlignPanel(colourWithAlignPanel);
-
- /*
- * Default colour by viewer to true if not specified (e.g. for
- * pre-2.7 projects)
- */
- boolean colourByViewer = jmoldat.isColourByViewer();
- colourByViewer &= structureState.isColourByJmol();
- jmoldat.setColourByViewer(colourByViewer);
-
- if (jmoldat.getStateData().length() < structureState
- .getValue()/*Content()*/.length())
- {
- jmoldat.setStateData(structureState.getValue());// Content());
- }
- if (pdbid.getFile() != null)
- {
- File mapkey = new File(pdbid.getFile());
- StructureData seqstrmaps = jmoldat.getFileData().get(mapkey);
- if (seqstrmaps == null)
- {
- jmoldat.getFileData().put(mapkey,
- seqstrmaps = jmoldat.new StructureData(pdbFile,
- pdbid.getId()));
- }
- if (!seqstrmaps.getSeqList().contains(seq))
- {
- seqstrmaps.getSeqList().add(seq);
- // TODO and chains?
- }
- }
- else
- {
- errorMessage = ("The Jmol views in this project were imported\nfrom an older version of Jalview.\nPlease review the sequence colour associations\nin the Colour by section of the Jmol View menu.\n\nIn the case of problems, see note at\nhttp://issues.jalview.org/browse/JAL-747");
- warn(errorMessage);
- }
- }
- }
- }
- }
- // Instantiate the associated structure views
- for (Entry<String, StructureViewerModel> entry : structureViewers
- .entrySet())
- {
- try
- {
- createOrLinkStructureViewer(entry, af, ap, jprovider);
- } catch (Exception e)
- {
- System.err.println(
- "Error loading structure viewer: " + e.getMessage());
- // failed - try the next one
- }
- }
- }
-
- /**
- *
- * @param viewerData
- * @param af
- * @param ap
- * @param jprovider
- */
- protected void createOrLinkStructureViewer(
- Entry<String, StructureViewerModel> viewerData, AlignFrame af,
- AlignmentPanel ap, jarInputStreamProvider jprovider)
- {
- final StructureViewerModel stateData = viewerData.getValue();
-
- /*
- * Search for any viewer windows already open from other alignment views
- * that exactly match the stored structure state
- */
- StructureViewerBase comp = findMatchingViewer(viewerData);
-
- if (comp != null)
- {
- linkStructureViewer(ap, comp, stateData);
- return;
- }
-
- String type = stateData.getType();
- try
- {
- ViewerType viewerType = ViewerType.valueOf(type);
- createStructureViewer(viewerType, viewerData, af, jprovider);
- } catch (IllegalArgumentException | NullPointerException e)
- {
- // TODO JAL-3619 show error dialog / offer an alternative viewer
- Cache.log.error("Invalid structure viewer type: " + type);
- }
-
- }
-
- /**
- * 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();
-// BH again was invokeAndWait
- // try
- // {
- javax.swing.SwingUtilities.invokeLater(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;
- }
-
- /**
- * Generates a name for the entry in the project jar file to hold state
- * information for a structure viewer
- *
- * @param viewId
- * @return
- */
- protected String getViewerJarEntryName(String viewId)
- {
- return VIEWER_PREFIX + viewId;
- }
-
- /**
- * Returns any open frame that matches given structure viewer data. The match
- * is based on the unique viewId, or (for older project versions) the frame's
- * geometry.
- *
- * @param viewerData
- * @return
- */
- protected StructureViewerBase findMatchingViewer(
- Entry<String, StructureViewerModel> viewerData)
- {
- final String sviewid = viewerData.getKey();
- final StructureViewerModel svattrib = viewerData.getValue();
- StructureViewerBase comp = null;
- JInternalFrame[] frames = getAllFrames();
- for (JInternalFrame frame : frames)
- {
- if (frame instanceof StructureViewerBase)
- {
- /*
- * Post jalview 2.4 schema includes structure view id
- */
- if (sviewid != null && ((StructureViewerBase) frame).getViewId()
- .equals(sviewid))
- {
- comp = (StructureViewerBase) frame;
- break; // break added in 2.9
- }
- /*
- * Otherwise test for matching position and size of viewer frame
- */
- else if (frame.getX() == svattrib.getX()
- && frame.getY() == svattrib.getY()
- && frame.getHeight() == svattrib.getHeight()
- && frame.getWidth() == svattrib.getWidth())
- {
- comp = (StructureViewerBase) frame;
- // no break in faint hope of an exact match on viewId
- }
- }
- }
- return comp;
- }
-
- /**
- * Link an AlignmentPanel to an existing structure viewer.
- *
- * @param ap
- * @param viewer
- * @param oldFiles
- * @param useinViewerSuperpos
- * @param usetoColourbyseq
- * @param viewerColouring
- */
- protected void linkStructureViewer(AlignmentPanel ap,
- StructureViewerBase viewer, StructureViewerModel stateData)
- {
- // NOTE: if the jalview project is part of a shared session then
- // view synchronization should/could be done here.
-
- final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
- final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
- final boolean viewerColouring = stateData.isColourByViewer();
- Map<File, StructureData> oldFiles = stateData.getFileData();
-
- /*
- * Add mapping for sequences in this view to an already open viewer
- */
- final AAStructureBindingModel binding = viewer.getBinding();
- for (File id : oldFiles.keySet())
- {
- // add this and any other pdb files that should be present in the
- // viewer
- StructureData filedat = oldFiles.get(id);
- String pdbFile = filedat.getFilePath();
- SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
- binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
- null);
- binding.addSequenceForStructFile(pdbFile, seq);
- }
- // and add the AlignmentPanel's reference to the view panel
- viewer.addAlignmentPanel(ap);
- if (useinViewerSuperpos)
- {
- viewer.useAlignmentPanelForSuperposition(ap);
- }
- else
+ * Generates a name for the entry in the project jar file to hold state
+ * information for a structure viewer
+ *
+ * @param viewId
+ * @return
+ */
+ protected String getViewerJarEntryName(String viewId)
{
- viewer.excludeAlignmentPanelForSuperposition(ap);
+ return VIEWER_PREFIX + viewId;
}
- if (usetoColourbyseq)
- {
- viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
+
+ /**
+ * Returns any open frame that matches given structure viewer data. The match
+ * is based on the unique viewId, or (for older project versions) the frame's
+ * geometry.
+ *
+ * @param viewerData
+ * @return
+ */
+ protected StructureViewerBase findMatchingViewer(
+ Entry<String, StructureViewerModel> viewerData)
+ {
+ final String sviewid = viewerData.getKey();
+ final StructureViewerModel svattrib = viewerData.getValue();
+ StructureViewerBase comp = null;
+ JInternalFrame[] frames = getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof StructureViewerBase)
+ {
+ /*
+ * Post jalview 2.4 schema includes structure view id
+ */
+ if (sviewid != null && ((StructureViewerBase) frame).getViewId()
+ .equals(sviewid))
+ {
+ comp = (StructureViewerBase) frame;
+ break; // break added in 2.9
+ }
+ /*
+ * Otherwise test for matching position and size of viewer frame
+ */
+ else if (frame.getX() == svattrib.getX()
+ && frame.getY() == svattrib.getY()
+ && frame.getHeight() == svattrib.getHeight()
+ && frame.getWidth() == svattrib.getWidth())
+ {
+ comp = (StructureViewerBase) frame;
+ // no break in faint hope of an exact match on viewId
+ }
+ }
+ }
+ return comp;
}
- else
- {
- viewer.excludeAlignmentPanelForColourbyseq(ap);
+
+ /**
+ * Link an AlignmentPanel to an existing structure viewer.
+ *
+ * @param ap
+ * @param viewer
+ * @param oldFiles
+ * @param useinViewerSuperpos
+ * @param usetoColourbyseq
+ * @param viewerColouring
+ */
+ protected void linkStructureViewer(AlignmentPanel ap,
+ StructureViewerBase viewer, StructureViewerModel stateData)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
+
+ final boolean useinViewerSuperpos = stateData.isAlignWithPanel();
+ final boolean usetoColourbyseq = stateData.isColourWithAlignPanel();
+ final boolean viewerColouring = stateData.isColourByViewer();
+ Map<File, StructureData> oldFiles = stateData.getFileData();
+
+ /*
+ * Add mapping for sequences in this view to an already open viewer
+ */
+ final AAStructureBindingModel binding = viewer.getBinding();
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ StructureData filedat = oldFiles.get(id);
+ String pdbFile = filedat.getFilePath();
+ SequenceI[] seq = filedat.getSeqList().toArray(new SequenceI[0]);
+ binding.getSsm().setMapping(seq, null, pdbFile, DataSourceType.FILE,
+ null);
+ binding.addSequenceForStructFile(pdbFile, seq);
+ }
+ // and add the AlignmentPanel's reference to the view panel
+ viewer.addAlignmentPanel(ap);
+ if (useinViewerSuperpos)
+ {
+ viewer.useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ viewer.useAlignmentPanelForColourbyseq(ap, !viewerColouring);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForColourbyseq(ap);
+ }
}
- }
- /**
- * Get all frames within the Desktop.
- *
- * @return
- */
- protected JInternalFrame[] getAllFrames()
- {
- JInternalFrame[] frames = null;
- // TODO is this necessary - is it safe - risk of hanging?
- do
- {
- try
- {
- frames = Desktop.getDesktopPane().getAllFrames();
- } catch (ArrayIndexOutOfBoundsException e)
- {
- // occasional No such child exceptions are thrown here...
- try
- {
- Thread.sleep(10);
- } catch (InterruptedException f)
- {
- }
- }
- } while (frames == null);
- return frames;
- }
+ /**
+ * Get all frames within the Desktop.
+ *
+ * @return
+ */
+ protected JInternalFrame[] getAllFrames()
+ {
+ JInternalFrame[] frames = null;
+ // TODO is this necessary - is it safe - risk of hanging?
+ do
+ {
+ try
+ {
+ frames = Desktop.getDesktopPane().getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException f)
+ {
+ }
+ }
+ } while (frames == null);
+ return frames;
+ }
- /**
- * Answers true if 'version' is equal to or later than 'supported', where each
- * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
- * changes. Development and test values for 'version' are leniently treated
- * i.e. answer true.
- *
- * @param supported
- * - minimum version we are comparing against
- * @param version
- * - version of data being processsed
- * @return
- */
- public static boolean isVersionStringLaterThan(String supported,
- String version)
+ /**
+ * Answers true if 'version' is equal to or later than 'supported', where each
+ * is formatted as major/minor versions like "2.8.3" or "2.3.4b1" for bugfix
+ * changes. Development and test values for 'version' are leniently treated
+ * i.e. answer true.
+ *
+ * @param supported
+ * - minimum version we are comparing against
+ * @param version
+ * - version of data being processsed
+ * @return
+ */
+ public static boolean isVersionStringLaterThan(String supported,
+ String version)
{
if (supported == null || version == null
|| version.equalsIgnoreCase("DEVELOPMENT BUILD")
}
else
{
- warn("Couldn't recover parameters for "
+ Console.warn("Couldn't recover parameters for "
+ calcIdParam.getCalcId());
}
}
String id = object.getViewport().get(0).getSequenceSetId();
if (skipList.containsKey(id))
{
- if (Cache.log != null && Cache.log.isDebugEnabled())
- {
- Cache.log.debug("Skipping seuqence set id " + id);
- }
+ Console.debug("Skipping seuqence set id " + id);
return true;
}
return false;
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
}
- Vector dseqs = null;
+ Vector<SequenceI> dseqs = null;
if (!ignoreUnrefed)
{
// recovering an alignment View
{
if (ds != null && ds != seqSetDS)
{
- warn("JAL-3171 regression: Overwriting a dataset reference for an alignment"
- + " - CDS/Protein crossreference data may be lost");
+ Console.warn(
+ "JAL-3171 regression: Overwriting a dataset reference for an alignment"
+ + " - CDS/Protein crossreference data may be lost");
if (xtant_ds != null)
{
// This can only happen if the unique sequence set ID was bound to a
// dataset that did not contain any of the sequences in the view
// currently being restored.
- warn("JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
+ Console.warn(
+ "JAL-3171 SERIOUS! TOTAL CONFUSION - please consider contacting the Jalview Development team so they can investigate why your project caused this message to be displayed.");
}
}
ds = seqSetDS;
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
-// debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
+// Console.debug("Jalview2XML Created new dataset " + vamsasSet.getDatasetId()
// + " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
AlignmentI prevDS = seqToDataset.put(restoredSeq.getDsseqid(), ds);
if (prevDS != null && prevDS != ds)
{
- warn("Dataset sequence appears in many datasets: "
+ Console.warn("Dataset sequence appears in many datasets: "
+ restoredSeq.getDsseqid());
// TODO: try to merge!
}
}
}
+
/**
*
* @param vamsasSeq
{
if (dataset.getDataset() != null)
{
- warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ Console.warn(
+ "Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
String datasetId = makeHashCode(dataset, null);
if (datasetId == null)
seqRefIds.put(sqid, djs);
}
- jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ Console.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
}
private Hashtable jvids2vobj;
- private void warn(String msg)
- {
- warn(msg, null);
- }
-
- private void warn(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.warn(msg, e);
- }
- else
- {
- Cache.log.warn(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
- private void debug(String string)
- {
- debug(string, null);
- }
-
- private void debug(String msg, Exception e)
- {
- if (Cache.log != null)
- {
- if (e != null)
- {
- Cache.log.debug(msg, e);
- }
- else
- {
- Cache.log.debug(msg);
- }
- }
- else
- {
- System.err.println("Warning: " + msg);
- if (e != null)
- {
- e.printStackTrace();
- }
- }
- }
-
/**
* set the object to ID mapping tables used to write/recover objects and XML
* ID strings for the jalview project. If external tables are provided then
if (!jvann.annotationId.equals(anid))
{
// TODO verify that this is the correct behaviour
- this.warn("Overriding Annotation ID for " + anid
+ Console.warn("Overriding Annotation ID for " + anid
+ " from different id : " + jvann.annotationId);
jvann.annotationId = anid;
}
}
else
{
- Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ Console.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
}
}
}
}
else
{
- warn("Couldn't find entry in Jalview Jar for " + jarEntryName);
+ Console.warn(
+ "Couldn't find entry in Jalview Jar for " + jarEntryName);
}
} catch (Exception ex)
{
}
} catch (Exception ex)
{
- Cache.log.error("Error loading PCA: " + ex.toString());
+ Console.error("Error loading PCA: " + ex.toString());
+ }
+ }
+
+ /**
+ * 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();
+// BH again was invokeAndWait
+ // try
+ // {
+ javax.swing.SwingUtilities.invokeLater(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)
+// {
+// Console.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)
+ {
+ Console.error("Error restoring Jmol session: " + e.toString());
}
+ return null;
}
/**
boolean and)
{
jalview.xml.binding.jalview.FeatureMatcherSet result = new jalview.xml.binding.jalview.FeatureMatcherSet();
+
if (filters.hasNext())
{
/*
}
result.setMatchCondition(matcherModel);
}
+
return result;
}
featureType, e.getMessage()));
// return as much as was parsed up to the error
}
+
return result;
}
else if (filterBy == FilterBy.BY_SCORE)
{
matchCondition = FeatureMatcher.byScore(cond, pattern);
+
}
else if (filterBy == FilterBy.BY_ATTRIBUTE)
{
matchCondition = FeatureMatcher.byAttribute(cond, pattern,
attNames);
}
+
/*
* note this throws IllegalStateException if AND-ing to a
* previously OR-ed compound condition, or vice versa
public static FeatureColourI parseColour(Colour colourModel)
{
FeatureColourI colour = null;
+
if (colourModel.getMax() != null)
{
Color mincol = null;
Color maxcol = null;
Color noValueColour = null;
+
try
{
mincol = new Color(Integer.parseInt(colourModel.getMinRGB(), 16));
maxcol = new Color(Integer.parseInt(colourModel.getRGB(), 16));
} catch (Exception e)
{
- Cache.log.warn("Couldn't parse out graduated feature color.", e);
+ Console.warn("Couldn't parse out graduated feature color.", e);
}
+
NoValueColour noCol = colourModel.getNoValueColour();
if (noCol == NoValueColour.MIN)
{
{
noValueColour = maxcol;
}
+
colour = new FeatureColour(maxcol, mincol, maxcol, noValueColour,
safeFloat(colourModel.getMin()),
safeFloat(colourModel.getMax()));
Color color = new Color(Integer.parseInt(colourModel.getRGB(), 16));
colour = new FeatureColour(color);
}
+
return colour;
}
}
+
git://source.jalview.org / jalview.git / blobdiff