/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * Copyright (C) 2014 The Jalview Authors
*
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation; either version 2
- * of the License, or (at your option) any later version.
+ * This file is part of Jalview.
*
- * This program is distributed in the hope that it will be useful,
- * but WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
- * GNU General Public License for more details.
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
- * along with this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.Rectangle;
-import java.io.*;
-import java.net.*;
-import java.util.*;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-
-import uk.ac.vamsas.objects.utils.MapList;
+import jalview.api.structures.JalviewStructureDisplayI;
import jalview.bin.Cache;
import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceI;
-import jalview.schemabinding.version2.*;
-import jalview.schemes.*;
+import jalview.schemabinding.version2.AlcodMap;
+import jalview.schemabinding.version2.Alcodon;
+import jalview.schemabinding.version2.AlcodonFrame;
+import jalview.schemabinding.version2.Annotation;
+import jalview.schemabinding.version2.AnnotationColours;
+import jalview.schemabinding.version2.AnnotationElement;
+import jalview.schemabinding.version2.CalcIdParam;
+import jalview.schemabinding.version2.DBRef;
+import jalview.schemabinding.version2.Features;
+import jalview.schemabinding.version2.Group;
+import jalview.schemabinding.version2.HiddenColumns;
+import jalview.schemabinding.version2.JGroup;
+import jalview.schemabinding.version2.JSeq;
+import jalview.schemabinding.version2.JalviewModel;
+import jalview.schemabinding.version2.JalviewModelSequence;
+import jalview.schemabinding.version2.MapListFrom;
+import jalview.schemabinding.version2.MapListTo;
+import jalview.schemabinding.version2.Mapping;
+import jalview.schemabinding.version2.MappingChoice;
+import jalview.schemabinding.version2.OtherData;
+import jalview.schemabinding.version2.PdbentryItem;
+import jalview.schemabinding.version2.Pdbids;
+import jalview.schemabinding.version2.Property;
+import jalview.schemabinding.version2.Sequence;
+import jalview.schemabinding.version2.SequenceSet;
+import jalview.schemabinding.version2.SequenceSetProperties;
+import jalview.schemabinding.version2.Setting;
+import jalview.schemabinding.version2.StructureState;
+import jalview.schemabinding.version2.ThresholdLine;
+import jalview.schemabinding.version2.Tree;
+import jalview.schemabinding.version2.UserColours;
+import jalview.schemabinding.version2.Viewport;
+import jalview.schemes.AnnotationColourGradient;
+import jalview.schemes.ColourSchemeI;
+import jalview.schemes.ColourSchemeProperty;
+import jalview.schemes.GraduatedColor;
+import jalview.schemes.ResidueColourScheme;
+import jalview.schemes.ResidueProperties;
+import jalview.schemes.UserColourScheme;
import jalview.structure.StructureSelectionManager;
+import jalview.structures.models.AAStructureBindingModel;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
import jalview.util.jarInputStreamProvider;
+import jalview.viewmodel.AlignmentViewport;
+import jalview.ws.jws2.Jws2Discoverer;
+import jalview.ws.jws2.dm.AAConSettings;
+import jalview.ws.jws2.jabaws2.Jws2Instance;
+import jalview.ws.params.ArgumentI;
+import jalview.ws.params.AutoCalcSetting;
+import jalview.ws.params.WsParamSetI;
+
+import java.awt.Rectangle;
+import java.io.BufferedReader;
+import java.io.DataInputStream;
+import java.io.DataOutputStream;
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.InputStreamReader;
+import java.io.OutputStreamWriter;
+import java.io.PrintWriter;
+import java.lang.reflect.InvocationTargetException;
+import java.net.MalformedURLException;
+import java.net.URL;
+import java.util.ArrayList;
+import java.util.Enumeration;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Hashtable;
+import java.util.IdentityHashMap;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Map.Entry;
+import java.util.Set;
+import java.util.StringTokenizer;
+import java.util.Vector;
+import java.util.jar.JarEntry;
+import java.util.jar.JarInputStream;
+import java.util.jar.JarOutputStream;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JOptionPane;
+import javax.swing.SwingUtilities;
+
+import org.exolab.castor.xml.Unmarshaller;
/**
* Write out the current jalview desktop state as a Jalview XML stream.
* will be :)
*
* @author $author$
- * @version $Revision$
+ * @version $Revision: 1.134 $
*/
public class Jalview2XML
{
+
+ private class ViewerData
+ {
+
+ private int x;
+
+ private int y;
+
+ private int width;
+
+ private int height;
+
+ private boolean alignWithPanel;
+
+ private boolean colourWithAlignPanel;
+
+ private boolean colourByViewer;
+
+ private String stateData = "";
+
+ // todo: java bean in place of Object []
+ private Map<File, Object[]> fileData = new HashMap<File, Object[]>();
+
+ public ViewerData(int x, int y, int width, int height,
+ boolean alignWithPanel, boolean colourWithAlignPanel,
+ boolean colourByViewer)
+ {
+ this.x = x;
+ this.y = y;
+ this.width = width;
+ this.height = height;
+ this.alignWithPanel = alignWithPanel;
+ this.colourWithAlignPanel = colourWithAlignPanel;
+ this.colourByViewer = colourByViewer;
+ }
+
+ }
+
+ /*
+ * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
+ * of sequence objects are created.
+ */
+ IdentityHashMap<SequenceI, String> seqsToIds = null;
+
+ /**
+ * 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;
+
+ Vector frefedSequence = null;
+
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+
/**
* create/return unique hash string for sq
*
}
if (seqsToIds.containsKey(sq))
{
- return (String) seqsToIds.get(sq);
+ return seqsToIds.get(sq);
}
else
{
{
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap();
+ seqsToIds = new IdentityHashMap<SequenceI, String>();
}
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap<String, SequenceI>();
}
}
- /**
- * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
- * of sequence objects are created.
- */
- java.util.IdentityHashMap seqsToIds = null;
-
- /**
- * jalview XML Sequence ID to jalview sequence object reference (both dataset
- * and alignment sequences. Populated as XML reps of sequence objects are
- * created.)
- */
- java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
-
- Vector frefedSequence = null;
-
- boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
-
public Jalview2XML()
{
}
{
if (ref[1] instanceof jalview.datamodel.Mapping)
{
- SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ SequenceI seq = seqRefIds.get(sref);
while (seq.getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
{
if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
{
- SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ SequenceI seq = seqRefIds.get(sref);
while (seq.getDatasetSequence() != null)
{
seq = seq.getDatasetSequence();
/**
* List of pdbfiles added to Jar
*/
- Vector pdbfiles = null;
+ List<String> pdbfiles = null;
// SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
- public void SaveState(File statefile)
+ public void saveState(File statefile)
{
+ FileOutputStream fos = null;
try
{
- FileOutputStream fos = new FileOutputStream(statefile);
+ fos = new FileOutputStream(statefile);
JarOutputStream jout = new JarOutputStream(fos);
- SaveState(jout);
+ saveState(jout);
} catch (Exception e)
{
errorMessage += "(output file was '" + statefile + "')";
}
e.printStackTrace();
+ } finally
+ {
+ if (fos != null)
+ {
+ try
+ {
+ fos.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
reportErrors();
}
*
* @param jout
*/
- public void SaveState(JarOutputStream jout)
+ public void saveState(JarOutputStream jout)
{
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
return;
}
+ Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
+
try
{
// NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
// //////////////////////////////////////////////////
- // NOTE ALSO new PrintWriter must be used for each new JarEntry
- PrintWriter out = null;
Vector shortNames = new Vector();
}
int ap, apSize = af.alignPanels.size();
+
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
fileName = fileName + ".xml";
}
- SaveState(apanel, fileName, jout);
+ saveState(apanel, fileName, jout);
+
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
+
}
}
}
+
+ writeDatasetFor(dsses, "" + jout.hashCode() + " " + uniqueSetSuffix,
+ jout);
+
try
{
jout.flush();
}
// USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
- public boolean SaveAlignment(AlignFrame af, String jarFile,
+ public boolean saveAlignment(AlignFrame af, String jarFile,
String fileName)
{
try
int ap, apSize = af.alignPanels.size();
FileOutputStream fos = new FileOutputStream(jarFile);
JarOutputStream jout = new JarOutputStream(fos);
+ Hashtable<String, AlignFrame> dsses = new Hashtable<String, AlignFrame>();
for (ap = 0; ap < apSize; ap++)
{
AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
{
jfileName = jfileName + ".xml";
}
- SaveState(apanel, jfileName, jout);
+ saveState(apanel, jfileName, jout);
+ String dssid = getDatasetIdRef(af.getViewport().getAlignment()
+ .getDataset());
+ if (!dsses.containsKey(dssid))
+ {
+ dsses.put(dssid, af);
+ }
}
-
+ writeDatasetFor(dsses, fileName, jout);
try
{
jout.flush();
}
}
+ private void writeDatasetFor(Hashtable<String, AlignFrame> dsses,
+ String fileName, JarOutputStream jout)
+ {
+
+ 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);
+ }
+ }
+
/**
- * create a JalviewModel from an algnment view and marshall it to a
+ * create a JalviewModel from an alignment view and marshall it to a
* JarOutputStream
*
* @param ap
- * panel to create jalview model for
+ * panel to create jalview model for
* @param fileName
- * name of alignment panel written to output stream
+ * name of alignment panel written to output stream
* @param jout
- * jar output stream
+ * jar output stream
* @param out
- * jar entry name
+ * jar entry name
*/
- public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ public JalviewModel saveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
{
- initSeqRefs();
+ return saveState(ap, fileName, false, jout);
+ }
- Vector userColours = new Vector();
+ /**
+ * 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
+ */
+ public JalviewModel saveState(AlignmentPanel ap, String fileName,
+ boolean storeDS, JarOutputStream jout)
+ {
+ initSeqRefs();
+ List<UserColourScheme> userColours = new ArrayList<UserColourScheme>();
AlignViewport av = ap.av;
object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
- object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+ object.setVersion(jalview.bin.Cache.getDefault("VERSION",
+ "Development Build"));
- jalview.datamodel.AlignmentI jal = av.alignment;
+ jalview.datamodel.AlignmentI jal = av.getAlignment();
- if (av.hasHiddenRows)
+ if (av.hasHiddenRows())
{
jal = jal.getHiddenSequences().getFullAlignment();
}
{
// dataset id is the dataset's hashcode
vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ if (storeDS)
+ {
+ // switch jal and the dataset
+ jal = jal.getDataset();
+ }
}
if (jal.getProperties() != null)
{
}
JSeq jseq;
+ Set<String> calcIdSet = new HashSet<String>();
// SAVE SEQUENCES
String id = "";
- jalview.datamodel.SequenceI jds;
+ jalview.datamodel.SequenceI jds, jdatasq;
for (int i = 0; i < jal.getHeight(); i++)
{
jds = jal.getSequenceAt(i);
+ jdatasq = jds.getDatasetSequence() == null ? jds : jds
+ .getDatasetSequence();
id = seqHash(jds);
if (seqRefIds.get(id) != null)
jseq.setColour(av.getSequenceColour(jds).getRGB());
jseq.setId(id); // jseq id should be a string not a number
-
- if (av.hasHiddenRows)
+ if (!storeDS)
{
- jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
-
- if (av.hiddenRepSequences != null
- && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ // Store any sequences this sequence represents
+ if (av.hasHiddenRows())
{
- jalview.datamodel.SequenceI[] reps = ((jalview.datamodel.SequenceGroup) av.hiddenRepSequences
- .get(jal.getSequenceAt(i))).getSequencesInOrder(jal);
+ jseq.setHidden(av.getAlignment().getHiddenSequences()
+ .isHidden(jds));
- for (int h = 0; h < reps.length; h++)
+ if (av.isHiddenRepSequence(jal.getSequenceAt(i)))
{
- if (reps[h] != jal.getSequenceAt(i))
+ jalview.datamodel.SequenceI[] reps = av
+ .getRepresentedSequences(jal.getSequenceAt(i))
+ .getSequencesInOrder(jal);
+
+ for (int h = 0; h < reps.length; h++)
{
- jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ if (reps[h] != jal.getSequenceAt(i))
+ {
+ jseq.addHiddenSequences(jal.findIndex(reps[h]));
+ }
}
}
}
}
- if (jds.getDatasetSequence().getSequenceFeatures() != null)
+ if (jdatasq.getSequenceFeatures() != null)
{
- jalview.datamodel.SequenceFeature[] sf = jds.getDatasetSequence()
+ jalview.datamodel.SequenceFeature[] sf = jdatasq
.getSequenceFeatures();
int index = 0;
while (index < sf.length)
}
}
- if (jds.getDatasetSequence().getPDBId() != null)
+ if (jdatasq.getPDBId() != null)
{
- Enumeration en = jds.getDatasetSequence().getPDBId().elements();
+ Enumeration en = jdatasq.getPDBId().elements();
while (en.hasMoreElements())
{
Pdbids pdb = new Pdbids();
pdb.setId(entry.getId());
pdb.setType(entry.getType());
- AppJmol jmol;
+ /*
+ * Store any JMol or Chimera views associated with this sequence. This
+ * section copes with duplicate entries in the project, so a dataset
+ * only view *should* be coped with sensibly.
+ */
+ List<String> viewIds = new ArrayList<String>();
// This must have been loaded, is it still visible?
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ String matchedFile = null;
for (int f = frames.length - 1; f > -1; f--)
{
- if (frames[f] instanceof AppJmol)
+ if (frames[f] instanceof StructureViewerBase)
{
- jmol = (AppJmol) frames[f];
- if (!jmol.pdbentry.getId().equals(entry.getId())
- && !(entry.getId().length()>4
- && entry.getId().startsWith(jmol.pdbentry.getId())))
- continue;
-
- StructureState state = new StructureState();
- state.setVisible(true);
- state.setXpos(jmol.getX());
- state.setYpos(jmol.getY());
- state.setWidth(jmol.getWidth());
- state.setHeight(jmol.getHeight());
- state.setViewId(jmol.getViewId());
- String statestring = jmol.viewer.getStateInfo();
- if (state != null)
- {
- state.setContent(statestring.replaceAll("\n", ""));
- }
- for (int s = 0; s < jmol.sequence.length; s++)
- {
- if (jal.findIndex(jmol.sequence[s]) > -1)
- {
- pdb.addStructureState(state);
- }
- }
+ StructureViewerBase viewFrame = (StructureViewerBase) frames[f];
+ matchedFile = saveStructureState(ap, jds, pdb, entry,
+ viewIds, matchedFile, viewFrame);
}
}
- if (entry.getFile() != null)
+ if (matchedFile != null || entry.getFile() != null)
{
- pdb.setFile(entry.getFile());
+ if (entry.getFile() != null)
+ {
+ // use entry's file
+ matchedFile = entry.getFile();
+ }
+ pdb.setFile(matchedFile); // entry.getFile());
if (pdbfiles == null)
{
- pdbfiles = new Vector();
+ pdbfiles = new ArrayList<String>();
}
if (!pdbfiles.contains(entry.getId()))
{
- pdbfiles.addElement(entry.getId());
+ pdbfiles.add(entry.getId());
+ DataInputStream dis = null;
try
{
- File file = new File(entry.getFile());
+ File file = new File(matchedFile);
if (file.exists() && jout != null)
{
byte[] data = new byte[(int) file.length()];
jout.putNextEntry(new JarEntry(entry.getId()));
- DataInputStream dis = new DataInputStream(
+ dis = new DataInputStream(
new FileInputStream(file));
dis.readFully(data);
} catch (Exception ex)
{
ex.printStackTrace();
+ } finally
+ {
+ if (dis != null)
+ {
+ try
+ {
+ dis.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
}
}
jms.addJSeq(jseq);
}
- if (av.hasHiddenRows)
+ if (!storeDS && av.hasHiddenRows())
{
- jal = av.alignment;
+ jal = av.getAlignment();
}
// SAVE MAPPINGS
if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
for (int p = 0; p < jac[i].aaWidth; p++)
{
Alcodon cmap = new Alcodon();
- if (jac[i].codons[p]!=null)
+ if (jac[i].codons[p] != null)
{
- // Null codons indicate a gapped column in the translated peptide alignment.
+ // Null codons indicate a gapped column in the translated peptide
+ // alignment.
cmap.setPos1(jac[i].codons[p][0]);
cmap.setPos2(jac[i].codons[p][1]);
cmap.setPos3(jac[i].codons[p][2]);
for (int m = 0; m < pmaps.length; m++)
{
AlcodMap alcmap = new AlcodMap();
- alcmap.setDnasq(seqHash(dnas[m]));
+ alcmap.setDnasq(seqHash(dnas[m]));
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
// SAVE TREES
// /////////////////////////////////
- if (av.currentTree != null)
+ if (!storeDS && av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
// NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
{
TreePanel tp = (TreePanel) frames[t];
- if (tp.treeCanvas.av.alignment == jal)
+ if (tp.treeCanvas.av.getAlignment() == jal)
{
Tree tree = new Tree();
tree.setTitle(tp.getTitle());
}
}
}
-
// SAVE ANNOTATIONS
- if (jal.getAlignmentAnnotation() != null)
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap groupRefs = new IdentityHashMap();
+ if (storeDS)
{
- jalview.datamodel.AlignmentAnnotation[] aa = jal
- .getAlignmentAnnotation();
-
- for (int i = 0; i < aa.length; i++)
+ for (SequenceI sq : jal.getSequences())
{
- Annotation an = new Annotation();
-
- if (aa[i].annotationId != null)
- {
- annotationIds.put(aa[i].annotationId, aa[i]);
- }
-
- an.setId(aa[i].annotationId);
-
- if (aa[i] == av.quality || aa[i] == av.conservation
- || aa[i] == av.consensus)
- {
- an.setLabel(aa[i].label);
- an.setGraph(true);
- vamsasSet.addAnnotation(an);
- continue;
- }
-
- an.setVisible(aa[i].visible);
-
- an.setDescription(aa[i].description);
-
- if (aa[i].sequenceRef != null)
- {
- // TODO later annotation sequenceRef should be the XML ID of the
- // sequence rather than its display name
- an.setSequenceRef(aa[i].sequenceRef.getName());
- }
-
- if (aa[i].graph > 0)
- {
- an.setGraph(true);
- an.setGraphType(aa[i].graph);
- an.setGraphGroup(aa[i].graphGroup);
- if (aa[i].getThreshold() != null)
- {
- ThresholdLine line = new ThresholdLine();
- line.setLabel(aa[i].getThreshold().label);
- line.setValue(aa[i].getThreshold().value);
- line.setColour(aa[i].getThreshold().colour.getRGB());
- an.setThresholdLine(line);
- }
- }
- else
- {
- an.setGraph(false);
- }
-
- an.setLabel(aa[i].label);
- if (aa[i].hasScore())
- {
- an.setScore(aa[i].getScore());
- }
- AnnotationElement ae;
- if (aa[i].annotations != null)
- {
- an.setScoreOnly(false);
- for (int a = 0; a < aa[i].annotations.length; a++)
- {
- if ((aa[i] == null) || (aa[i].annotations[a] == null))
- {
- continue;
- }
-
- ae = new AnnotationElement();
- if (aa[i].annotations[a].description != null)
- ae.setDescription(aa[i].annotations[a].description);
- if (aa[i].annotations[a].displayCharacter != null)
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
-
- if (!Float.isNaN(aa[i].annotations[a].value))
- ae.setValue(aa[i].annotations[a].value);
-
- ae.setPosition(a);
- if (aa[i].annotations[a].secondaryStructure != ' '
- && aa[i].annotations[a].secondaryStructure != '\0')
- ae
- .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
- + "");
-
- if (aa[i].annotations[a].colour != null
- && aa[i].annotations[a].colour != java.awt.Color.black)
- {
- ae.setColour(aa[i].annotations[a].colour.getRGB());
- }
-
- an.addAnnotationElement(ae);
- }
- }
- else
+ // Store annotation on dataset sequences only
+ jalview.datamodel.AlignmentAnnotation[] aa = sq.getAnnotation();
+ if (aa != null && aa.length > 0)
{
- an.setScoreOnly(true);
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
}
- vamsasSet.addAnnotation(an);
}
}
-
+ else
+ {
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ // Store the annotation shown on the alignment.
+ jalview.datamodel.AlignmentAnnotation[] aa = jal
+ .getAlignmentAnnotation();
+ storeAlignmentAnnotation(aa, groupRefs, av, calcIdSet, storeDS,
+ vamsasSet);
+ }
+ }
// SAVE GROUPS
if (jal.getGroups() != null)
{
JGroup[] groups = new JGroup[jal.getGroups().size()];
-
- for (int i = 0; i < groups.length; i++)
+ int i = -1;
+ for (jalview.datamodel.SequenceGroup sg : jal.getGroups())
{
- groups[i] = new JGroup();
+ groups[++i] = new JGroup();
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal
- .getGroups().elementAt(i);
groups[i].setStart(sg.getStartRes());
groups[i].setEnd(sg.getEndRes());
- groups[i].setName(sg.getName()); // TODO later sequence group should
- // specify IDs of sequences, not just
- // names
+ groups[i].setName(sg.getName());
+ if (groupRefs.containsKey(sg))
+ {
+ // group has references so set it's ID field
+ groups[i].setId(groupRefs.get(sg).toString());
+ }
if (sg.cs != null)
{
if (sg.cs.conservationApplied())
if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ groups[i].setColour(setUserColourScheme(sg.cs, userColours,
jms));
}
else
}
else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
{
- groups[i]
- .setColour(ColourSchemeProperty
- .getColourName(((jalview.schemes.AnnotationColourGradient) sg.cs)
- .getBaseColour()));
+ groups[i].setColour("AnnotationColourGradient");
+ groups[i].setAnnotationColours(constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) sg.cs,
+ userColours, jms));
}
else if (sg.cs instanceof jalview.schemes.UserColourScheme)
{
groups[i]
- .setColour(SetUserColourScheme(sg.cs, userColours, jms));
+ .setColour(setUserColourScheme(sg.cs, userColours, jms));
}
else
{
groups[i].setTextCol1(sg.textColour.getRGB());
groups[i].setTextCol2(sg.textColour2.getRGB());
groups[i].setTextColThreshold(sg.thresholdTextColour);
- groups[i].setShowUnconserved(sg.getShowunconserved());
+ groups[i].setShowUnconserved(sg.getShowNonconserved());
+ groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
+ groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+ groups[i].setNormaliseSequenceLogo(sg.isNormaliseSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
jms.setJGroup(groups);
}
-
- // /////////SAVE VIEWPORT
- Viewport view = new Viewport();
- view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(makeHashCode(av.getSequenceSetId(), av
- .getSequenceSetId()));
- view.setId(av.getViewId());
- view.setViewName(av.viewName);
- view.setGatheredViews(av.gatherViewsHere);
-
- if (ap.av.explodedPosition != null)
- {
- view.setXpos(av.explodedPosition.x);
- view.setYpos(av.explodedPosition.y);
- view.setWidth(av.explodedPosition.width);
- view.setHeight(av.explodedPosition.height);
- }
- else
+ if (!storeDS)
{
- view.setXpos(ap.alignFrame.getBounds().x);
- view.setYpos(ap.alignFrame.getBounds().y);
- view.setWidth(ap.alignFrame.getBounds().width);
- view.setHeight(ap.alignFrame.getBounds().height);
- }
-
- view.setStartRes(av.startRes);
- view.setStartSeq(av.startSeq);
+ // /////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
+ av.getSequenceSetId()));
+ view.setId(av.getViewId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
+
+ if (ap.av.explodedPosition != null)
+ {
+ view.setXpos(av.explodedPosition.x);
+ view.setYpos(av.explodedPosition.y);
+ view.setWidth(av.explodedPosition.width);
+ view.setHeight(av.explodedPosition.height);
+ }
+ else
+ {
+ view.setXpos(ap.alignFrame.getBounds().x);
+ view.setYpos(ap.alignFrame.getBounds().y);
+ view.setWidth(ap.alignFrame.getBounds().width);
+ view.setHeight(ap.alignFrame.getBounds().height);
+ }
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
- {
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
- userColours, jms));
- }
- else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
- {
- jalview.schemes.AnnotationColourGradient acg = (jalview.schemes.AnnotationColourGradient) av
- .getGlobalColourScheme();
+ view.setStartRes(av.startRes);
+ view.setStartSeq(av.startSeq);
- AnnotationColours ac = new AnnotationColours();
- ac.setAboveThreshold(acg.getAboveThreshold());
- ac.setThreshold(acg.getAnnotationThreshold());
- ac.setAnnotation(acg.getAnnotation());
- if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
{
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ view.setBgColour(setUserColourScheme(av.getGlobalColourScheme(),
userColours, jms));
}
+ else if (av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ AnnotationColours ac = constructAnnotationColours(
+ (jalview.schemes.AnnotationColourGradient) av
+ .getGlobalColourScheme(),
+ userColours, jms);
+
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
else
{
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg
- .getBaseColour()));
+ view.setBgColour(ColourSchemeProperty.getColourName(av
+ .getGlobalColourScheme()));
}
- ac.setMaxColour(acg.getMaxColour().getRGB());
- ac.setMinColour(acg.getMinColour().getRGB());
- view.setAnnotationColours(ac);
- view.setBgColour("AnnotationColourGradient");
- }
- else
- {
- view.setBgColour(ColourSchemeProperty.getColourName(av
- .getGlobalColourScheme()));
- }
+ ColourSchemeI cs = av.getGlobalColourScheme();
- ColourSchemeI cs = av.getGlobalColourScheme();
-
- if (cs != null)
- {
- if (cs.conservationApplied())
+ if (cs != null)
{
- view.setConsThreshold(cs.getConservationInc());
- if (cs instanceof jalview.schemes.UserColourScheme)
+ if (cs.conservationApplied())
+ {
+ view.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(setUserColourScheme(cs, userColours, jms));
+ }
+ }
+
+ if (cs instanceof ResidueColourScheme)
{
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ view.setPidThreshold(cs.getThreshold());
}
}
- if (cs instanceof ResidueColourScheme)
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ view.setFontName(av.font.getName());
+ view.setFontSize(av.font.getSize());
+ view.setFontStyle(av.font.getStyle());
+ view.setRenderGaps(av.renderGaps);
+ view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.isRightAlignIds());
+ view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowText(av.getShowText());
+ view.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.textColour.getRGB());
+ view.setTextCol2(av.textColour2.getRGB());
+ view.setTextColThreshold(av.thresholdTextColour);
+ 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.followHighlight);
+ view.setFollowSelection(av.followSelection);
+ view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+ if (av.getFeaturesDisplayed() != null)
{
- view.setPidThreshold(cs.getThreshold());
- }
- }
+ jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
- view.setConservationSelected(av.getConservationSelected());
- view.setPidSelected(av.getAbovePIDThreshold());
- view.setFontName(av.font.getName());
- view.setFontSize(av.font.getSize());
- view.setFontStyle(av.font.getStyle());
- view.setRenderGaps(av.renderGaps);
- view.setShowAnnotation(av.getShowAnnotation());
- view.setShowBoxes(av.getShowBoxes());
- view.setShowColourText(av.getColourText());
- view.setShowFullId(av.getShowJVSuffix());
- view.setRightAlignIds(av.rightAlignIds);
- view.setShowSequenceFeatures(av.showSequenceFeatures);
- view.setShowText(av.getShowText());
- view.setShowUnconserved(av.getShowUnconserved());
- view.setWrapAlignment(av.getWrapAlignment());
- view.setTextCol1(av.textColour.getRGB());
- view.setTextCol2(av.textColour2.getRGB());
- view.setTextColThreshold(av.thresholdTextColour);
+ String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder;
- if (av.featuresDisplayed != null)
- {
- jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
+ Vector settingsAdded = new Vector();
+ Object gstyle = null;
+ GraduatedColor gcol = null;
+ if (renderOrder != null)
+ {
+ for (int ro = 0; ro < renderOrder.length; ro++)
+ {
+ gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
+
+ setting.setDisplay(av.getFeaturesDisplayed()
+ .containsKey(renderOrder[ro]));
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getOrder(renderOrder[ro]);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
+ }
+ }
- String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+ // Make sure we save none displayed feature settings
+ Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours
+ .keySet().iterator();
+ while (en.hasNext())
+ {
+ String key = en.next().toString();
+ if (settingsAdded.contains(key))
+ {
+ continue;
+ }
- Vector settingsAdded = new Vector();
- for (int ro = 0; ro < renderOrder.length; ro++)
- {
- Setting setting = new Setting();
- setting.setType(renderOrder[ro]);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getColour(key).getRGB());
- setting.setDisplay(av.featuresDisplayed
- .containsKey(renderOrder[ro]));
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
- renderOrder[ro]);
- if (rorder > -1)
+ setting.setDisplay(false);
+ float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer()
+ .getOrder(key);
+ if (rorder > -1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(key);
+ }
+ en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups
+ .keySet().iterator();
+ Vector groupsAdded = new Vector();
+ while (en.hasNext())
{
- setting.setOrder(rorder);
+ String grp = en.next().toString();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas
+ .getFeatureRenderer().featureGroups.get(grp))
+ .booleanValue());
+ fs.addGroup(g);
+ groupsAdded.addElement(grp);
}
- fs.addSetting(setting);
- settingsAdded.addElement(renderOrder[ro]);
+ jms.setFeatureSettings(fs);
+
}
- // Make sure we save none displayed feature settings
- Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
- .keys();
- while (en.hasMoreElements())
+ if (av.hasHiddenColumns())
{
- String key = en.nextElement().toString();
- if (settingsAdded.contains(key))
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
{
- continue;
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
}
-
- Setting setting = new Setting();
- setting.setType(key);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(key).getRGB());
-
- setting.setDisplay(false);
- float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(
- key);
- if (rorder > -1)
+ else
{
- setting.setOrder(rorder);
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns()
+ .size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection()
+ .getHiddenColumns().elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
}
- fs.addSetting(setting);
- settingsAdded.addElement(key);
}
- en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
- Vector groupsAdded = new Vector();
- while (en.hasMoreElements())
+ if (calcIdSet.size() > 0)
{
- String grp = en.nextElement().toString();
- if (groupsAdded.contains(grp))
+ for (String calcId : calcIdSet)
{
- continue;
+ if (calcId.trim().length() > 0)
+ {
+ CalcIdParam cidp = createCalcIdParam(calcId, av);
+ // Some calcIds have no parameters.
+ if (cidp != null)
+ {
+ view.addCalcIdParam(cidp);
+ }
+ }
}
- Group g = new Group();
- g.setName(grp);
- g
- .setDisplay(((Boolean) ap.seqPanel.seqCanvas
- .getFeatureRenderer().featureGroups.get(grp))
- .booleanValue());
- fs.addGroup(g);
- groupsAdded.addElement(grp);
}
- jms.setFeatureSettings(fs);
-
- }
- if (av.hasHiddenColumns)
- {
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
- {
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
- }
+ jms.addViewport(view);
}
-
- jms.addViewport(view);
-
object.setJalviewModelSequence(jms);
object.getVamsasModel().addSequenceSet(vamsasSet);
}
/**
- * 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.
+ * 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 saveStructureState(AlignmentPanel ap, SequenceI jds,
+ Pdbids pdb, PDBEntry entry, List<String> viewIds,
+ String matchedFile, StructureViewerBase viewFrame)
+ {
+ final AAStructureBindingModel bindingModel = viewFrame
+ .getBinding();
+ 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()
+ .startsWith(pdbId.toLowerCase())))
+ {
+ 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)
+ String statestring = viewFrame.getStateInfo();
+
+ 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());
+ /*
+ * Only store each structure viewer's state once in each XML document.
+ */
+ if (!viewIds.contains(viewId))
+ {
+ viewIds.add(viewId);
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
+ else
+ {
+ state.setContent("# duplicate state");
+ }
+ pdb.addStructureState(state);
+ }
+ }
+ }
+ return matchedFile;
+ }
+
+ private AnnotationColours constructAnnotationColours(
+ AnnotationColourGradient acg, List<UserColourScheme> userColours,
+ JalviewModelSequence jms)
+ {
+ AnnotationColours ac = new AnnotationColours();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ ac.setAnnotation(acg.getAnnotation());
+ if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ {
+ ac.setColourScheme(setUserColourScheme(acg.getBaseColour(),
+ userColours, jms));
+ }
+ 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 groupRefs, AlignmentViewport av,
+ Set<String> calcIdSet, boolean storeDS, SequenceSet vamsasSet)
+ {
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
+
+ if (aa[i].annotationId != null)
+ {
+ annotationIds.put(aa[i].annotationId, aa[i]);
+ }
+
+ an.setId(aa[i].annotationId);
+
+ an.setVisible(aa[i].visible);
+
+ an.setDescription(aa[i].description);
+
+ if (aa[i].sequenceRef != null)
+ {
+ // TODO later annotation sequenceRef should be the XML ID of the
+ // sequence rather than its display name
+ an.setSequenceRef(aa[i].sequenceRef.getName());
+ }
+ if (aa[i].groupRef != null)
+ {
+ Object groupIdr = groupRefs.get(aa[i].groupRef);
+ if (groupIdr == null)
+ {
+ // make a locally unique String
+ groupRefs.put(aa[i].groupRef,
+ groupIdr = ("" + System.currentTimeMillis()
+ + aa[i].groupRef.getName() + groupRefs.size()));
+ }
+ an.setGroupRef(groupIdr.toString());
+ }
+
+ // store all visualization attributes for annotation
+ an.setGraphHeight(aa[i].graphHeight);
+ an.setCentreColLabels(aa[i].centreColLabels);
+ an.setScaleColLabels(aa[i].scaleColLabel);
+ an.setShowAllColLabels(aa[i].showAllColLabels);
+ an.setBelowAlignment(aa[i].belowAlignment);
+
+ if (aa[i].graph > 0)
+ {
+ an.setGraph(true);
+ an.setGraphType(aa[i].graph);
+ an.setGraphGroup(aa[i].graphGroup);
+ if (aa[i].getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(aa[i].getThreshold().label);
+ line.setValue(aa[i].getThreshold().value);
+ line.setColour(aa[i].getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
+
+ an.setLabel(aa[i].label);
+
+ if (aa[i] == av.getAlignmentQualityAnnot()
+ || aa[i] == av.getAlignmentConservationAnnotation()
+ || aa[i] == av.getAlignmentConsensusAnnotation()
+ || aa[i].autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ }
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
+
+ if (aa[i].getCalcId() != null)
+ {
+ calcIdSet.add(aa[i].getCalcId());
+ an.setCalcId(aa[i].getCalcId());
+ }
+ if (aa[i].hasProperties())
+ {
+ for (String pr : aa[i].getProperties())
+ {
+ Property prop = new Property();
+ prop.setName(pr);
+ prop.setValue(aa[i].getProperty(pr));
+ an.addProperty(prop);
+ }
+ }
+ AnnotationElement ae;
+ if (aa[i].annotations != null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ if (aa[i].annotations[a].description != null)
+ {
+ ae.setDescription(aa[i].annotations[a].description);
+ }
+ if (aa[i].annotations[a].displayCharacter != null)
+ {
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+ }
+
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ {
+ ae.setValue(aa[i].annotations[a].value);
+ }
+
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure > ' ')
+ {
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+ }
+
+ if (aa[i].annotations[a].colour != null
+ && aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
+
+ an.addAnnotationElement(ae);
+ if (aa[i].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 && !aa[i].autoCalculated))
+ {
+ // skip autocalculated annotation - these are only provided for
+ // alignments
+ vamsasSet.addAnnotation(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());
+ // generic URI allowing a third party to resolve another instance of the
+ // service used for this calculation
+ for (String urls : settings.getServiceURLs())
+ {
+ vCalcIdParam.addServiceURL(urls);
+ }
+ 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"))
+ {
+ Jws2Instance service = Jws2Discoverer.getDiscoverer()
+ .getPreferredServiceFor(calcIdParam.getServiceURL());
+ if (service != null)
+ {
+ WsParamSetI parmSet = null;
+ try
+ {
+ parmSet = service.getParamStore().parseServiceParameterFile(
+ calcIdParam.getName(), calcIdParam.getDescription(),
+ calcIdParam.getServiceURL(),
+ 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;
+ }
+ AAConSettings 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 JABAWS server.");
+ return false;
+ }
+ }
+ throw new Error(MessageManager.formatMessage("error.unsupported_version_calcIdparam", new String[]{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;
* exist, the result of the hashcode call for the object.
*
* @param jvobj
- * jalview data object
+ * jalview data object
* @return unique ID for referring to jvobj
*/
private String makeHashCode(Object jvobj, String altCode)
* return local jalview object mapped to ID, if it exists
*
* @param idcode
- * (may be null)
+ * (may be null)
* @return null or object bound to idcode
*/
private Object retrieveExistingObj(String idcode)
return mp;
}
- String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
- Vector userColours, JalviewModelSequence jms)
+ String setUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ List<UserColourScheme> userColours, JalviewModelSequence jms)
{
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();
jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();
jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();
}
}
- id = "ucs" + userColours.indexOf(ucs);
uc.setId(id);
uc.setUserColourScheme(jbucs);
jms.addUserColours(uc);
return id;
}
- jalview.schemes.UserColourScheme GetUserColourScheme(
+ jalview.schemes.UserColourScheme getUserColourScheme(
JalviewModelSequence jms, String id)
{
UserColours[] uc = jms.getUserColours();
/**
* Load a jalview project archive from a jar file
*
- * @param file -
- * HTTP URL or filename
+ * @param file
+ * - HTTP URL or filename
*/
- public AlignFrame LoadJalviewAlign(final String file)
+ public AlignFrame loadJalviewAlign(final String file)
{
jalview.gui.AlignFrame af = null;
try
{
+ // create list to store references for any new Jmol viewers created
+ newStructureViewers = new Vector<JalviewStructureDisplayI>();
// 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);
+ af = loadJalviewAlign(jprovider);
+
} catch (MalformedURLException e)
{
errorMessage = "Invalid URL format for '" + file + "'";
reportErrors();
+ } finally
+ {
+ try
+ {
+ SwingUtilities.invokeAndWait(new Runnable()
+ {
+ public void run()
+ {
+ setLoadingFinishedForNewStructureViewers();
+ };
+ });
+ } catch (Exception x)
+ {
+
+ }
}
return af;
}
return new jarInputStreamProvider()
{
+ @Override
public JarInputStream getJarInputStream() throws IOException
{
if (_url != null)
}
}
+ @Override
public String getFilename()
{
return file;
* @param jprovider
* @return
*/
- public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ public AlignFrame loadJalviewAlign(final jarInputStreamProvider jprovider)
{
errorMessage = null;
if (uniqueSetSuffix == null)
}
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap<String, SequenceI>();
}
if (viewportsAdded == null)
{
frefedSequence = new Vector();
}
- jalview.gui.AlignFrame af = null;
+ jalview.gui.AlignFrame af = null, _af = null;
Hashtable gatherToThisFrame = new Hashtable();
final String file = jprovider.getFilename();
try
object = (JalviewModel) unmar.unmarshal(in);
if (true) // !skipViewport(object))
{
- af = LoadFromObject(object, file, true, jprovider);
- if (af.viewport.gatherViewsHere)
+ _af = loadFromObject(object, file, true, jprovider);
+ if (object.getJalviewModelSequence().getViewportCount() > 0)
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ af = _af;
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
}
entryCount++;
+ ex + "\n");
} catch (OutOfMemoryError e)
{
- new jalview.gui.OOMWarning("loading jalview XML file", e,
- Desktop.instance);
+ // 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();
}
if (Desktop.instance != null)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
+ @Override
public void run()
{
JOptionPane.showInternalMessageDialog(Desktop.desktop,
errorMessage = null;
}
- Hashtable alreadyLoadedPDB;
+ Hashtable<String, String> alreadyLoadedPDB;
/**
* 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 boolean updateLocalViews = false;
+ private final boolean updateLocalViews = false;
String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
if (alreadyLoadedPDB == null)
+ {
alreadyLoadedPDB = new Hashtable();
+ }
if (alreadyLoadedPDB.containsKey(pdbId))
+ {
return alreadyLoadedPDB.get(pdbId).toString();
+ }
try
{
}
;
out.close();
-
- alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
- return outFile.getAbsolutePath();
+ String t = outFile.getAbsolutePath();
+ alreadyLoadedPDB.put(pdbId, t);
+ return t;
}
else
{
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
*
* @param object
- * DOM
+ * DOM
* @param file
- * filename source string
+ * filename source string
* @param loadTreesAndStructures
- * when false only create Viewport
+ * when false only create Viewport
* @param jprovider
- * data source provider
+ * data source provider
* @return alignment frame created from view stored in DOM
*/
- AlignFrame LoadFromObject(JalviewModel object, String file,
+ AlignFrame loadFromObject(JalviewModel object, String file,
boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
JalviewModelSequence jms = object.getJalviewModelSequence();
- Viewport view = jms.getViewport(0);
+ Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0)
+ : null;
+
// ////////////////////////////////
// LOAD SEQUENCES
boolean multipleView = false;
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ JSeq[] jseqs = object.getJalviewModelSequence().getJSeq();
int vi = 0; // counter in vamsasSeq array
- for (int i = 0; i < JSEQ.length; i++)
+ for (int i = 0; i < jseqs.length; i++)
{
- String seqId = JSEQ[i].getId();
+ String seqId = jseqs[i].getId();
if (seqRefIds.get(seqId) != null)
{
- tmpseqs.add((jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ tmpseqs.add(seqRefIds.get(seqId));
multipleView = true;
}
else
jseq = new jalview.datamodel.Sequence(vamsasSeq[vi].getName(),
vamsasSeq[vi].getSequence());
jseq.setDescription(vamsasSeq[vi].getDescription());
- jseq.setStart(JSEQ[i].getStart());
- jseq.setEnd(JSEQ[i].getEnd());
+ jseq.setStart(jseqs[i].getStart());
+ jseq.setEnd(jseqs[i].getEnd());
jseq.setVamsasId(uniqueSetSuffix + seqId);
seqRefIds.put(vamsasSeq[vi].getId(), jseq);
tmpseqs.add(jseq);
vi++;
}
- if (JSEQ[i].getHidden())
+ if (jseqs[i].getHidden())
{
if (hiddenSeqs == null)
{
hiddenSeqs = new Vector();
}
- hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
- .get(seqId));
+ hiddenSeqs.addElement(seqRefIds.get(seqId));
}
}
}
else
{
- recoverDatasetFor(vamsasSet, al);
+ // recover dataset - passing on flag indicating if this a 'viewless'
+ // sequence set (a.k.a. a stored dataset for the project)
+ recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence()
+ .getViewportCount() == 0);
}
// ///////////////////////////////
// structures for the alignment
for (int i = 0; i < vamsasSeq.length; i++)
{
- if (JSEQ[i].getFeaturesCount() > 0)
+ if (jseqs[i].getFeaturesCount() > 0)
{
- Features[] features = JSEQ[i].getFeatures();
+ Features[] features = jseqs[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
{
addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
}
- if (JSEQ[i].getPdbidsCount() > 0)
+ if (jseqs[i].getPdbidsCount() > 0)
{
- Pdbids[] ids = JSEQ[i].getPdbids();
+ Pdbids[] ids = jseqs[i].getPdbids();
for (int p = 0; p < ids.length; p++)
{
jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
entry.setFile(pdbloaded.get(ids[p].getId()).toString());
}
}
-
+ StructureSelectionManager.getStructureSelectionManager(
+ Desktop.instance)
+ .registerPDBEntry(entry);
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
}
}
Alcodon[] alcods = alc[i].getAlcodon();
for (int p = 0; p < cf.codons.length; p++)
{
- if (alcods[p].hasPos1() && alcods[p].hasPos2() && alcods[p].hasPos3())
+ if (alcods[p].hasPos1() && alcods[p].hasPos2()
+ && alcods[p].hasPos3())
{
// translated codons require three valid positions
cf.codons[p] = new int[3];
cf.codons[p][0] = (int) alcods[p].getPos1();
cf.codons[p][1] = (int) alcods[p].getPos2();
cf.codons[p][2] = (int) alcods[p].getPos3();
- } else {
+ }
+ else
+ {
cf.codons[p] = null;
}
}
AlcodMap[] maps = alc[i].getAlcodMap();
for (int m = 0; m < maps.length; m++)
{
- SequenceI dnaseq = (SequenceI) seqRefIds
+ SequenceI dnaseq = seqRefIds
.get(maps[m].getDnasq());
// Load Mapping
jalview.datamodel.Mapping mapping = null;
// ////////////////////////////////
// LOAD ANNOTATIONS
- boolean hideQuality = true, hideConservation = true, hideConsensus = true;
+ ArrayList<JvAnnotRow> autoAlan = new ArrayList<JvAnnotRow>();
+ /**
+ * store any annotations which forward reference a group's ID
+ */
+ Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>> groupAnnotRefs = new Hashtable<String, ArrayList<jalview.datamodel.AlignmentAnnotation>>();
if (vamsasSet.getAnnotationCount() > 0)
{
for (int i = 0; i < an.length; i++)
{
- // set visibility for automatic annotation for this view
- if (an[i].getLabel().equals("Quality"))
- {
- hideQuality = false;
- continue;
- }
- else if (an[i].getLabel().equals("Conservation"))
+ /**
+ * test if annotation is automatically calculated for this view only
+ */
+ boolean autoForView = false;
+ if (an[i].getLabel().equals("Quality")
+ || an[i].getLabel().equals("Conservation")
+ || an[i].getLabel().equals("Consensus"))
{
- hideConservation = false;
- continue;
+ // Kludge for pre 2.5 projects which lacked the autocalculated flag
+ autoForView = true;
+ if (!an[i].hasAutoCalculated())
+ {
+ an[i].setAutoCalculated(true);
+ }
}
- else if (an[i].getLabel().equals("Consensus"))
+ if (autoForView
+ || (an[i].hasAutoCalculated() && an[i].isAutoCalculated()))
{
- hideConsensus = false;
- continue;
+ // remove ID - we don't recover annotation from other views for
+ // view-specific annotation
+ an[i].setId(null);
}
+
// set visiblity for other annotation in this view
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
// in principle Visible should always be true for annotation displayed
// in multiple views
if (an[i].hasVisible())
+ {
jda.visible = an[i].getVisible();
+ }
al.addAnnotation(jda);
// Construct new annotation from model.
AnnotationElement[] ae = an[i].getAnnotationElement();
jalview.datamodel.Annotation[] anot = null;
-
+ java.awt.Color firstColour = null;
+ int anpos;
if (!an[i].getScoreOnly())
{
anot = new jalview.datamodel.Annotation[al.getWidth()];
-
for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
{
- if (ae[aa].getPosition() >= anot.length)
+ anpos = ae[aa].getPosition();
+
+ if (anpos >= anot.length)
+ {
continue;
+ }
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+ anot[anpos] = new jalview.datamodel.Annotation(
- ae[aa].getDisplayCharacter(), ae[aa].getDescription(), (ae[aa]
- .getSecondaryStructure() == null || ae[aa]
- .getSecondaryStructure().length() == 0) ? ' ' : ae[aa]
- .getSecondaryStructure().charAt(0), ae[aa].getValue()
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure() == null || ae[aa]
+ .getSecondaryStructure().length() == 0) ? ' '
+ : ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue()
);
// JBPNote: Consider verifying dataflow for IO of secondary
// {
// anot[ae[aa].getPosition()].displayCharacter = "";
// }
- anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
- .getColour());
+ anot[anpos].colour = new java.awt.Color(ae[aa].getColour());
+ if (firstColour == null)
+ {
+ firstColour = anot[anpos].colour;
+ }
}
}
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
{
+ float llim = 0, hlim = 0;
+ // if (autoForView || an[i].isAutoCalculated()) {
+ // hlim=11f;
+ // }
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
- an[i].getDescription(), anot, 0, 0, an[i].getGraphType());
+ an[i].getDescription(), anot, llim, hlim,
+ an[i].getGraphType());
jaa.graphGroup = an[i].getGraphGroup();
-
+ jaa._linecolour = firstColour;
if (an[i].getThresholdLine() != null)
{
jaa.setThreshold(new jalview.datamodel.GraphLine(an[i]
an[i].getThresholdLine().getColour())));
}
-
+ if (autoForView || an[i].isAutoCalculated())
+ {
+ // Hardwire the symbol display line to ensure that labels for
+ // histograms are displayed
+ jaa.hasText = true;
+ }
}
else
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
+ jaa._linecolour = firstColour;
}
// register new annotation
if (an[i].getId() != null)
al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
}
}
+ // and make a note of any group association
+ if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
+ {
+ ArrayList<jalview.datamodel.AlignmentAnnotation> aal = groupAnnotRefs
+ .get(an[i].getGroupRef());
+ if (aal == null)
+ {
+ aal = new ArrayList<jalview.datamodel.AlignmentAnnotation>();
+ groupAnnotRefs.put(an[i].getGroupRef(), aal);
+ }
+ aal.add(jaa);
+ }
+
if (an[i].hasScore())
{
jaa.setScore(an[i].getScore());
}
-
if (an[i].hasVisible())
+ {
jaa.visible = an[i].getVisible();
+ }
- al.addAnnotation(jaa);
+ if (an[i].hasCentreColLabels())
+ {
+ jaa.centreColLabels = an[i].getCentreColLabels();
+ }
+
+ if (an[i].hasScaleColLabels())
+ {
+ jaa.scaleColLabel = an[i].getScaleColLabels();
+ }
+ if (an[i].hasAutoCalculated() && an[i].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 (an[i].hasGraphHeight())
+ {
+ jaa.graphHeight = an[i].getGraphHeight();
+ }
+ if (an[i].hasBelowAlignment())
+ {
+ jaa.belowAlignment = an[i].isBelowAlignment();
+ }
+ jaa.setCalcId(an[i].getCalcId());
+ if (an[i].getPropertyCount() > 0)
+ {
+ for (jalview.schemabinding.version2.Property prop : an[i]
+ .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 (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
-
+ boolean addAnnotSchemeGroup = false;
for (int i = 0; i < groups.length; i++)
{
ColourSchemeI cs = null;
{
if (groups[i].getColour().startsWith("ucs"))
{
- cs = GetUserColourScheme(jms, groups[i].getColour());
+ cs = getUserColourScheme(jms, groups[i].getColour());
+ }
+ else if (groups[i].getColour().equals("AnnotationColourGradient")
+ && groups[i].getAnnotationColours() != null)
+ {
+ addAnnotSchemeGroup = true;
+ cs = null;
}
else
{
for (int s = 0; s < groups[i].getSeqCount(); s++)
{
String seqId = groups[i].getSeq(s) + "";
- jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) seqRefIds
+ jalview.datamodel.SequenceI ts = seqRefIds
.get(seqId);
if (ts != null)
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
- sg
- .setOutlineColour(new java.awt.Color(groups[i]
- .getOutlineColour()));
+ sg.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
sg.textColour = new java.awt.Color(groups[i].getTextCol1());
sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
- sg.setShowunconserved(groups[i].hasShowUnconserved() ? groups[i].isShowUnconserved() : false);
+ sg.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
+ .isShowUnconserved() : false);
sg.thresholdTextColour = groups[i].getTextColThreshold();
-
+ if (groups[i].hasShowConsensusHistogram())
+ {
+ sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
+ }
+ ;
+ if (groups[i].hasShowSequenceLogo())
+ {
+ sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
+ }
+ if (groups[i].hasNormaliseSequenceLogo())
+ {
+ sg.setNormaliseSequenceLogo(groups[i].isNormaliseSequenceLogo());
+ }
+ if (groups[i].hasIgnoreGapsinConsensus())
+ {
+ sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
+ }
if (groups[i].getConsThreshold() != 0)
{
jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3, sg
- .getSequences(null), 0, sg.getWidth() - 1);
+ "All", ResidueProperties.propHash, 3,
+ sg.getSequences(null), 0, sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
}
- al.addGroup(sg);
- }
+ if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
+ {
+ // re-instate unique group/annotation row reference
+ ArrayList<jalview.datamodel.AlignmentAnnotation> jaal = groupAnnotRefs
+ .get(groups[i].getId());
+ if (jaal != null)
+ {
+ for (jalview.datamodel.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.cs = constructAnnotationColour(
+ groups[i].getAnnotationColours(), null, al, jms, false);
+ }
+ }
+ }
+ if (view == null)
+ {
+ // only dataset in this model, so just return.
+ return null;
}
-
// ///////////////////////////////
// LOAD VIEWPORT
}
}
+ /**
+ * indicate that annotation colours are applied across all groups (pre
+ * Jalview 2.8.1 behaviour)
+ */
+ boolean doGroupAnnColour = isVersionStringLaterThan("2.8.1",
+ object.getVersion());
+
AlignmentPanel ap = null;
boolean isnewview = true;
if (viewId != null)
if (isnewview)
{
- af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
- hideQuality, hideConservation, jms, view, uniqueSeqSetId,
- viewId);
+ af = loadViewport(file, jseqs, hiddenSeqs, al, jms, view,
+ uniqueSeqSetId, viewId, autoAlan);
av = af.viewport;
ap = af.alignPanel;
}
TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
if (tp == null)
{
- tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
- .getNewick()), tree.getTitle(), tree.getWidth(), tree
- .getHeight(), tree.getXpos(), tree.getYpos());
+ tp = af.ShowNewickTree(
+ new jalview.io.NewickFile(tree.getNewick()),
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
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(tree.getXpos(), tree.getYpos(), tree
.getWidth(), tree.getHeight()));
tp.treeCanvas.ap = ap; // af.alignPanel;
}
- if (tp==null)
+ if (tp == null)
{
- warn("There was a problem recovering stored Newick tree: \n"+tree.getNewick());
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
continue;
}
// //LOAD STRUCTURES
if (loadTreesAndStructures)
{
- for (int i = 0; i < JSEQ.length; i++)
+ loadStructures(jprovider, jseqs, af, ap);
+ }
+ // and finally return.
+ return af;
+ }
+
+ /**
+ * Load and link any saved structure viewers.
+ *
+ * @param jprovider
+ * @param jseqs
+ * @param af
+ * @param ap
+ */
+ protected void loadStructures(jarInputStreamProvider jprovider,
+ JSeq[] jseqs, AlignFrame af, AlignmentPanel ap)
+ {
+ // run through all PDB ids on the alignment, and collect mappings between
+ // jmol view ids and all sequences referring to it
+ Map<String, ViewerData> jmolViewIds = new HashMap<String, ViewerData>();
+
+ for (int i = 0; i < jseqs.length; i++)
+ {
+ if (jseqs[i].getPdbidsCount() > 0)
{
- if (JSEQ[i].getPdbidsCount() > 0)
+ Pdbids[] ids = jseqs[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
{
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
+ final int structureStateCount = ids[p].getStructureStateCount();
+ for (int s = 0; s < structureStateCount; s++)
+ {
+ // check to see if we haven't already created this structure view
+ final StructureState structureState = ids[p].getStructureState(s);
+ String sviewid = (structureState.getViewId() == null) ? null
+ : structureState.getViewId()
+ + uniqueSetSuffix;
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+ // Originally : ids[p].getFile()
+ // : TODO: verify external PDB file recovery still works in normal
+ // jalview project load
+ jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
+ jpdb.setId(ids[p].getId());
+
+ int x = structureState.getXpos();
+ int y = structureState.getYpos();
+ int width = structureState.getWidth();
+ int height = structureState.getHeight();
+
+ // Probably don't need to do this anymore...
+ // Desktop.desktop.getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ jalview.datamodel.SequenceI seq = seqRefIds
+ .get(jseqs[i].getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ + "," + height;
+ }
+ if (!jmolViewIds.containsKey(sviewid))
+ {
+ jmolViewIds.put(sviewid, new ViewerData(x, y, width, height,
+ false, false, true));
+ // 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
+ ViewerData jmoldat = jmolViewIds.get(sviewid);
+ jmoldat.alignWithPanel |= structureState
+ .hasAlignwithAlignPanel() ? structureState.getAlignwithAlignPanel() : false;
+ // never colour by linked panel if not specified
+ jmoldat.colourWithAlignPanel |= structureState
+ .hasColourwithAlignPanel() ? structureState.getColourwithAlignPanel()
+ : false;
+ // default for pre-2.7 projects is that Jmol colouring is enabled
+ jmoldat.colourByViewer &= structureState
+ .hasColourByJmol() ? structureState
+ .getColourByJmol() : true;
+
+ if (jmoldat.stateData.length() < structureState.getContent()
+ .length())
+ {
+ {
+ jmoldat.stateData = structureState.getContent();
+ }
+ }
+ if (ids[p].getFile() != null)
+ {
+ File mapkey = new File(ids[p].getFile());
+ Object[] seqstrmaps = jmoldat.fileData.get(mapkey);
+ if (seqstrmaps == null)
+ {
+ jmoldat.fileData.put(mapkey,
+ seqstrmaps = new Object[]
+ { pdbFile, ids[p].getId(), new Vector(),
+ new Vector() });
+ }
+ if (!((Vector) seqstrmaps[2]).contains(seq))
+ {
+ ((Vector) seqstrmaps[2]).addElement(seq);
+ // ((Vector)seqstrmaps[3]).addElement(n) :
+ // in principle, chains
+ // should be stored here : do we need to
+ // TODO: store and recover seq/pdb_id :
+ // chain mappings
+ }
+ }
+ 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 Jmol views
+ for (Entry<String, ViewerData> entry : jmolViewIds.entrySet())
+ {
+ String sviewid = entry.getKey();
+ ViewerData svattrib = entry.getValue();
+ String state = svattrib.stateData;
+ Map<File, Object[]> oldFiles = svattrib.fileData;
+ final boolean useinJmolsuperpos = svattrib.alignWithPanel;
+ final boolean usetoColourbyseq = svattrib.colourWithAlignPanel;
+ final boolean jmolColouring = svattrib.colourByViewer;
+ int x = svattrib.x;
+ int y = svattrib.y;
+ int width = svattrib.width;
+ int height = svattrib.height;
+ // collate the pdbfile -> sequence mappings from this view
+ Vector<String> pdbfilenames = new Vector<String>();
+ Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
+ Vector<String> pdbids = new Vector<String>();
+
+ /*
+ * Search for any Jmol windows already open from other alignment views
+ * that exactly match the stored structure state
+ */
+ AppJmol comp = null;
+ JInternalFrame[] frames = getAllFrames();
+ for (JInternalFrame frame : frames)
+ {
+ if (frame instanceof AppJmol)
{
- for (int s = 0; s < ids[p].getStructureStateCount(); s++)
+ /*
+ * Post jalview 2.4 schema includes structure view id
+ */
+ if (sviewid != null
+ && ((StructureViewerBase) frame).getViewId().equals(
+ sviewid))
{
- // check to see if we haven't already created this structure view
- String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
- : ids[p].getStructureState(s).getViewId()
- + uniqueSetSuffix;
- jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
- // Originally : ids[p].getFile()
- // : TODO: verify external PDB file recovery still works in normal
- // jalview project load
- jpdb.setFile(loadPDBFile(jprovider, ids[p].getId()));
- jpdb.setId(ids[p].getId());
-
- int x = ids[p].getStructureState(s).getXpos();
- int y = ids[p].getStructureState(s).getYpos();
- int width = ids[p].getStructureState(s).getWidth();
- int height = ids[p].getStructureState(s).getHeight();
- AppJmol comp = null;
- JInternalFrame[] frames = null;
- do
+ comp = (AppJmol) frame;
+ }
+ /*
+ * Otherwise test for matching position and size of viewer frame
+ */
+ else if (frame.getX() == x && frame.getY() == y
+ && frame.getHeight() == height
+ && frame.getWidth() == width)
+ {
+ comp = (AppJmol) frame;
+ }
+ }
+ }
+
+ if (comp == null)
+ {
+ /*
+ * Create a new Jmol window. First parse the Jmol state to translate
+ * filenames loaded into the view, and record the order in which files
+ * are shown in the Jmol view, so we can add the sequence mappings in
+ * same order.
+ */
+ StringBuffer newFileLoc = null;
+ int cp = 0, ncp, ecp;
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ if (newFileLoc == null)
+ {
+ newFileLoc = new StringBuffer();
+ }
+ do
+ {
+ // look for next filename in load statement
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do
+ // filename
+ // translation differently.
+ Object[] filedat = oldFiles.get(new File(oldfilenam));
+ newFileLoc.append(Platform
+ .escapeString((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement(((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ } while ((ncp = state.indexOf("/*file*/", cp)) > -1);
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err
+ .print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuffer(state);
+ newFileLoc.append("; load append ");
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in
+ // the viewer
+ Object[] filedat = oldFiles.get(id);
+ String nfilename;
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement(((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append((String) filedat[0]);
+ newFileLoc.append("\"");
+
+ }
+ newFileLoc.append(";");
+ }
+
+ if (newFileLoc != null)
+ {
+ int histbug = newFileLoc.indexOf("history = ");
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
+ histbug);
+ String val = (diff == -1) ? null : newFileLoc.substring(
+ histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e"))
{
- try
+ if (val.trim().equals("true"))
{
- frames = Desktop.desktop.getAllFrames();
- } catch (ArrayIndexOutOfBoundsException e)
+ val = "1";
+ }
+ else
{
- // occasional No such child exceptions are thrown here...
- frames = null;
- try
- {
- Thread.sleep(10);
- } catch (Exception f)
- {
- }
- ;
+ val = "0";
}
- } while (frames == null);
- // search for any Jmol windows already open from other
- // alignment views that exactly match the stored structure state
- for (int f = 0; comp == null && f < frames.length; f++)
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
+ // TODO: assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}} from hash
+ final String[] pdbf = pdbfilenames
+ .toArray(new String[pdbfilenames.size()]), id = pdbids
+ .toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString(), vid = sviewid;
+ final AlignFrame alf = af;
+ final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
+ width, height);
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
{
- if (frames[f] instanceof AppJmol)
+ @Override
+ public void run()
{
- if (sviewid != null
- && ((AppJmol) frames[f]).getViewId().equals(
- sviewid))
+ JalviewStructureDisplayI sview = null;
+ try
{
- // post jalview 2.4 schema includes structure view id
- comp = (AppJmol) frames[f];
- }
- else if (frames[f].getX() == x && frames[f].getY() == y
- && frames[f].getHeight() == height
- && frames[f].getWidth() == width)
+ // JAL-1333 note - we probably can't migrate Jmol views to UCSF Chimera!
+ sview = new StructureViewer(alf.alignPanel
+ .getStructureSelectionManager()).createView(
+ StructureViewer.ViewerType.JMOL, pdbf, id, sq,
+ alf.alignPanel,
+ useinJmolsuperpos, usetoColourbyseq,
+ jmolColouring, fileloc, rect, vid);
+ addNewStructureViewer(sview);
+ } catch (OutOfMemoryError ex)
{
- comp = (AppJmol) frames[f];
+ new OOMWarning("restoring structure view for PDB id "
+ + id, (OutOfMemoryError) ex.getCause());
+ if (sview != null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
}
}
- }
- Desktop.desktop.getComponentAt(x, y);
-
- String pdbFile = loadPDBFile(jprovider, ids[p].getId());
-
- jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
- { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
- + "") };
-
- if (comp == null)
- {
- // create a new Jmol window
- String state = ids[p].getStructureState(s).getContent();
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.", ex);
- StringBuffer newFileLoc = new StringBuffer(state.substring(
- 0, state.indexOf("\"", state.indexOf("load")) + 1));
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
- newFileLoc.append(jpdb.getFile());
- newFileLoc.append(state.substring(state.indexOf("\"", state
- .indexOf("load \"") + 6)));
+ }
+ else
+ // if (comp != null)
+ {
+ linkStructureViewer(ap, comp, oldFiles, useinJmolsuperpos,
+ usetoColourbyseq, jmolColouring);
+ }
+ }
+ }
+ }
- new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
- newFileLoc.toString(), new java.awt.Rectangle(x, y,
- width, height), sviewid);
+ /**
+ * Link an AlignmentPanel to an existing JMol viewer.
+ *
+ * @param ap
+ * @param viewer
+ * @param oldFiles
+ * @param useinJmolsuperpos
+ * @param usetoColourbyseq
+ * @param jmolColouring
+ */
+ protected void linkStructureViewer(AlignmentPanel ap, AppJmol viewer,
+ Map<File, Object[]> oldFiles,
+ final boolean useinJmolsuperpos, final boolean usetoColourbyseq,
+ final boolean jmolColouring)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
- }
- else
- // if (comp != null)
- {
- // NOTE: if the jalview project is part of a shared session then
- // view synchronization should/could be done here.
+ // add mapping for sequences in this view to an already open Jmol
+ // instance
+ for (File id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ Object[] filedat = oldFiles.get(id);
+ String pdbFile = (String) filedat[0];
+ SequenceI[] seq = ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]);
+ viewer.jmb.getSsm().setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+ viewer.jmb.addSequenceForStructFile(pdbFile, seq);
+ }
+ // and add the AlignmentPanel's reference to the Jmol view
+ viewer.addAlignmentPanel(ap);
+ if (useinJmolsuperpos)
+ {
+ viewer.useAlignmentPanelForSuperposition(ap);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForSuperposition(ap);
+ }
+ if (usetoColourbyseq)
+ {
+ viewer.useAlignmentPanelForColourbyseq(ap, !jmolColouring);
+ }
+ else
+ {
+ viewer.excludeAlignmentPanelForColourbyseq(ap);
+ }
+ }
- // add mapping for this sequence to the already open Jmol
- // instance (if it doesn't already exist)
- // These
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
+ /**
+ * 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.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ try
+ {
+ Thread.sleep(10);
+ } catch (InterruptedException f)
+ {
+ }
+ }
+ } while (frames == null);
+ return frames;
+ }
- ((AppJmol) comp).addSequence(seq);
- }
- }
+ /**
+ *
+ * @param supported
+ * - minimum version we are comparing against
+ * @param version
+ * - version of data being processsed.
+ * @return true if version is development/null or evaluates to the same or
+ * later X.Y.Z (where X,Y,Z are like [0-9]+b?[0-9]*)
+ */
+ private boolean isVersionStringLaterThan(String supported, String version)
+ {
+ if (version == null || version.equalsIgnoreCase("DEVELOPMENT BUILD")
+ || version.equalsIgnoreCase("Test")
+ || version.equalsIgnoreCase("AUTOMATED BUILD"))
+ {
+ System.err.println("Assuming project file with "
+ + (version == null ? "null" : version)
+ + " is compatible with Jalview version " + supported);
+ return true;
+ }
+ else
+ {
+ StringTokenizer currentV = new StringTokenizer(supported, "."), fileV = new StringTokenizer(
+ version, ".");
+ while (currentV.hasMoreTokens() && fileV.hasMoreTokens())
+ {
+ // convert b to decimal to catch bugfix releases within a series
+ String curT = currentV.nextToken().toLowerCase().replace('b', '.');
+ String fileT = fileV.nextToken().toLowerCase().replace('b', '.');
+ try
+ {
+ if (Float.valueOf(curT) > Float.valueOf(fileT))
+ {
+ // current version is newer than the version that wrote the file
+ return false;
}
+ } catch (NumberFormatException nfe)
+ {
+ System.err
+ .println("** WARNING: Version comparison failed for tokens ("
+ + curT
+ + ") and ("
+ + fileT
+ + ")\n** Current: '"
+ + supported + "' and Version: '" + version + "'");
}
}
+ if (currentV.hasMoreElements())
+ {
+ // fileV has no minor version but identical series to current
+ return false;
+ }
}
+ return true;
+ }
- return af;
+ Vector<JalviewStructureDisplayI> newStructureViewers = null;
+
+ protected void addNewStructureViewer(JalviewStructureDisplayI sview)
+ {
+ if (newStructureViewers != null)
+ {
+ sview.getBinding().setFinishedLoadingFromArchive(false);
+ newStructureViewers.add(sview);
+ }
+ }
+
+ protected void setLoadingFinishedForNewStructureViewers()
+ {
+ if (newStructureViewers != null)
+ {
+ for (JalviewStructureDisplayI sview : newStructureViewers)
+ {
+ sview.getBinding().setFinishedLoadingFromArchive(true);
+ }
+ newStructureViewers.clear();
+ newStructureViewers = null;
+ }
}
AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
- Alignment al, boolean hideConsensus, boolean hideQuality,
- boolean hideConservation, JalviewModelSequence jms,
- Viewport view, String uniqueSeqSetId, String viewId)
+ Alignment al, JalviewModelSequence jms, Viewport view,
+ String uniqueSeqSetId, String viewId,
+ ArrayList<JvAnnotRow> autoAlan)
{
AlignFrame af = null;
af = new AlignFrame(al, view.getWidth(), view.getHeight(),
for (int i = 0; i < JSEQ.length; i++)
{
- af.viewport.setSequenceColour(af.viewport.alignment.getSequenceAt(i),
- new java.awt.Color(JSEQ[i].getColour()));
+ af.viewport.setSequenceColour(af.viewport.getAlignment()
+ .getSequenceAt(i), new java.awt.Color(JSEQ[i].getColour()));
}
af.viewport.gatherViewsHere = view.getGatheredViews();
jalview.gui.AlignViewport av = (jalview.gui.AlignViewport) viewportsAdded
.get(uniqueSeqSetId);
- af.viewport.sequenceSetID = uniqueSeqSetId;
+ af.viewport.setSequenceSetId(uniqueSeqSetId);
if (av != null)
{
// propagate shared settings to this new view
for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
{
- hidden.addSequence(al
- .getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
+ hidden.addSequence(
+ al.getSequenceAt(JSEQ[s].getHiddenSequences(r)), false);
}
af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
}
af.viewport.hideSequence(hseqs);
}
- // set visibility of annotation in view
- if ((hideConsensus || hideQuality || hideConservation)
- && al.getAlignmentAnnotation() != null)
- {
- int hSize = al.getAlignmentAnnotation().length;
- for (int h = 0; h < hSize; h++)
- {
- if ((hideConsensus && al.getAlignmentAnnotation()[h].label
- .equals("Consensus"))
- || (hideQuality && al.getAlignmentAnnotation()[h].label
- .equals("Quality"))
- || (hideConservation && al.getAlignmentAnnotation()[h].label
- .equals("Conservation")))
- {
- al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
- hSize--;
- h--;
- }
- }
- af.alignPanel.adjustAnnotationHeight();
- }
// recover view properties and display parameters
if (view.getViewName() != null)
{
af.viewport.viewName = view.getViewName();
af.setInitialTabVisible();
}
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view
- .getHeight());
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
- af.viewport.rightAlignIds = view.getRightAlignIds();
+ af.viewport.setRightAlignIds(view.getRightAlignIds());
af.viewport.setFont(new java.awt.Font(view.getFontName(), view
.getFontStyle(), view.getFontSize()));
af.alignPanel.fontChanged();
af.viewport.textColour = new java.awt.Color(view.getTextCol1());
af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
af.viewport.thresholdTextColour = view.getTextColThreshold();
- af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view.isShowUnconserved() : false);
+ af.viewport.setShowUnconserved(view.hasShowUnconserved() ? view
+ .isShowUnconserved() : false);
af.viewport.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
{
if (view.getBgColour().startsWith("ucs"))
{
- cs = GetUserColourScheme(jms, view.getBgColour());
+ cs = getUserColourScheme(jms, view.getBgColour());
}
else if (view.getBgColour().startsWith("Annotation"))
{
- // int find annotation
- for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
- {
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label
- .equals(view.getAnnotationColours().getAnnotation()))
- {
- if (af.viewport.alignment.getAlignmentAnnotation()[i]
- .getThreshold() == null)
- {
- af.viewport.alignment.getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(view
- .getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
+ AnnotationColours viewAnnColour = view.getAnnotationColours();
+ cs = constructAnnotationColour(viewAnnColour, af, al, jms, true);
- );
- }
+ // annpos
- if (view.getAnnotationColours().getColourScheme()
- .equals("None"))
- {
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], new java.awt.Color(view
- .getAnnotationColours().getMinColour()),
- new java.awt.Color(view.getAnnotationColours()
- .getMaxColour()), view.getAnnotationColours()
- .getAboveThreshold());
- }
- else if (view.getAnnotationColours().getColourScheme()
- .startsWith("ucs"))
- {
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], GetUserColourScheme(
- jms, view.getAnnotationColours().getColourScheme()),
- view.getAnnotationColours().getAboveThreshold());
- }
- else
- {
- cs = new AnnotationColourGradient(af.viewport.alignment
- .getAlignmentAnnotation()[i], ColourSchemeProperty
- .getColour(al, view.getAnnotationColours()
- .getColourScheme()), view
- .getAnnotationColours().getAboveThreshold());
- }
-
- // Also use these settings for all the groups
- if (al.getGroups() != null)
- {
- for (int g = 0; g < al.getGroups().size(); g++)
- {
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
- .getGroups().elementAt(g);
-
- if (sg.cs == null)
- {
- continue;
- }
-
- /*
- * if
- * (view.getAnnotationColours().getColourScheme().equals("None")) {
- * sg.cs = new AnnotationColourGradient(
- * af.viewport.alignment.getAlignmentAnnotation()[i], new
- * java.awt.Color(view.getAnnotationColours(). getMinColour()),
- * new java.awt.Color(view.getAnnotationColours().
- * getMaxColour()),
- * view.getAnnotationColours().getAboveThreshold()); } else
- */
- {
- sg.cs = new AnnotationColourGradient(
- af.viewport.alignment.getAlignmentAnnotation()[i],
- sg.cs, view.getAnnotationColours()
- .getAboveThreshold());
- }
-
- }
- }
-
- break;
- }
-
- }
}
else
{
if (cs != null)
{
cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.hconsensus);
+ cs.setConsensus(af.viewport.getSequenceConsensusHash());
}
}
{
af.viewport.showSequenceFeatures = true;
}
+ if (view.hasCentreColumnLabels())
+ {
+ af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
+ }
+ if (view.hasIgnoreGapsinConsensus())
+ {
+ af.viewport.setIgnoreGapsConsensus(view.getIgnoreGapsinConsensus(),
+ null);
+ }
+ if (view.hasFollowHighlight())
+ {
+ af.viewport.followHighlight = view.getFollowHighlight();
+ }
+ if (view.hasFollowSelection())
+ {
+ af.viewport.followSelection = view.getFollowSelection();
+ }
+ if (view.hasShowConsensusHistogram())
+ {
+ af.viewport.setShowConsensusHistogram(view
+ .getShowConsensusHistogram());
+ }
+ else
+ {
+ af.viewport.setShowConsensusHistogram(true);
+ }
+ if (view.hasShowSequenceLogo())
+ {
+ af.viewport.setShowSequenceLogo(view.getShowSequenceLogo());
+ }
+ else
+ {
+ af.viewport.setShowSequenceLogo(false);
+ }
+ if (view.hasNormaliseSequenceLogo())
+ {
+ af.viewport.setNormaliseSequenceLogo(view.getNormaliseSequenceLogo());
+ }
+ if (view.hasShowDbRefTooltip())
+ {
+ af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
+ }
+ if (view.hasShowNPfeatureTooltip())
+ {
+ af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
+ }
+ if (view.hasShowGroupConsensus())
+ {
+ af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
+ }
+ else
+ {
+ af.viewport.setShowGroupConsensus(false);
+ }
+ if (view.hasShowGroupConservation())
+ {
+ af.viewport.setShowGroupConservation(view.getShowGroupConservation());
+ }
+ else
+ {
+ af.viewport.setShowGroupConservation(false);
+ }
+
// recover featre settings
if (jms.getFeatureSettings() != null)
{
- af.viewport.featuresDisplayed = new Hashtable();
+ af.viewport.setFeaturesDisplayed(new Hashtable());
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
Setting setting = jms.getFeatureSettings().getSetting(fs);
if (setting.hasMincolour())
{
- // TODO: determine how to set data independent bounds for a graduated colour scheme's range.
- GraduatedColor gc = new GraduatedColor(new java.awt.Color(setting.getMincolour()), new java.awt.Color(setting.getColour()),
- 0,1);
- if (setting.hasThreshold()) {
+ GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
+ new java.awt.Color(setting.getMincolour()),
+ new java.awt.Color(setting.getColour()),
+ setting.getMin(), setting.getMax()) : new GraduatedColor(
+ new java.awt.Color(setting.getMincolour()),
+ new java.awt.Color(setting.getColour()), 0, 1);
+ if (setting.hasThreshold())
+ {
gc.setThresh(setting.getThreshold());
gc.setThreshType(setting.getThreshstate());
}
- } else {
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ gc.setAutoScaled(true); // default
+ if (setting.hasAutoScale())
+ {
+ gc.setAutoScaled(setting.getAutoScale());
+ }
+ if (setting.hasColourByLabel())
+ {
+ gc.setColourByLabel(setting.getColourByLabel());
+ }
+ // and put in the feature colour table.
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), gc);
+ }
+ else
+ {
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(),
+ new java.awt.Color(setting.getColour()));
}
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ {
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
setting.getType(), setting.getOrder());
+ }
else
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
+ {
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder(
setting.getType(),
fs / jms.getFeatureSettings().getSettingCount());
+ }
if (setting.getDisplay())
{
- af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
+ af.viewport.getFeaturesDisplayed().put(setting.getType(), new Integer(
setting.getColour()));
}
}
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
Hashtable fgtable;
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
+ af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable();
for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++)
{
Group grp = jms.getFeatureSettings().getGroup(gs);
);
}
}
-
+ if (view.getCalcIdParam() != null)
+ {
+ for (CalcIdParam calcIdParam : view.getCalcIdParam())
+ {
+ if (calcIdParam != null)
+ {
+ if (recoverCalcIdParam(calcIdParam, af.viewport))
+ {
+ }
+ else
+ {
+ warn("Couldn't recover parameters for "
+ + calcIdParam.getCalcId());
+ }
+ }
+ }
+ }
af.setMenusFromViewport(af.viewport);
// TODO: we don't need to do this if the viewport is aready visible.
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
- .getHeight());
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ af.alignPanel.updateAnnotation(false, true); // recompute any autoannotation
+ reorderAutoannotation(af, al, autoAlan);
+ af.alignPanel.alignmentChanged();
return af;
}
+ private ColourSchemeI constructAnnotationColour(
+ AnnotationColours viewAnnColour, AlignFrame af, Alignment al,
+ JalviewModelSequence jms, boolean checkGroupAnnColour)
+ {
+ boolean propagateAnnColour = false;
+ ColourSchemeI cs = null;
+ AlignmentI annAlignment = af != null ? af.viewport.getAlignment() : al;
+ if (checkGroupAnnColour && al.getGroups() != null
+ && al.getGroups().size() > 0)
+ {
+ // pre 2.8.1 behaviour
+ // check to see if we should transfer annotation colours
+ propagateAnnColour = true;
+ for (jalview.datamodel.SequenceGroup sg : al.getGroups())
+ {
+ if (sg.cs instanceof AnnotationColourGradient)
+ {
+ propagateAnnColour = false;
+ }
+ }
+ }
+ // int find annotation
+ if (annAlignment.getAlignmentAnnotation() != null)
+ {
+ for (int i = 0; i < annAlignment.getAlignmentAnnotation().length; i++)
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].label
+ .equals(viewAnnColour.getAnnotation()))
+ {
+ if (annAlignment.getAlignmentAnnotation()[i].getThreshold() == null)
+ {
+ annAlignment.getAlignmentAnnotation()[i]
+ .setThreshold(new jalview.datamodel.GraphLine(
+ viewAnnColour.getThreshold(), "Threshold",
+ java.awt.Color.black)
+
+ );
+ }
+
+ if (viewAnnColour.getColourScheme().equals("None"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(viewAnnColour.getMinColour()),
+ new java.awt.Color(viewAnnColour.getMaxColour()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else if (viewAnnColour.getColourScheme().startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ getUserColourScheme(jms,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al,
+ viewAnnColour.getColourScheme()),
+ viewAnnColour.getAboveThreshold());
+ }
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs).setSeqAssociated(viewAnnColour
+ .isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ if (propagateAnnColour && al.getGroups() != null)
+ {
+ // Also use these settings for all the groups
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ jalview.datamodel.SequenceGroup sg = al.getGroups().get(g);
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /*
+ * if (viewAnnColour.getColourScheme().equals("None" )) { sg.cs =
+ * new AnnotationColourGradient(
+ * annAlignment.getAlignmentAnnotation()[i], new
+ * java.awt.Color(viewAnnColour. getMinColour()), new
+ * java.awt.Color(viewAnnColour. getMaxColour()),
+ * viewAnnColour.getAboveThreshold()); } else
+ */
+ {
+ sg.cs = new AnnotationColourGradient(
+ annAlignment.getAlignmentAnnotation()[i], sg.cs,
+ viewAnnColour.getAboveThreshold());
+ if (cs instanceof AnnotationColourGradient)
+ {
+ if (viewAnnColour.hasPerSequence())
+ {
+ ((AnnotationColourGradient) cs)
+ .setSeqAssociated(viewAnnColour.isPerSequence());
+ }
+ if (viewAnnColour.hasPredefinedColours())
+ {
+ ((AnnotationColourGradient) cs)
+ .setPredefinedColours(viewAnnColour
+ .isPredefinedColours());
+ }
+ }
+ }
+
+ }
+ }
+
+ break;
+ }
+
+ }
+ }
+ return cs;
+ }
+
+ private void reorderAutoannotation(AlignFrame af, Alignment al,
+ ArrayList<JvAnnotRow> autoAlan)
+ {
+ // copy over visualization settings for autocalculated annotation in the
+ // view
+ if (al.getAlignmentAnnotation() != null)
+ {
+ /**
+ * Kludge for magic autoannotation names (see JAL-811)
+ */
+ String[] magicNames = new String[]
+ { "Consensus", "Quality", "Conservation" };
+ JvAnnotRow nullAnnot = new JvAnnotRow(-1, null);
+ Hashtable<String, JvAnnotRow> visan = new Hashtable<String, JvAnnotRow>();
+ for (String nm : magicNames)
+ {
+ visan.put(nm, nullAnnot);
+ }
+ for (JvAnnotRow auan : autoAlan)
+ {
+ visan.put(auan.template.label
+ + (auan.template.getCalcId() == null ? "" : "\t"
+ + auan.template.getCalcId()), auan);
+ }
+ int hSize = al.getAlignmentAnnotation().length;
+ ArrayList<JvAnnotRow> reorder = new ArrayList<JvAnnotRow>();
+ // work through any autoCalculated annotation already on the view
+ // removing it if it should be placed in a different location on the
+ // annotation panel.
+ List<String> remains = new ArrayList(visan.keySet());
+ for (int h = 0; h < hSize; h++)
+ {
+ jalview.datamodel.AlignmentAnnotation jalan = al
+ .getAlignmentAnnotation()[h];
+ if (jalan.autoCalculated)
+ {
+ String k;
+ JvAnnotRow valan = visan.get(k = jalan.label);
+ if (jalan.getCalcId() != null)
+ {
+ valan = visan.get(k = jalan.label + "\t" + jalan.getCalcId());
+ }
+
+ if (valan != null)
+ {
+ // delete the auto calculated row from the alignment
+ al.deleteAnnotation(jalan, false);
+ remains.remove(k);
+ hSize--;
+ h--;
+ if (valan != nullAnnot)
+ {
+ if (jalan != valan.template)
+ {
+ // newly created autoannotation row instance
+ // so keep a reference to the visible annotation row
+ // and copy over all relevant attributes
+ if (valan.template.graphHeight >= 0)
+
+ {
+ jalan.graphHeight = valan.template.graphHeight;
+ }
+ jalan.visible = valan.template.visible;
+ }
+ reorder.add(new JvAnnotRow(valan.order, jalan));
+ }
+ }
+ }
+ }
+ // Add any (possibly stale) autocalculated rows that were not appended to
+ // the view during construction
+ for (String other : remains)
+ {
+ JvAnnotRow othera = visan.get(other);
+ if (othera != nullAnnot && othera.template.getCalcId() != null
+ && othera.template.getCalcId().length() > 0)
+ {
+ reorder.add(othera);
+ }
+ }
+ // now put the automatic annotation in its correct place
+ int s = 0, srt[] = new int[reorder.size()];
+ JvAnnotRow[] rws = new JvAnnotRow[reorder.size()];
+ for (JvAnnotRow jvar : reorder)
+ {
+ rws[s] = jvar;
+ srt[s++] = jvar.order;
+ }
+ reorder.clear();
+ jalview.util.QuickSort.sort(srt, rws);
+ // and re-insert the annotation at its correct position
+ for (JvAnnotRow jvar : rws)
+ {
+ al.addAnnotation(jvar.template, jvar.order);
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+ }
+
Hashtable skipList = null;
/**
return false;
}
- public void AddToSkipList(AlignFrame af)
+ public void addToSkipList(AlignFrame af)
{
if (skipList == null)
{
}
}
- private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al,
+ boolean ignoreUnrefed)
{
jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
Vector dseqs = null;
for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
{
Sequence vamsasSeq = vamsasSet.getSequence(i);
- ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed);
}
// create a new dataset
if (ds == null)
SequenceI[] dsseqs = new SequenceI[dseqs.size()];
dseqs.copyInto(dsseqs);
ds = new jalview.datamodel.Alignment(dsseqs);
+ debug("Created new dataset " + vamsasSet.getDatasetId()
+ + " for alignment " + System.identityHashCode(al));
addDatasetRef(vamsasSet.getDatasetId(), ds);
}
// set the dataset for the newly imported alignment.
- if (al.getDataset() == null)
+ if (al.getDataset() == null && !ignoreUnrefed)
{
al.setDataset(ds);
}
/**
*
* @param vamsasSeq
- * sequence definition to create/merge dataset sequence for
+ * sequence definition to create/merge dataset sequence for
* @param ds
- * dataset alignment
+ * dataset alignment
* @param dseqs
- * vector to add new dataset sequence to
+ * vector to add new dataset sequence to
*/
private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
- AlignmentI ds, Vector dseqs)
+ AlignmentI ds, Vector dseqs, boolean ignoreUnrefed)
{
// JBP TODO: Check this is called for AlCodonFrames to support recovery of
// xRef Codon Maps
jalview.datamodel.SequenceI dsq = null;
if (sq != null && sq.getDatasetSequence() != null)
{
- dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+ dsq = sq.getDatasetSequence();
+ }
+ if (sq == null && ignoreUnrefed)
+ {
+ return;
}
-
String sqid = vamsasSeq.getDsseqid();
if (dsq == null)
{
// need to create or add a new dataset sequence reference to this sequence
if (sqid != null)
{
- dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+ dsq = seqRefIds.get(sqid);
}
// check again
if (dsq == null)
if (sq != dsq)
{ // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
+ // and update the current dataset alignment
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
+ if (!dseqs.contains(dsq))
+ {
+ dseqs.add(dsq);
+ }
+ }
+ else
+ {
+ if (ds.findIndex(dsq) < 0)
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ }
}
}
}
* sb.append(newres.substring(newres.length() - sq.getEnd() -
* dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
*/
- dsq.setSequence(sb.toString());
+ dsq.setSequence(newres);
}
// TODO: merges will never happen if we 'know' we have the real dataset
// sequence - this should be detected when id==dssid
- System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
+ System.err
+ .println("DEBUG Notice: Merged dataset sequence (if you see this often, post at http://issues.jalview.org/browse/JAL-1474)"); // ("
// + (pre ? "prepended" : "") + " "
// + (post ? "appended" : ""));
}
}
java.util.Hashtable datasetIds = null;
+
java.util.IdentityHashMap dataset2Ids = null;
+
private Alignment getDatasetFor(String datasetId)
{
if (datasetIds == null)
}
datasetIds.put(datasetId, dataset);
}
+
/**
* make a new dataset ID for this jalview dataset alignment
+ *
* @param dataset
* @return
*/
private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
{
- if (dataset.getDataset()!=null)
+ if (dataset.getDataset() != null)
{
warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
}
- String datasetId=makeHashCode(dataset, null);
- if (datasetId==null)
+ String datasetId = makeHashCode(dataset, null);
+ if (datasetId == null)
{
// make a new datasetId and record it
if (dataset2Ids == null)
{
dataset2Ids = new IdentityHashMap();
- } else {
+ }
+ else
+ {
datasetId = (String) dataset2Ids.get(dataset);
}
- if (datasetId==null)
+ if (datasetId == null)
{
- datasetId = "ds"+dataset2Ids.size()+1;
- dataset2Ids.put(dataset,datasetId);
+ datasetId = "ds" + dataset2Ids.size() + 1;
+ dataset2Ids.put(dataset, datasetId);
}
}
return datasetId;
}
+
private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
{
for (int d = 0; d < sequence.getDBRefCount(); d++)
MappingChoice mc = m.getMappingChoice();
if (mc.getDseqFor() != null)
{
- String dsfor = ""+mc.getDseqFor();
+ String dsfor = "" + mc.getDseqFor();
if (seqRefIds.containsKey(dsfor))
{
/**
* recover from hash
*/
- jmap.setTo((SequenceI) seqRefIds.get(dsfor));
+ jmap.setTo(seqRefIds.get(dsfor));
}
else
{
/**
* make a new dataset sequence and add it to refIds hash
*/
- djs = new jalview.datamodel.Sequence(ms.getName(), ms
- .getSequence());
+ djs = new jalview.datamodel.Sequence(ms.getName(),
+ ms.getSequence());
djs.setStart(jmap.getMap().getToLowest());
djs.setEnd(jmap.getMap().getToHighest());
djs.setVamsasId(uniqueSetSuffix + sqid);
boolean keepSeqRefs)
{
initSeqRefs();
- jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+ jalview.schemabinding.version2.JalviewModel jm = saveState(ap, null,
null);
if (!keepSeqRefs)
else
{
uniqueSetSuffix = "";
- jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't overwrite the view we just copied
+ jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
+ // overwrite the
+ // view we just
+ // copied
}
- if (this.frefedSequence==null)
+ if (this.frefedSequence == null)
{
frefedSequence = new Vector();
}
viewportsAdded = new Hashtable();
- AlignFrame af = LoadFromObject(jm, null, false, null);
+ AlignFrame af = loadFromObject(jm, null, false, null);
af.alignPanels.clear();
af.closeMenuItem_actionPerformed(true);
/*
- * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0; i<ap.av.alignment.getAlignmentAnnotation().length;
- * i++) { if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
- * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
- * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
+ * if(ap.av.getAlignment().getAlignmentAnnotation()!=null) { for(int i=0;
+ * i<ap.av.getAlignment().getAlignmentAnnotation().length; i++) {
+ * if(!ap.av.getAlignment().getAlignmentAnnotation()[i].autoCalculated) {
+ * af.alignPanel.av.getAlignment().getAlignmentAnnotation()[i] =
+ * ap.av.getAlignment().getAlignmentAnnotation()[i]; } } }
*/
return af.alignPanel;
* flag indicating if hashtables should be cleared on finalization TODO this
* flag may not be necessary
*/
- private boolean _cleartables = true;
+ private final boolean _cleartables = true;
private Hashtable jvids2vobj;
*
* @see java.lang.Object#finalize()
*/
+ @Override
protected void finalize() throws Throwable
{
// really make sure we have no buried refs left.
}
}
+ 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
* alignment objects containing dataset sequences
*
* @param vobj2jv
- * Map from ID strings to jalview datamodel
+ * Map from ID strings to jalview datamodel
* @param jv2vobj
- * Map from jalview datamodel to ID strings
+ * Map from jalview datamodel to ID strings
*
*
*/
// register sequence object so the XML parser can recover it.
if (seqRefIds == null)
{
- seqRefIds = new Hashtable();
+ seqRefIds = new HashMap<String, SequenceI>();
}
if (seqsToIds == null)
{
- seqsToIds = new IdentityHashMap();
+ seqsToIds = new IdentityHashMap<SequenceI, String>();
}
- seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
- seqsToIds.put(jvobj, id);
+ seqRefIds.put(jv2vobj.get(jvobj).toString(), (SequenceI) jvobj);
+ seqsToIds.put((SequenceI) jvobj, id);
}
else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
{
}
}
else
+ {
Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
}
}
git://source.jalview.org / jalview.git / blobdiff