/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * 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 Jalview. If not, see <http://www.gnu.org/licenses/>.
*/
package jalview.gui;
+import java.awt.Rectangle;
import java.io.*;
+import java.lang.reflect.InvocationTargetException;
import java.net.*;
import java.util.*;
+import java.util.Map.Entry;
import java.util.jar.*;
import javax.swing.*;
import org.exolab.castor.xml.*;
import uk.ac.vamsas.objects.utils.MapList;
+import jalview.bin.Cache;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.SequenceI;
import jalview.schemabinding.version2.*;
import jalview.schemes.*;
import jalview.structure.StructureSelectionManager;
+import jalview.util.jarInputStreamProvider;
/**
- * Write out the current jalview desktop state
- * as a Jalview XML stream.
+ * Write out the current jalview desktop state as a Jalview XML stream.
+ *
+ * Note: the vamsas objects referred to here are primitive versions of the
+ * VAMSAS project schema elements - they are not the same and most likely never
+ * will be :)
*
- * Note: the vamsas objects referred to here are primitive
- * versions of the VAMSAS project schema elements - they are
- * not the same and most likely never will be :)
- *
* @author $author$
* @version $Revision$
*/
{
/**
* create/return unique hash string for sq
+ *
* @param sq
* @return new or existing unique string for sq
*/
String seqHash(SequenceI sq)
{
- if (seqsToIds==null)
+ if (seqsToIds == null)
{
initSeqRefs();
}
if (seqsToIds.containsKey(sq))
{
return (String) seqsToIds.get(sq);
- } else {
- // create sequential key
- String key = "sq"+(seqsToIds.size()+1);
+ }
+ else
+ {
+ // create sequential key
+ String key = "sq" + (seqsToIds.size() + 1);
+ key = makeHashCode(sq, key); // check we don't have an external reference
+ // for it already.
seqsToIds.put(sq, key);
return key;
}
}
+
void clearSeqRefs()
{
- seqRefIds.clear();
- seqsToIds.clear();
+ if (_cleartables)
+ {
+ if (seqRefIds != null)
+ {
+ seqRefIds.clear();
+ }
+ if (seqsToIds != null)
+ {
+ seqsToIds.clear();
+ }
+ // seqRefIds = null;
+ // seqsToIds = null;
+ }
+ else
+ {
+ // do nothing
+ warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
+ // seqRefIds = new Hashtable();
+ // seqsToIds = new IdentityHashMap();
+ }
}
+
void initSeqRefs()
{
- if (seqsToIds==null)
+ if (seqsToIds == null)
{
seqsToIds = new IdentityHashMap();
}
- if (seqRefIds==null)
+ if (seqRefIds == null)
{
seqRefIds = new Hashtable();
}
}
- java.util.IdentityHashMap seqsToIds = null; // SequenceI->key resolution
+
+ /**
+ * 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()
{
}
+
public Jalview2XML(boolean raiseGUI)
{
this.raiseGUI = raiseGUI;
}
else
{
- System.err
- .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
- + ref[1].getClass() + " type objects.");
+ if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ if (ref[2] != null
+ && ref[2] instanceof jalview.datamodel.Mapping)
+ {
+ jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
+ ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
+ seq, mp.getTo(), mp.getMap());
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
+ + ref[2].getClass() + " type objects.");
+ }
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+ + ref[1].getClass() + " type objects.");
+ }
}
frefedSequence.remove(r);
rSize--;
}
else
{
+ System.err
+ .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
+ + ref[0]
+ + " with objecttype "
+ + ref[1].getClass());
r++;
}
}
else
{
+ // empty reference
frefedSequence.remove(r);
rSize--;
}
}
/**
- * This maintains a list of viewports, the key being the
- * seqSetId. Important to set historyItem and redoList
- * for multiple views
+ * This maintains a list of viewports, the key being the seqSetId. Important
+ * to set historyItem and redoList for multiple views
*/
Hashtable viewportsAdded;
// SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
public void SaveState(File statefile)
{
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ SaveState(jout);
+
+ } catch (Exception e)
+ {
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive to output file '"
+ + statefile + "' - See console error log for details";
+ }
+ else
+ {
+ errorMessage += "(output file was '" + statefile + "')";
+ }
+ e.printStackTrace();
+ }
+ reportErrors();
+ }
+
+ /**
+ * Writes a jalview project archive to the given Jar output stream.
+ *
+ * @param jout
+ */
+ public void SaveState(JarOutputStream jout)
+ {
JInternalFrame[] frames = Desktop.desktop.getAllFrames();
if (frames == null)
try
{
- FileOutputStream fos = new FileOutputStream(statefile);
- JarOutputStream jout = new JarOutputStream(fos);
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
- ////////////////////////////////////////////////////
- //NOTE ALSO new PrintWriter must be used for each new JarEntry
+ // 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();
- //REVERSE ORDER
+ // REVERSE ORDER
for (int i = frames.length - 1; i > -1; i--)
{
if (frames[i] instanceof AlignFrame)
{
AlignFrame af = (AlignFrame) frames[i];
+ // skip ?
+ if (skipList != null
+ && skipList.containsKey(af.getViewport()
+ .getSequenceSetId()))
+ {
+ continue;
+ }
String shortName = af.getTitle();
}
}
}
- try { jout.flush(); } catch (Exception foo) {};
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
jout.close();
} catch (Exception ex)
{
- //TODO: inform user of the problem - they need to know if their data was not saved !
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive - see error output for details";
+ }
ex.printStackTrace();
}
}
SaveState(apanel, jfileName, jout);
}
- try { jout.flush(); } catch (Exception foo) {};
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
jout.close();
return true;
} catch (Exception ex)
{
+ errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
ex.printStackTrace();
return false;
}
}
/**
- * create a JalviewModel from an algnment view and marshall it
- * to a JarOutputStream
- *
- * @param ap panel to create jalview model for
- * @param fileName name of alignment panel written to output stream
- * @param jout jar output stream
- * @param out jar entry name
+ * create a JalviewModel from an algnment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
*/
public JalviewModel SaveState(AlignmentPanel ap, String fileName,
JarOutputStream jout)
{
initSeqRefs();
-
+ Vector jmolViewIds = new Vector(); //
Vector userColours = new Vector();
AlignViewport av = ap.av;
if (jal.getDataset() != null)
{
// dataset id is the dataset's hashcode
- vamsasSet.setDatasetId(jal.getDataset().hashCode() + "");
+ vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
}
if (jal.getProperties() != null)
{
JSeq jseq;
- //SAVE SEQUENCES
+ // SAVE SEQUENCES
String id = "";
jalview.datamodel.SequenceI jds;
for (int i = 0; i < jal.getHeight(); i++)
if (seqRefIds.get(id) != null)
{
- // This happens for two reasons: 1. multiple views are being serialised. 2. the hashCode has collided with another sequence's code. This DOES HAPPEN! (PF00072.15.stk does this)
- // JBPNote: Uncomment to debug writing out of files that do not read back in due to ArrayOutOfBoundExceptions.
- //System.err.println("vamsasSeq backref: "+id+"");
- //System.err.println(jds.getName()+" "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
- //System.err.println("Hashcode: "+seqHash(jds));
- //SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
- //System.err.println(rsq.getName()+" "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
- //System.err.println("Hashcode: "+seqHash(rsq));
+ // This happens for two reasons: 1. multiple views are being serialised.
+ // 2. the hashCode has collided with another sequence's code. This DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
}
else
{
pdb.setType(entry.getType());
AppJmol jmol;
- //This must have been loaded, is it still visible?
+ // 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)
{
+ // TODO: revise schema to allow many:one PDB id binding to viewer
jmol = (AppJmol) frames[f];
- if (!jmol.pdbentry.getId().equals(entry.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());
-
- String statestring = jmol.viewer.getStateInfo();
- if (state != null)
- {
- state.setContent(statestring.replaceAll("\n", ""));
- }
- for (int s = 0; s < jmol.sequence.length; s++)
+ for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
{
- if (jal.findIndex(jmol.sequence[s]) > -1)
+ if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry
+ .getId()
+ .toLowerCase()
+ .startsWith(
+ jmol.jmb.pdbentry[peid].getId()
+ .toLowerCase())))
+ continue;
+ if (matchedFile == null)
+ {
+ matchedFile = jmol.jmb.pdbentry[peid].getFile();
+ }
+ else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
+ .getFile()))
+ {
+ Cache.log
+ .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + jmol.jmb.pdbentry[peid].getFile());
+ ; // record the
+ }
+ // file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
+ String statestring = jmol.jmb.viewer.getStateInfo();
+
+ for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
{
- pdb.addStructureState(state);
+ if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ {
+ 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());
+ if (!jmolViewIds.contains(state.getViewId()))
+ {
+ // Make sure we only store a Jmol state once in each XML
+ // document.
+ jmolViewIds.addElement(state.getViewId());
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
+ else
+ {
+ state.setContent("# duplicate state");
+ }
+ pdb.addStructureState(state);
+ }
}
}
}
}
- 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.addElement(entry.getId());
try
{
- File file = new File(entry.getFile());
+ File file = new File(matchedFile);
if (file.exists() && jout != null)
{
byte[] data = new byte[(int) file.length()];
for (int p = 0; p < jac[i].aaWidth; p++)
{
Alcodon cmap = new Alcodon();
- cmap.setPos1(jac[i].codons[p][0]);
- cmap.setPos2(jac[i].codons[p][1]);
- cmap.setPos3(jac[i].codons[p][2]);
+ if (jac[i].codons[p] != null)
+ {
+ // 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]);
+ }
alc.addAlcodon(cmap);
}
if (jac[i].getProtMappings() != null
for (int m = 0; m < pmaps.length; m++)
{
AlcodMap alcmap = new AlcodMap();
- alcmap.setDnasq("" + dnas[m].hashCode());
+ alcmap.setDnasq(seqHash(dnas[m]));
alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
false));
alc.addAlcodMap(alcmap);
}
}
- //SAVE TREES
- ///////////////////////////////////
+ // SAVE TREES
+ // /////////////////////////////////
if (av.currentTree != null)
{
// FIND ANY ASSOCIATED TREES
tree.setWidth(tp.getWidth());
tree.setXpos(tp.getX());
tree.setYpos(tp.getY());
-
+ tree.setId(makeHashCode(tp, null));
jms.addTree(tree);
}
}
}
}
- //SAVE ANNOTATIONS
+ // SAVE ANNOTATIONS
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap groupRefs = new IdentityHashMap();
if (jal.getAlignmentAnnotation() != null)
{
jalview.datamodel.AlignmentAnnotation[] aa = jal
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].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());
+ }
+ if (aa[i] == av.quality || aa[i] == av.conservation
+ || aa[i] == av.consensus || aa[i].autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ // write a stub for this annotation - indicate presence of autocalc
+ // rows
+ an.setLabel(aa[i].label);
+ an.setGraph(true);
+ vamsasSet.addAnnotation(an);
+ continue;
+ }
if (aa[i].graph > 0)
{
ae.setPosition(a);
if (aa[i].annotations[a].secondaryStructure != ' '
&& aa[i].annotations[a].secondaryStructure != '\0')
- ae
- .setSecondaryStructure(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)
vamsasSet.addAnnotation(an);
}
}
-
- //SAVE GROUPS
+ // SAVE GROUPS
if (jal.getGroups() != null)
{
JGroup[] groups = new JGroup[jal.getGroups().size()];
groups[i].setStart(sg.getStartRes());
groups[i].setEnd(sg.getEndRes());
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())
groups[i].setTextCol1(sg.textColour.getRGB());
groups[i].setTextCol2(sg.textColour2.getRGB());
groups[i].setTextColThreshold(sg.thresholdTextColour);
-
+ groups[i].setShowUnconserved(sg.getShowNonconserved());
+ groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
+ groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
for (int s = 0; s < sg.getSize(); s++)
{
jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
jms.setJGroup(groups);
}
- ///////////SAVE VIEWPORT
+ // /////////SAVE VIEWPORT
Viewport view = new Viewport();
view.setTitle(ap.alignFrame.getTitle());
- view.setSequenceSetId(av.getSequenceSetId());
+ view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
+ av.getSequenceSetId()));
+ view.setId(av.getViewId());
view.setViewName(av.viewName);
view.setGatheredViews(av.gatherViewsHere);
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);
-
+ view.setShowConsensusHistogram(av.isShowConsensusHistogram());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
+ 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.featuresDisplayed != null)
{
jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings();
String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
Vector settingsAdded = new Vector();
+ Object gstyle = null;
+ GraduatedColor gcol = null;
for (int ro = 0; ro < renderOrder.length; ro++)
{
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
Setting setting = new Setting();
setting.setType(renderOrder[ro]);
- setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer()
- .getColour(renderOrder[ro]).getRGB());
+ 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.seqPanel.seqCanvas.getFeatureRenderer()
+ .getColour(renderOrder[ro]).getRGB());
+ }
setting.setDisplay(av.featuresDisplayed
.containsKey(renderOrder[ro]));
settingsAdded.addElement(renderOrder[ro]);
}
- //Make sure we save none displayed feature settings
+ // Make sure we save none displayed feature settings
Enumeration en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours
.keys();
while (en.hasMoreElements())
}
Group g = new Group();
g.setName(grp);
- g
- .setDisplay(((Boolean) ap.seqPanel.seqCanvas
- .getFeatureRenderer().featureGroups.get(grp))
- .booleanValue());
+ g.setDisplay(((Boolean) ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups
+ .get(grp)).booleanValue());
fs.addGroup(g);
groupsAdded.addElement(grp);
}
if (av.hasHiddenColumns)
{
- for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
+ {
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ }
+ else
{
- int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
- .elementAt(c);
- HiddenColumns hc = new HiddenColumns();
- hc.setStart(region[0]);
- hc.setEnd(region[1]);
- view.addHiddenColumns(hc);
+ 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);
+ }
}
}
object.setJalviewModelSequence(jms);
object.getVamsasModel().addSequenceSet(vamsasSet);
- if (jout!=null && fileName!=null)
+ if (jout != null && fileName != null)
{
- //We may not want to write the object to disk,
- //eg we can copy the alignViewport to a new view object
- //using save and then load
+ // We may not want to write the object to disk,
+ // eg we can copy the alignViewport to a new view object
+ // using save and then load
try
{
JarEntry entry = new JarEntry(fileName);
jout.putNextEntry(entry);
PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
- "UTF-8"));
- org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(pout);
+ "UTF-8"));
+ org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
+ pout);
marshaller.marshal(object);
pout.flush();
jout.closeEntry();
return object;
}
+ /**
+ * External mapping between jalview objects and objects yielding a valid and
+ * unique object ID string. This is null for normal Jalview project IO, but
+ * non-null when a jalview project is being read or written as part of a
+ * vamsas session.
+ */
+ IdentityHashMap jv2vobj = null;
+
+ /**
+ * Construct a unique ID for jvobj using either existing bindings or if none
+ * exist, the result of the hashcode call for the object.
+ *
+ * @param jvobj
+ * jalview data object
+ * @return unique ID for referring to jvobj
+ */
+ private String makeHashCode(Object jvobj, String altCode)
+ {
+ if (jv2vobj != null)
+ {
+ Object id = jv2vobj.get(jvobj);
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // check string ID mappings
+ if (jvids2vobj != null && jvobj instanceof String)
+ {
+ id = jvids2vobj.get(jvobj);
+ }
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // give up and warn that something has gone wrong
+ warn("Cannot find ID for object in external mapping : " + jvobj);
+ }
+ return altCode;
+ }
+
+ /**
+ * return local jalview object mapped to ID, if it exists
+ *
+ * @param idcode
+ * (may be null)
+ * @return null or object bound to idcode
+ */
+ private Object retrieveExistingObj(String idcode)
+ {
+ if (idcode != null && vobj2jv != null)
+ {
+ return vobj2jv.get(idcode);
+ }
+ return null;
+ }
+
+ /**
+ * binding from ID strings from external mapping table to jalview data model
+ * objects.
+ */
+ private Hashtable vobj2jv;
+
private Sequence createVamsasSequence(String id, SequenceI jds)
{
return createVamsasSequence(true, id, jds, null);
}
else
{
- vamsasSeq.setDsseqid(id); // so we can tell which sequences really are dataset sequences only
+ vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+ // dataset sequences only
dbrefs = jds.getDBRef();
}
if (dbrefs != null)
&& (parentseq != jmp.getTo() || parentseq
.getDatasetSequence() != jmp.getTo()))
{
- mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo())
- , jmp.getTo(), jds));
+ mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
+ jmp.getTo(), jds));
}
else
{
{
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);
}
/**
- * DOCUMENT ME!
- *
- * @param file DOCUMENT ME!
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
+
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = true;
+
+ /**
+ * Load a jalview project archive from a jar file
+ *
+ * @param file
+ * - HTTP URL or filename
*/
public AlignFrame LoadJalviewAlign(final String file)
{
- uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
jalview.gui.AlignFrame af = null;
- seqRefIds = new Hashtable();
- viewportsAdded = new Hashtable();
- frefedSequence = new Vector();
- Hashtable gatherToThisFrame = new Hashtable();
+ try
+ {
+ // 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.
- String errorMessage = null;
+ jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
+ af = LoadJalviewAlign(jprovider);
+ } catch (MalformedURLException e)
+ {
+ errorMessage = "Invalid URL format for '" + file + "'";
+ reportErrors();
+ }
+ return af;
+ }
- try
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final String file) throws MalformedURLException
+ {
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded = null;
+ frefedSequence = null;
+
+ if (file.startsWith("http://"))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
{
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
- URL url = null;
- if (file.startsWith("http://"))
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ if (_url != null)
+ {
+ return new JarInputStream(_url.openStream());
+ }
+ else
+ {
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ public String getFilename()
{
- url = new URL(file);
+ return file;
}
+ };
+ }
+
+ /**
+ * Recover jalview session from a jalview project archive. Caller may
+ * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
+ * themselves. Any null fields will be initialised with default values,
+ * non-null fields are left alone.
+ *
+ * @param jprovider
+ * @return
+ */
+ public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ {
+ errorMessage = null;
+ if (uniqueSetSuffix == null)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ if (viewportsAdded == null)
+ {
+ viewportsAdded = new Hashtable();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new Vector();
+ }
+ jalview.gui.AlignFrame af = null;
+ Hashtable gatherToThisFrame = new Hashtable();
+ final String file = jprovider.getFilename();
+ try
+ {
JarInputStream jin = null;
JarEntry jarentry = null;
int entryCount = 1;
do
{
- if (url != null)
- {
- jin = new JarInputStream(url.openStream());
- }
- else
- {
- jin = new JarInputStream(new FileInputStream(file));
- }
-
+ jin = jprovider.getJarInputStream();
for (int i = 0; i < entryCount; i++)
{
jarentry = jin.getNextJarEntry();
Unmarshaller unmar = new Unmarshaller(object);
unmar.setValidation(false);
object = (JalviewModel) unmar.unmarshal(in);
-
- af = LoadFromObject(object, file, true);
- if (af.viewport.gatherViewsHere)
+ if (true) // !skipViewport(object))
{
- gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ af = LoadFromObject(object, file, true, jprovider);
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
}
entryCount++;
}
else if (jarentry != null)
{
- //Some other file here.
+ // Some other file here.
entryCount++;
}
} while (jarentry != null);
{
System.err.println("Parsing as Jalview Version 2 file failed.");
ex.printStackTrace(System.err);
-
- //Is Version 1 Jar file?
- try {
- af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(file);
- } catch (Exception ex2) {
- System.err.println("Exception whilst loading as jalviewXMLV1:");
- ex2.printStackTrace();
- af = null;
+ if (attemptversion1parse)
+ {
+ // Is Version 1 Jar file?
+ try
+ {
+ af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
+ } catch (Exception ex2)
+ {
+ System.err.println("Exception whilst loading as jalviewXMLV1:");
+ ex2.printStackTrace();
+ af = null;
+ }
}
-
if (Desktop.instance != null)
{
Desktop.instance.stopLoading();
System.err.println("Exception whilst loading jalview XML file : "
+ ex + "\n");
+ } catch (OutOfMemoryError e)
+ {
+ // Don't use the OOM Window here
+ errorMessage = "Out of memory loading jalview XML file";
+ System.err.println("Out of memory whilst loading jalview XML file");
+ e.printStackTrace();
}
if (Desktop.instance != null)
{
Desktop.instance.gatherViews((AlignFrame) en.nextElement());
}
+ if (errorMessage != null)
+ {
+ reportErrors();
+ }
+ return af;
+ }
+
+ /**
+ * check errorMessage for a valid error message and raise an error box in the
+ * GUI or write the current errorMessage to stderr and then clear the error
+ * state.
+ */
+ protected void reportErrors()
+ {
+ reportErrors(false);
+ }
+ protected void reportErrors(final boolean saving)
+ {
if (errorMessage != null)
{
final String finalErrorMessage = errorMessage;
if (raiseGUI)
- {
+ {
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
public void run()
- {
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- finalErrorMessage, "Error loading Jalview file",
- JOptionPane.WARNING_MESSAGE);
- }
- });
- } else {
- System.err.println("Problem loading Jalview file: "+errorMessage);
- }
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error "
+ + (saving ? "saving" : "loading")
+ + " Jalview file", JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println("Problem loading Jalview file: " + errorMessage);
+ }
}
-
- return af;
+ errorMessage = null;
}
Hashtable alreadyLoadedPDB;
- String loadPDBFile(String file, String pdbId)
+ /**
+ * 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;
+
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
{
if (alreadyLoadedPDB == null)
alreadyLoadedPDB = new Hashtable();
try
{
- JarInputStream jin = null;
-
- if (file.startsWith("http://"))
- {
- jin = new JarInputStream(new URL(file).openStream());
- }
- else
- {
- jin = new JarInputStream(new FileInputStream(file));
- }
+ JarInputStream jin = jprovider.getJarInputStream();
+ /*
+ * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
+ * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
+ * FileInputStream(jprovider)); }
+ */
JarEntry entry = null;
do
{
entry = jin.getNextJarEntry();
- } while (!entry.getName().equals(pdbId));
+ } while (entry != null && !entry.getName().equals(pdbId));
+ if (entry != null)
+ {
+ BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+ File outFile = File.createTempFile("jalview_pdb", ".txt");
+ outFile.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
- BufferedReader in = new BufferedReader(new InputStreamReader(jin));
- File outFile = File.createTempFile("jalview_pdb", ".txt");
- outFile.deleteOnExit();
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
- String data;
+ while ((data = in.readLine()) != null)
+ {
+ out.println(data);
+ }
+ try
+ {
+ out.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ out.close();
- while ((data = in.readLine()) != null)
+ alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
+ return outFile.getAbsolutePath();
+ }
+ else
{
- out.println(data);
+ warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
}
- try { out.flush(); } catch (Exception foo) {};
- out.close();
-
- alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
- return outFile.getAbsolutePath();
-
} catch (Exception ex)
{
ex.printStackTrace();
return null;
}
+ /**
+ * Load alignment frame from jalview XML DOM object
+ *
+ * @param object
+ * DOM
+ * @param file
+ * filename source string
+ * @param loadTreesAndStructures
+ * when false only create Viewport
+ * @param jprovider
+ * data source provider
+ * @return alignment frame created from view stored in DOM
+ */
AlignFrame LoadFromObject(JalviewModel object, String file,
- boolean loadTreesAndStructures)
+ boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
{
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
Sequence[] vamsasSeq = vamsasSet.getSequence();
JalviewModelSequence jms = object.getJalviewModelSequence();
Viewport view = jms.getViewport(0);
-
- //////////////////////////////////
- //LOAD SEQUENCES
+ // ////////////////////////////////
+ // LOAD SEQUENCES
Vector hiddenSeqs = null;
jalview.datamodel.Sequence jseq;
boolean multipleView = false;
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
- int vi=0; // counter in vamsasSeq array
+ int vi = 0; // counter in vamsasSeq array
for (int i = 0; i < JSEQ.length; i++)
{
- String seqId = JSEQ[i].getId() + "";
+ String seqId = JSEQ[i].getId();
if (seqRefIds.get(seqId) != null)
{
jseq.setStart(JSEQ[i].getStart());
jseq.setEnd(JSEQ[i].getEnd());
jseq.setVamsasId(uniqueSetSuffix + seqId);
- seqRefIds.put(vamsasSeq[vi].getId()+"", jseq);
+ seqRefIds.put(vamsasSeq[vi].getId(), jseq);
tmpseqs.add(jseq);
vi++;
}
}
- ///
+ // /
// Create the alignment object from the sequence set
- /////////////////////////////////
+ // ///////////////////////////////
jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
.size()];
jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
orderedSeqs);
- /// Add the alignment properties
+ // / Add the alignment properties
for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
{
SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
al.setProperty(ssp.getKey(), ssp.getValue());
}
- ///
+ // /
// SequenceFeatures are added to the DatasetSequence,
// so we must create or recover the dataset before loading features
- /////////////////////////////////
+ // ///////////////////////////////
if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
{
// older jalview projects do not have a dataset id.
{
recoverDatasetFor(vamsasSet, al);
}
- /////////////////////////////////
+ // ///////////////////////////////
Hashtable pdbloaded = new Hashtable();
if (!multipleView)
{
+ // load sequence features, database references and any associated PDB
+ // structures for the alignment
for (int i = 0; i < vamsasSeq.length; i++)
{
if (JSEQ[i].getFeaturesCount() > 0)
{
if (!pdbloaded.containsKey(ids[p].getFile()))
{
- entry.setFile(loadPDBFile(file, ids[p].getId()));
+ entry.setFile(loadPDBFile(jprovider, ids[p].getId()));
}
else
{
}
}
}
- }
+ } // end !multipleview
- /////////////////////////////////
+ // ///////////////////////////////
// LOAD SEQUENCE MAPPINGS
+
if (vamsasSet.getAlcodonFrameCount() > 0)
{
+ // TODO Potentially this should only be done once for all views of an
+ // alignment
AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
for (int i = 0; i < alc.length; i++)
{
Alcodon[] alcods = alc[i].getAlcodon();
for (int p = 0; p < cf.codons.length; p++)
{
- 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();
+ 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
+ {
+ cf.codons[p] = null;
+ }
}
}
if (alc[i].getAlcodMapCount() > 0)
SequenceI dnaseq = (SequenceI) seqRefIds
.get(maps[m].getDnasq());
// Load Mapping
+ jalview.datamodel.Mapping mapping = null;
// attach to dna sequence reference.
+ if (maps[m].getMapping() != null)
+ {
+ mapping = addMapping(maps[m].getMapping());
+ }
if (dnaseq != null)
{
- if (maps[m].getMapping() != null)
- {
- jalview.datamodel.Mapping mapping = addMapping(maps[m]
- .getMapping());
- cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
- }
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(new Object[]
+ { maps[m].getDnasq(), cf, mapping });
}
}
}
}
- //////////////////////////////////
- //LOAD ANNOTATIONS
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
boolean hideQuality = true, hideConservation = true, hideConsensus = true;
+ /**
+ * store any annotations which forward reference a group's ID
+ */
+ Hashtable groupAnnotRefs = new Hashtable();
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;
hideConsensus = false;
continue;
}
-
+ // set visiblity for other annotation in this view
if (an[i].getId() != null
&& annotationIds.containsKey(an[i].getId()))
{
jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
.get(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();
continue;
}
-
+ // Construct new annotation from model.
AnnotationElement[] ae = an[i].getAnnotationElement();
jalview.datamodel.Annotation[] anot = null;
anot[ae[aa].getPosition()] = 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 structure annotation read from Stockholm files
- // this was added to try to ensure that
- //if (anot[ae[aa].getPosition()].secondaryStructure>' ')
- //{
- // anot[ae[aa].getPosition()].displayCharacter = "";
- //}
- anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]
- .getColour());
+ // JBPNote: Consider verifying dataflow for IO of secondary
+ // structure annotation read from Stockholm files
+ // this was added to try to ensure that
+ // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
+ // {
+ // anot[ae[aa].getPosition()].displayCharacter = "";
+ // }
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(
+ ae[aa].getColour());
}
}
jalview.datamodel.AlignmentAnnotation jaa = null;
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
}
-
+ // register new annotation
if (an[i].getId() != null)
{
annotationIds.put(an[i].getId(), jaa);
jaa.annotationId = an[i].getId();
}
-
+ // recover sequence association
if (an[i].getSequenceRef() != null)
{
if (al.findName(an[i].getSequenceRef()) != 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)
+ {
+ groupAnnotRefs.put(an[i].getGroupRef(), jaa);
+ }
+
if (an[i].hasScore())
{
jaa.setScore(an[i].getScore());
}
-
if (an[i].hasVisible())
jaa.visible = an[i].getVisible();
+ 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.
+ }
al.addAnnotation(jaa);
}
}
- /////////////////////////
- //LOAD GROUPS
+ // ///////////////////////
+ // LOAD GROUPS
+ // Create alignment markup and styles for this view
if (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
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.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].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);
}
+ if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
+ {
+ // re-instate unique group/annotation row reference
+ jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
+ .get(groups[i].getId());
+ if (jaa != null)
+ {
+ jaa.groupRef = sg;
+ }
+ }
al.addGroup(sg);
+
}
}
- /////////////////////////////////
+ // ///////////////////////////////
// LOAD VIEWPORT
- AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
+ // If we just load in the same jar file again, the sequenceSetId
+ // will be the same, and we end up with multiple references
+ // to the same sequenceSet. We must modify this id on load
+ // so that each load of the file gives a unique id
+ String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+ String viewId = (view.getId() == null ? null : view.getId()
+ + uniqueSetSuffix);
+ AlignFrame af = null;
+ AlignViewport av = null;
+ // now check to see if we really need to create a new viewport.
+ if (multipleView && viewportsAdded.size() == 0)
+ {
+ // We recovered an alignment for which a viewport already exists.
+ // TODO: fix up any settings necessary for overlaying stored state onto
+ // state recovered from another document. (may not be necessary).
+ // we may need a binding from a viewport in memory to one recovered from
+ // XML.
+ // and then recover its containing af to allow the settings to be applied.
+ // TODO: fix for vamsas demo
+ System.err
+ .println("About to recover a viewport for existing alignment: Sequence set ID is "
+ + uniqueSeqSetId);
+ Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
+ if (seqsetobj != null)
+ {
+ if (seqsetobj instanceof String)
+ {
+ uniqueSeqSetId = (String) seqsetobj;
+ System.err
+ .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ + uniqueSeqSetId);
+ }
+ else
+ {
+ System.err
+ .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
+ }
+
+ }
+ }
+ AlignmentPanel ap = null;
+ boolean isnewview = true;
+ if (viewId != null)
+ {
+ // Check to see if this alignment already has a view id == viewId
+ jalview.gui.AlignmentPanel views[] = Desktop
+ .getAlignmentPanels(uniqueSeqSetId);
+ if (views != null && views.length > 0)
+ {
+ for (int v = 0; v < views.length; v++)
+ {
+ if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+ {
+ // recover the existing alignpanel, alignframe, viewport
+ af = views[v].alignFrame;
+ av = views[v].av;
+ ap = views[v];
+ // TODO: could even skip resetting view settings if we don't want to
+ // change the local settings from other jalview processes
+ isnewview = false;
+ }
+ }
+ }
+ }
+
+ if (isnewview)
+ {
+ af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
+ hideQuality, hideConservation, jms, view, uniqueSeqSetId,
+ viewId);
+ av = af.viewport;
+ ap = af.alignPanel;
+ }
+ // LOAD TREES
+ // /////////////////////////////////////
+ if (loadTreesAndStructures && jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
+ {
+
+ Tree tree = jms.getTree(t);
+
+ 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());
+ 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.av = av; // af.viewport; // TODO: verify 'associate with all
+ // views'
+ // works still
+ tp.treeCanvas.av = av; // af.viewport;
+ tp.treeCanvas.ap = ap; // af.alignPanel;
+
+ }
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
+
+ tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow_actionPerformed(null);
+
+ if (tree.getFontName() != null)
+ {
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
+ .getFontStyle(), tree.getFontSize()));
+ }
+ else
+ {
+ tp.setTreeFont(new java.awt.Font(view.getFontName(), view
+ .getFontStyle(), tree.getFontSize()));
+ }
+
+ tp.showPlaceholders(tree.getMarkUnlinked());
+ tp.showBootstrap(tree.getShowBootstrap());
+ tp.showDistances(tree.getShowDistances());
+
+ tp.treeCanvas.threshold = tree.getThreshold();
+
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ // //LOAD STRUCTURES
+ if (loadTreesAndStructures)
+ {
+ // run through all PDB ids on the alignment, and collect mappings between
+ // jmol view ids and all sequences referring to it
+ Hashtable<String, Object[]> jmolViewIds = new Hashtable();
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ if (JSEQ[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ for (int s = 0; s < ids[p].getStructureStateCount(); s++)
+ {
+ // 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();
+
+ // 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 = (jalview.datamodel.SequenceI) seqRefIds
+ .get(JSEQ[i].getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ + "," + height;
+ }
+ if (!jmolViewIds.containsKey(sviewid))
+ {
+ jmolViewIds.put(sviewid, new Object[]
+ { new int[]
+ { x, y, width, height }, "",
+ new Hashtable<String, Object[]>() });
+ }
+ // TODO: assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}} from hash
+ Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
+ if (((String) jmoldat[1]).length() < ids[p]
+ .getStructureState(s).getContent().length())
+ {
+ {
+ jmoldat[1] = ids[p].getStructureState(s).getContent();
+ }
+ }
+ Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
+ .get(ids[p].getFile());
+ if (seqstrmaps == null)
+ {
+ ((Hashtable) jmoldat[2]).put(
+ new File(ids[p].getFile()).toString(),
+ 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
+ }
+ }
+ }
+ }
+ }
+ {
+
+ // Instantiate the associated Jmol views
+ for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
+ {
+ String sviewid = entry.getKey();
+ Object[] svattrib = entry.getValue();
+ int[] geom = (int[]) svattrib[0];
+ String state = (String) svattrib[1];
+ Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
+
+ int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
+ // 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 to see if we've already created this Jmol view
+ AppJmol comp = null;
+ JInternalFrame[] frames = null;
+ do
+ {
+ try
+ {
+ frames = Desktop.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ frames = null;
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception f)
+ {
+ }
+ ;
+ }
+ } 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++)
+ {
+ if (frames[f] instanceof AppJmol)
+ {
+ if (sviewid != null
+ && ((AppJmol) frames[f]).getViewId().equals(sviewid))
+ {
+ // 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)
+ {
+ comp = (AppJmol) frames[f];
+ }
+ }
+ }
+
+ 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();
+ }
+ 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)
+ .toString());
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement((SequenceI[]) ((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.
+ }
+ 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 (String 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((SequenceI[]) ((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"))
+ {
+ if (val.trim().equals("true"))
+ {
+ val = "1";
+ }
+ else
+ {
+ val = "0";
+ }
+ 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 = (String[]) pdbfilenames
+ .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
+ .toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = (SequenceI[][]) 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()
+ {
+ public void run()
+ {
+ AppJmol sview=null;
+ try {
+ sview=new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc,
+
+ rect, vid);
+ }
+ catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id "+id,(OutOfMemoryError) ex.getCause());
+ if (sview!=null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.",ex);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
+
+ }
+ 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 (String 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 = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]);
+ StructureSelectionManager.getStructureSelectionManager()
+ .setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+ ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
+ }
+ }
+ }
+ }
+ }
+ // and finally return.
+ return af;
+ }
+
+ AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
+ Alignment al, boolean hideConsensus, boolean hideQuality,
+ boolean hideConservation, JalviewModelSequence jms,
+ Viewport view, String uniqueSeqSetId, String viewId)
+ {
+ AlignFrame af = null;
+ af = new AlignFrame(al, view.getWidth(), view.getHeight(),
+ uniqueSeqSetId, viewId);
af.setFileName(file, "Jalview");
new java.awt.Color(JSEQ[i].getColour()));
}
- //If we just load in the same jar file again, the sequenceSetId
- //will be the same, and we end up with multiple references
- //to the same sequenceSet. We must modify this id on load
- //so that each load of the file gives a unique id
- String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
-
af.viewport.gatherViewsHere = view.getGatheredViews();
if (view.getSequenceSetId() != null)
af.viewport.sequenceSetID = uniqueSeqSetId;
if (av != null)
{
-
+ // propagate shared settings to this new view
af.viewport.historyList = av.historyList;
af.viewport.redoList = av.redoList;
}
{
viewportsAdded.put(uniqueSeqSetId, af.viewport);
}
-
+ // TODO: check if this method can be called repeatedly without
+ // side-effects if alignpanel already registered.
PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
}
+ // apply Hidden regions to view.
if (hiddenSeqs != null)
{
for (int s = 0; s < JSEQ.length; s++)
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)
{
}
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.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.setStartRes(view.getStartRes());
af.viewport.setStartSeq(view.getStartSeq());
ColourSchemeI cs = null;
-
+ // apply colourschemes
if (view.getBgColour() != null)
{
if (view.getBgColour().startsWith("ucs"))
}
else if (view.getBgColour().startsWith("Annotation"))
{
- //int find annotation
- for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ // int find annotation
+ if (af.viewport.alignment.getAlignmentAnnotation() != null)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label
- .equals(view.getAnnotationColours().getAnnotation()))
+ for (int i = 0; i < af.viewport.alignment
+ .getAlignmentAnnotation().length; i++)
{
- if (af.viewport.alignment.getAlignmentAnnotation()[i]
- .getThreshold() == null)
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label
+ .equals(view.getAnnotationColours().getAnnotation()))
{
- af.viewport.alignment.getAlignmentAnnotation()[i]
- .setThreshold(new jalview.datamodel.GraphLine(view
- .getAnnotationColours().getThreshold(),
- "Threshold", java.awt.Color.black)
-
- );
- }
+ 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)
- 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++)
+ 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
{
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
- .getGroups().elementAt(g);
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al, view
+ .getAnnotationColours().getColourScheme()),
+ view.getAnnotationColours().getAboveThreshold());
+ }
- if (sg.cs == null)
+ // Also use these settings for all the groups
+ if (al.getGroups() != null)
+ {
+ for (int g = 0; g < al.getGroups().size(); g++)
{
- continue;
- }
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) al
+ .getGroups().elementAt(g);
- /* 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());
- }
+ 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;
}
- break;
}
-
}
}
else
{
af.viewport.showSequenceFeatures = true;
}
+ if (view.hasCentreColumnLabels())
+ {
+ af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
+ }
+ if (view.hasIgnoreGapsinConsensus())
+ {
+ af.viewport.ignoreGapsInConsensusCalculation = view
+ .getIgnoreGapsinConsensus();
+ }
+ 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.showSequenceLogo = view.getShowSequenceLogo();
+ }
+ else
+ {
+ af.viewport.showSequenceLogo = false;
+ }
+ 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();
for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
-
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
- setting.getType(), new java.awt.Color(setting.getColour()));
+ if (setting.hasMincolour())
+ {
+ 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());
+ }
+ 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.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), gc);
+ }
+ else
+ {
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(),
+ new java.awt.Color(setting.getColour()));
+ }
renderOrder[fs] = setting.getType();
if (setting.hasOrder())
af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(
for (int c = 0; c < view.getHiddenColumnsCount(); c++)
{
af.viewport.hideColumns(view.getHiddenColumns(c).getStart(), view
- .getHiddenColumns(c).getEnd() //+1
+ .getHiddenColumns(c).getEnd() // +1
);
}
}
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());
+ af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+ return af;
+ }
- Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(), view
- .getHeight());
-
- //LOAD TREES
- ///////////////////////////////////////
- if (loadTreesAndStructures && jms.getTreeCount() > 0)
- {
- try
- {
- for (int t = 0; t < jms.getTreeCount(); t++)
- {
-
- Tree tree = jms.getTree(t);
-
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(tree
- .getNewick()), tree.getTitle(), tree.getWidth(), tree
- .getHeight(), tree.getXpos(), tree.getYpos());
-
- tp.fitToWindow.setState(tree.getFitToWindow());
- tp.fitToWindow_actionPerformed(null);
-
- if (tree.getFontName() != null)
- {
- tp.setTreeFont(new java.awt.Font(tree.getFontName(), tree
- .getFontStyle(), tree.getFontSize()));
- }
- else
- {
- tp.setTreeFont(new java.awt.Font(view.getFontName(), view
- .getFontStyle(), tree.getFontSize()));
- }
-
- tp.showPlaceholders(tree.getMarkUnlinked());
- tp.showBootstrap(tree.getShowBootstrap());
- tp.showDistances(tree.getShowDistances());
-
- tp.treeCanvas.threshold = tree.getThreshold();
+ Hashtable skipList = null;
- if (tree.getCurrentTree())
- {
- af.viewport.setCurrentTree(tp.getTree());
- }
- }
+ /**
+ * TODO remove this method
+ *
+ * @param view
+ * @return AlignFrame bound to sequenceSetId from view, if one exists. private
+ * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
+ * throw new Error("Implementation Error. No skipList defined for this
+ * Jalview2XML instance."); } return (AlignFrame)
+ * skipList.get(view.getSequenceSetId()); }
+ */
- } catch (Exception ex)
+ /**
+ * Check if the Jalview view contained in object should be skipped or not.
+ *
+ * @param object
+ * @return true if view's sequenceSetId is a key in skipList
+ */
+ private boolean skipViewport(JalviewModel object)
+ {
+ if (skipList == null)
+ {
+ return false;
+ }
+ String id;
+ if (skipList.containsKey(id = object.getJalviewModelSequence()
+ .getViewport()[0].getSequenceSetId()))
+ {
+ if (Cache.log != null && Cache.log.isDebugEnabled())
{
- ex.printStackTrace();
+ Cache.log.debug("Skipping seuqence set id " + id);
}
+ return true;
}
+ return false;
+ }
- ////LOAD STRUCTURES
- if (loadTreesAndStructures)
+ public void AddToSkipList(AlignFrame af)
+ {
+ if (skipList == null)
{
- for (int i = 0; i < JSEQ.length; i++)
- {
- if (JSEQ[i].getPdbidsCount() > 0)
- {
- Pdbids[] ids = JSEQ[i].getPdbids();
- for (int p = 0; p < ids.length; p++)
- {
- for (int s = 0; s < ids[p].getStructureStateCount(); s++)
- {
- jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
-
- jpdb.setFile(loadPDBFile(ids[p].getFile(), 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();
-
- java.awt.Component comp = null;
-
- JInternalFrame[] frames = null;
- do {
- try {
- frames = Desktop.desktop.getAllFrames();
- }
- catch (ArrayIndexOutOfBoundsException e)
- {
- // occasional No such child exceptions are thrown here...
- frames = null;
- try {
- Thread.sleep(10);
- } catch (Exception f) {};
- }
- } while (frames==null);
- for (int f = 0; f < frames.length; f++)
- {
- if (frames[f] instanceof AppJmol)
- {
- if (frames[f].getX() == x && frames[f].getY() == y
- && frames[f].getHeight() == height
- && frames[f].getWidth() == width)
- {
- comp = frames[f];
- break;
- }
- }
- }
-
- Desktop.desktop.getComponentAt(x, y);
-
- String pdbFile = loadPDBFile(file, ids[p].getId());
-
- jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
- { (jalview.datamodel.SequenceI) seqRefIds.get(JSEQ[i].getId()
- + "") };
-
- if (comp == null)
- {
- String state = ids[p].getStructureState(s).getContent();
-
- StringBuffer newFileLoc = new StringBuffer(state.substring(
- 0, state.indexOf("\"", state.indexOf("load")) + 1));
-
- newFileLoc.append(jpdb.getFile());
- newFileLoc.append(state.substring(state.indexOf("\"", state
- .indexOf("load \"") + 6)));
-
- new AppJmol(pdbFile, ids[p].getId(), seq, af.alignPanel,
- newFileLoc.toString(), new java.awt.Rectangle(x, y,
- width, height));
-
- }
- else if (comp != null)
- {
- StructureSelectionManager.getStructureSelectionManager()
- .setMapping(seq, null, pdbFile,
- jalview.io.AppletFormatAdapter.FILE);
-
- ((AppJmol) comp).addSequence(seq);
- }
- }
- }
- }
- }
+ skipList = new Hashtable();
}
+ skipList.put(af.getViewport().getSequenceSetId(), af);
+ }
- return af;
+ public void clearSkipList()
+ {
+ if (skipList != null)
+ {
+ skipList.clear();
+ skipList = null;
+ }
}
private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
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.
al.setDataset(ds);
}
}
-
/**
*
- * @param vamsasSeq sequence definition to create/merge dataset sequence for
- * @param ds dataset alignment
- * @param dseqs vector to add new dataset sequence to
+ * @param vamsasSeq
+ * sequence definition to create/merge dataset sequence for
+ * @param ds
+ * dataset alignment
+ * @param dseqs
+ * vector to add new dataset sequence to
*/
- private void ensureJalviewDatasetSequence(Sequence vamsasSeq, AlignmentI ds, Vector dseqs)
+ private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
+ AlignmentI ds, Vector dseqs)
{
- jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds.get(vamsasSeq.getId());
+ // JBP TODO: Check this is called for AlCodonFrames to support recovery of
+ // xRef Codon Maps
+ jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
+ .get(vamsasSeq.getId());
jalview.datamodel.SequenceI dsq = null;
- if (sq!=null && sq.getDatasetSequence()!=null)
+ if (sq != null && sq.getDatasetSequence() != null)
{
dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
}
-
+
String sqid = vamsasSeq.getDsseqid();
- if (dsq==null)
+ if (dsq == null)
{
// need to create or add a new dataset sequence reference to this sequence
if (sqid != null)
seqRefIds.put(sqid, dsq);
if (ds == null)
{
- if (dseqs!=null)
+ if (dseqs != null)
{
dseqs.addElement(dsq);
}
{
ds.addSequence(dsq);
}
- } else {
- if (sq!=dsq)
- { // make this dataset sequence sq's dataset sequence
+ }
+ else
+ {
+ if (sq != dsq)
+ { // make this dataset sequence sq's dataset sequence
sq.setDatasetSequence(dsq);
}
}
}
// TODO: refactor this as a merge dataset sequence function
- // now check that sq (the dataset sequence) sequence really is the union of all references to it
- //boolean pre = sq.getStart() < dsq.getStart();
- //boolean post = sq.getEnd() > dsq.getEnd();
- //if (pre || post)
- if (sq!=dsq)
+ // now check that sq (the dataset sequence) sequence really is the union of
+ // all references to it
+ // boolean pre = sq.getStart() < dsq.getStart();
+ // boolean post = sq.getEnd() > dsq.getEnd();
+ // if (pre || post)
+ if (sq != dsq)
{
StringBuffer sb = new StringBuffer();
String newres = jalview.analysis.AlignSeq.extractGaps(
jalview.util.Comparison.GapChars, sq.getSequenceAsString());
- if (!newres.equalsIgnoreCase(dsq.getSequenceAsString()) && newres.length()>dsq.getLength())
+ if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
+ && newres.length() > dsq.getLength())
{
// Update with the longer sequence.
synchronized (dsq)
{
- /*if (pre)
- {
- sb.insert(0, newres
- .substring(0, dsq.getStart() - sq.getStart()));
- dsq.setStart(sq.getStart());
- }
- if (post)
- {
- sb.append(newres.substring(newres.length() - sq.getEnd()
- - dsq.getEnd()));
- dsq.setEnd(sq.getEnd());
- }
- */
- dsq.setSequence(sb.toString());
+ /*
+ * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
+ * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
+ * sb.append(newres.substring(newres.length() - sq.getEnd() -
+ * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
+ */
+ dsq.setSequence(sb.toString());
}
- //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"); // ("
- // + (pre ? "prepended" : "") + " "
- //+ (post ? "appended" : ""));
+ // 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"); // ("
+ // + (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)
+ {
+ warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ }
+ String datasetId = makeHashCode(dataset, null);
+ if (datasetId == null)
+ {
+ // make a new datasetId and record it
+ if (dataset2Ids == null)
+ {
+ dataset2Ids = new IdentityHashMap();
+ }
+ else
+ {
+ datasetId = (String) dataset2Ids.get(dataset);
+ }
+ if (datasetId == null)
+ {
+ 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)
{
- if (seqRefIds.containsKey(mc.getDseqFor()))
+ String dsfor = "" + mc.getDseqFor();
+ if (seqRefIds.containsKey(dsfor))
{
/**
* recover from hash
*/
- jmap.setTo((SequenceI) seqRefIds.get(mc.getDseqFor()));
+ jmap.setTo((SequenceI) seqRefIds.get(dsfor));
}
else
{
frefedSequence.add(new Object[]
- { mc.getDseqFor(), jmap });
+ { dsfor, jmap });
}
}
else
* local sequence definition
*/
Sequence ms = mc.getSequence();
- jalview.datamodel.Sequence djs=null;
+ jalview.datamodel.Sequence djs = null;
String sqid = ms.getDsseqid();
- if (sqid!=null && sqid.length()>0)
+ if (sqid != null && sqid.length() > 0)
{
/*
* recover dataset sequence
*/
djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
- } else {
- System.err.println("Warning - making up dataset sequence id for DbRef sequence map reference");
- sqid = ((Object)ms).toString(); // make up a new hascode for undefined dataset sequence hash (unlikely to happen)
}
-
- if (djs==null) {
+ else
+ {
+ System.err
+ .println("Warning - making up dataset sequence id for DbRef sequence map reference");
+ sqid = ((Object) ms).toString(); // make up a new hascode for
+ // undefined dataset sequence hash
+ // (unlikely to happen)
+ }
+
+ if (djs == null)
+ {
/**
* 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);
jmap.setTo(djs);
seqRefIds.put(sqid, djs);
-
+
}
jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
addDBRefs(djs, ms);
-
+
}
}
return (jmap);
public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
boolean keepSeqRefs)
{
- jalview.schemabinding.version2.JalviewModel jm =
- SaveState(ap, null, null);
+ initSeqRefs();
+ 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
+ }
+ if (this.frefedSequence == null)
+ {
+ frefedSequence = new Vector();
}
viewportsAdded = new Hashtable();
- AlignFrame af = LoadFromObject(jm, null, false);
+ 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.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]; } } }
+ */
return af.alignPanel;
}
- /* (non-Javadoc)
+
+ /**
+ * flag indicating if hashtables should be cleared on finalization TODO this
+ * flag may not be necessary
+ */
+ private boolean _cleartables = true;
+
+ private Hashtable jvids2vobj;
+
+ /*
+ * (non-Javadoc)
+ *
* @see java.lang.Object#finalize()
*/
protected void finalize() throws Throwable
{
// really make sure we have no buried refs left.
- clearSeqRefs();
+ if (_cleartables)
+ {
+ clearSeqRefs();
+ }
this.seqRefIds = null;
this.seqsToIds = null;
super.finalize();
}
-
+
+ private void warn(String msg)
+ {
+ warn(msg, null);
+ }
+
+ private void warn(String msg, Exception e)
+ {
+ if (Cache.log != null)
+ {
+ if (e != null)
+ {
+ Cache.log.warn(msg, e);
+ }
+ else
+ {
+ Cache.log.warn(msg);
+ }
+ }
+ else
+ {
+ System.err.println("Warning: " + msg);
+ if (e != null)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ private void debug(String string)
+ {
+ debug(string, null);
+ }
+
+ private void debug(String msg, Exception e)
+ {
+ if (Cache.log != null)
+ {
+ if (e != null)
+ {
+ Cache.log.debug(msg, e);
+ }
+ else
+ {
+ Cache.log.debug(msg);
+ }
+ }
+ else
+ {
+ System.err.println("Warning: " + msg);
+ if (e != null)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * set the object to ID mapping tables used to write/recover objects and XML
+ * ID strings for the jalview project. If external tables are provided then
+ * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
+ * object goes out of scope. - also populates the datasetIds hashtable with
+ * alignment objects containing dataset sequences
+ *
+ * @param vobj2jv
+ * Map from ID strings to jalview datamodel
+ * @param jv2vobj
+ * Map from jalview datamodel to ID strings
+ *
+ *
+ */
+ public void setObjectMappingTables(Hashtable vobj2jv,
+ IdentityHashMap jv2vobj)
+ {
+ this.jv2vobj = jv2vobj;
+ this.vobj2jv = vobj2jv;
+ Iterator ds = jv2vobj.keySet().iterator();
+ String id;
+ while (ds.hasNext())
+ {
+ Object jvobj = ds.next();
+ id = jv2vobj.get(jvobj).toString();
+ if (jvobj instanceof jalview.datamodel.Alignment)
+ {
+ if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
+ {
+ addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
+ }
+ }
+ else if (jvobj instanceof jalview.datamodel.Sequence)
+ {
+ // register sequence object so the XML parser can recover it.
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap();
+ }
+ seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
+ seqsToIds.put(jvobj, id);
+ }
+ else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
+ {
+ if (annotationIds == null)
+ {
+ annotationIds = new Hashtable();
+ }
+ String anid;
+ annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
+ jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
+ if (jvann.annotationId == null)
+ {
+ jvann.annotationId = anid;
+ }
+ if (!jvann.annotationId.equals(anid))
+ {
+ // TODO verify that this is the correct behaviour
+ this.warn("Overriding Annotation ID for " + anid
+ + " from different id : " + jvann.annotationId);
+ jvann.annotationId = anid;
+ }
+ }
+ else if (jvobj instanceof String)
+ {
+ if (jvids2vobj == null)
+ {
+ jvids2vobj = new Hashtable();
+ jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
+ }
+ }
+ else
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
+ }
+
+ /**
+ * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
+ * objects created from the project archive. If string is null (default for
+ * construction) then suffix will be set automatically.
+ *
+ * @param string
+ */
+ public void setUniqueSetSuffix(String string)
+ {
+ uniqueSetSuffix = string;
+
+ }
+
+ /**
+ * uses skipList2 as the skipList for skipping views on sequence sets
+ * associated with keys in the skipList
+ *
+ * @param skipList2
+ */
+ public void setSkipList(Hashtable skipList2)
+ {
+ skipList = skipList2;
+ }
+
}
git://source.jalview.org / jalview.git / blobdiff