/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* 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 .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
import jalview.analysis.Conservation;
import jalview.api.FeatureColourI;
import jalview.binding.Annotation;
import jalview.binding.AnnotationElement;
import jalview.binding.Features;
import jalview.binding.JGroup;
import jalview.binding.JSeq;
import jalview.binding.JalviewModel;
import jalview.binding.JalviewModelSequence;
import jalview.binding.Pdbids;
import jalview.binding.Sequence;
import jalview.binding.SequenceSet;
import jalview.binding.Setting;
import jalview.binding.Tree;
import jalview.binding.UserColours;
import jalview.binding.Viewport;
import jalview.datamodel.PDBEntry;
import jalview.datamodel.SequenceFeature;
import jalview.io.FileFormat;
import jalview.schemes.ColourSchemeI;
import jalview.schemes.ColourSchemeProperty;
import jalview.schemes.FeatureColour;
import jalview.structure.StructureSelectionManager;
import jalview.util.MessageManager;
import jalview.util.jarInputStreamProvider;
import jalview.viewmodel.seqfeatures.FeatureRendererSettings;
import java.io.InputStreamReader;
import java.io.Reader;
import java.net.UnknownHostException;
import java.util.Hashtable;
import java.util.Vector;
import java.util.jar.JarEntry;
import java.util.jar.JarInputStream;
/**
* DOCUMENT ME!
*
* @author $author$
* @version $Revision$
*/
public class Jalview2XML_V1
{
boolean raiseGUI = true;
public Jalview2XML_V1()
{
};
public Jalview2XML_V1(boolean raiseGUI)
{
this.raiseGUI = raiseGUI;
};
jalview.schemes.UserColourScheme GetUserColourScheme(
JalviewModelSequence jms, String id)
{
UserColours[] uc = jms.getUserColours();
UserColours colours = null;
for (int i = 0; i < uc.length; i++)
{
if (uc[i].getId().equals(id))
{
colours = uc[i];
break;
}
}
int csize = colours.getUserColourScheme().getColourCount();
java.awt.Color[] newColours = new java.awt.Color[csize];
for (int i = 0; i < csize; i++)
{
newColours[i] = new java.awt.Color(Integer.parseInt(
colours.getUserColourScheme().getColour(i).getRGB(), 16));
}
return new jalview.schemes.UserColourScheme(newColours);
}
/**
* DOCUMENT ME!
*
* @param file
* DOCUMENT ME!
*/
public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
{
final String file = jprovider.getFilename();
jalview.gui.AlignFrame af = null;
try
{
JarInputStream jin = null;
JarEntry jarentry = null;
int entryCount = 1;
do
{
jin = jprovider.getJarInputStream();
for (int i = 0; i < entryCount; i++)
{
jarentry = jin.getNextJarEntry();
}
if (jarentry != null)
{
entryCount++;
if (jarentry.getName().endsWith(".xml"))
{
Reader in = new InputStreamReader(jin, "UTF-8");
JalviewModel object = new JalviewModel();
object = object.unmarshal(in);
af = LoadFromObject(object, file);
}
}
jin.close();
} while (jarentry != null);
} catch (final UnknownHostException ex)
{
ex.printStackTrace();
if (raiseGUI)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
System.err.println(
"Couldn't locate Jalview XML file : " + ex + "\n");
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage("label.couldnt_locate",
new String[]
{ file }),
MessageManager.getString("label.url_not_found"),
JvOptionPane.WARNING_MESSAGE);
}
});
}
;
} catch (Exception ex)
{
System.err.println("Exception whilst loading jalview XML file : ");
ex.printStackTrace();
if (raiseGUI)
{
javax.swing.SwingUtilities.invokeLater(new Runnable()
{
@Override
public void run()
{
JvOptionPane.showInternalMessageDialog(Desktop.desktop,
MessageManager.formatMessage(
"label.error_loading_file_params", new String[]
{ file }),
MessageManager
.getString("label.error_loading_jalview_file"),
JvOptionPane.WARNING_MESSAGE);
}
});
}
}
return af;
}
AlignFrame LoadFromObject(JalviewModel object, String file)
{
Vector seqids = new Vector();
SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
Sequence[] vamsasSeq = vamsasSet.getSequence();
JalviewModelSequence jms = object.getJalviewModelSequence();
// ////////////////////////////////
// LOAD SEQUENCES
jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];
JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
for (int i = 0; i < vamsasSeq.length; i++)
{
jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
vamsasSeq[i].getSequence());
jseqs[i].setStart(JSEQ[i].getStart());
jseqs[i].setEnd(JSEQ[i].getEnd());
seqids.add(jseqs[i]);
}
// /SequenceFeatures are added to the DatasetSequence,
// so we must create the dataset before loading features
// ///////////////////////////////
jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);
al.setDataset(null);
// ///////////////////////////////
for (int i = 0; i < vamsasSeq.length; i++)
{
if (JSEQ[i].getFeaturesCount() > 0)
{
Features[] features = JSEQ[i].getFeatures();
for (int f = 0; f < features.length; f++)
{
SequenceFeature sf = new SequenceFeature(features[f].getType(),
features[f].getDescription(), features[f].getBegin(),
features[f].getEnd(), null);
sf.setStatus(features[f].getStatus());
al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
}
}
if (JSEQ[i].getPdbidsCount() > 0)
{
Pdbids[] ids = JSEQ[i].getPdbids();
for (int p = 0; p < ids.length; p++)
{
jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();
entry.setId(ids[p].getId());
if (ids[p].getType() != null)
{
if (ids[p].getType().equalsIgnoreCase("PDB"))
{
entry.setType(PDBEntry.Type.PDB);
}
else
{
entry.setType(PDBEntry.Type.FILE);
}
}
al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
StructureSelectionManager
.getStructureSelectionManager(Desktop.instance)
.registerPDBEntry(entry);
}
}
}
// ///////////////////////////////
// ////////////////////////////////
// LOAD ANNOTATIONS
if (vamsasSet.getAnnotation() != null)
{
Annotation[] an = vamsasSet.getAnnotation();
for (int i = 0; i < an.length; i++)
{
AnnotationElement[] ae = an[i].getAnnotationElement();
jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al
.getWidth()];
for (int aa = 0; aa < ae.length; aa++)
{
anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
ae[aa].getSecondaryStructure().charAt(0),
ae[aa].getValue());
}
jalview.datamodel.AlignmentAnnotation jaa = null;
if (an[i].getGraph())
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot, 0, 0,
jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);
}
else
{
jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
an[i].getDescription(), anot);
}
al.addAnnotation(jaa);
}
}
// ///////////////////////////////
// LOAD VIEWPORT
Viewport[] views = jms.getViewport();
Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER
AlignFrame af = new AlignFrame(al, view.getWidth(), view.getHeight());
af.setFileName(file, FileFormat.Jalview);
for (int i = 0; i < JSEQ.length; i++)
{
af.viewport.setSequenceColour(
af.viewport.getAlignment().getSequenceAt(i),
new java.awt.Color(JSEQ[i].getColour()));
}
// af.changeColour() );
// ///////////////////////
// LOAD GROUPS
if (jms.getJGroupCount() > 0)
{
JGroup[] groups = jms.getJGroup();
for (int i = 0; i < groups.length; i++)
{
ColourSchemeI cs = null;
if (groups[i].getColour() != null)
{
if (groups[i].getColour().startsWith("ucs"))
{
cs = GetUserColourScheme(jms, groups[i].getColour());
}
else
{
cs = ColourSchemeProperty.getColourScheme(al,
groups[i].getColour());
}
}
int pidThreshold = groups[i].getPidThreshold();
Vector seqs = new Vector();
int[] ids = groups[i].getSeq();
for (int s = 0; s < ids.length; s++)
{
seqs.addElement(seqids.elementAt(ids[s]));
}
jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(
seqs, groups[i].getName(), cs, groups[i].getDisplayBoxes(),
groups[i].getDisplayText(), groups[i].getColourText(),
groups[i].getStart(), groups[i].getEnd());
sg.getGroupColourScheme().setThreshold(pidThreshold, true);
sg.setOutlineColour(
new java.awt.Color(groups[i].getOutlineColour()));
if (groups[i].getConsThreshold() != 0)
{
Conservation c = new Conservation("All", sg.getSequences(null), 0,
sg.getWidth() - 1);
c.calculate();
c.verdict(false, 25);
sg.cs.setConservation(c);
}
al.addGroup(sg);
}
}
af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
view.getHeight());
af.viewport.getRanges().setStartRes(view.getStartRes());
// startSeq set in af.alignPanel.updateLayout below
af.viewport.setShowAnnotation(view.getShowAnnotation());
af.viewport.setAbovePIDThreshold(view.getPidSelected());
af.viewport.setColourText(view.getShowColourText());
af.viewport.setConservationSelected(view.getConservationSelected());
af.viewport.setShowJVSuffix(view.getShowFullId());
af.viewport.setFont(new java.awt.Font(view.getFontName(),
view.getFontStyle(), view.getFontSize()), true);
af.viewport.setRenderGaps(view.getRenderGaps());
af.viewport.setWrapAlignment(view.getWrapAlignment());
af.viewport.setShowAnnotation(view.isShowAnnotation());
af.viewport.setShowBoxes(view.getShowBoxes());
af.viewport.setShowText(view.getShowText());
ColourSchemeI cs = null;
if (view.getBgColour() != null)
{
if (view.getBgColour().startsWith("ucs"))
{
cs = GetUserColourScheme(jms, view.getBgColour());
}
else
{
cs = ColourSchemeProperty.getColourScheme(al, view.getBgColour());
}
// if (cs != null)
// {
// cs.setThreshold(view.getPidThreshold(), true);
// cs.setConsensus(af.viewport.getSequenceConsensusHash());
// }
}
af.viewport.getResidueShading().setThreshold(view.getPidThreshold(),
true);
af.viewport.getResidueShading()
.setConsensus(af.viewport.getSequenceConsensusHash());
af.viewport.setColourAppliesToAllGroups(false);
af.alignPanel.updateLayout();
af.changeColour(cs);
if (view.getConservationSelected() && cs != null)
{
af.viewport.getResidueShading()
.setConservationInc(view.getConsThreshold());
}
af.viewport.setColourAppliesToAllGroups(true);
af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures());
if (jms.getFeatureSettings() != null)
{
Hashtable featuresDisplayed = new Hashtable<>();
Hashtable featureColours = new Hashtable<>();
String[] renderOrder = new String[jms.getFeatureSettings()
.getSettingCount()];
for (int fs = 0; fs < jms.getFeatureSettings()
.getSettingCount(); fs++)
{
Setting setting = jms.getFeatureSettings().getSetting(fs);
featureColours.put(setting.getType(),
new FeatureColour(new java.awt.Color(setting.getColour())));
renderOrder[fs] = setting.getType();
if (setting.getDisplay())
{
featuresDisplayed.put(setting.getType(),
new Integer(setting.getColour()));
}
}
FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder,
new Hashtable(), featureColours, 1.0f, null,
null);
af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer()
.transferSettings(frs);
}
af.setMenusFromViewport(af.viewport);
Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
view.getHeight());
// LOAD TREES
// /////////////////////////////////////
if (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();
if (tree.getCurrentTree())
{
af.viewport.setCurrentTree(tp.getTree());
}
}
} catch (Exception ex)
{
ex.printStackTrace();
}
}
return af;
}
}