+++ /dev/null
-/*
- * 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 <http://www.gnu.org/licenses/>.
- * The Jalview Authors are detailed in the 'AUTHORS' file.
- */
-package jalview.gui;
-
-import jalview.analysis.Conservation;
-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.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 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);
- 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;
- }
-}
git://source.jalview.org / jalview.git / blobdiff