X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML_V1.java;h=9548839f83b633286676dc8f609fef3a1462ab5c;hb=7e82e1fed011077e5cd4cc40ac8ad3519d7c47a8;hp=e264b689c0d45787ddfe4e97b24675748ce51d48;hpb=d053a3c980cf4318b9a19a255f9fc870e74de989;p=jalview.git
diff --git a/src/jalview/gui/Jalview2XML_V1.java b/src/jalview/gui/Jalview2XML_V1.java
index e264b68..9548839 100755
--- a/src/jalview/gui/Jalview2XML_V1.java
+++ b/src/jalview/gui/Jalview2XML_V1.java
@@ -1,468 +1,513 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 .
- */
-package jalview.gui;
-
-import java.io.*;
-import java.net.*;
-import java.util.*;
-import java.util.jar.*;
-
-import javax.swing.*;
-
-import org.exolab.castor.xml.*;
-import jalview.binding.*;
-import jalview.schemes.*;
-import jalview.util.jarInputStreamProvider;
-
-/**
- * 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();
- }
-
- class NoDescIDResolver implements IDResolver
- {
- public Object resolve(String idref)
- {
- System.out.println(idref + " used");
- return null;
- }
- }
-
- if (jarentry != null)
- {
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");
- JalviewModel object = new JalviewModel();
-
- object = (JalviewModel) object.unmarshal(in);
-
- af = LoadFromObject(object, file);
- entryCount++;
- }
- } while (jarentry != null);
- } catch (final java.net.UnknownHostException ex)
- {
- ex.printStackTrace();
- if (raiseGUI)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
-
- System.err.println("Couldn't locate Jalview XML file : " + ex
- + "\n");
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Couldn't locate " + file, "URL not found",
- JOptionPane.WARNING_MESSAGE);
- }
- });
- }
- ;
- } catch (Exception ex)
- {
- System.err.println("Exception whilst loading jalview XML file : ");
- ex.printStackTrace();
- if (raiseGUI)
- {
- javax.swing.SwingUtilities.invokeLater(new Runnable()
- {
- public void run()
- {
-
- JOptionPane.showInternalMessageDialog(Desktop.desktop,
- "Error loading " + file, "Error loading Jalview file",
- JOptionPane.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++)
- {
- jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(
- features[f].getType(), features[f].getDescription(),
- features[f].getStatus(), features[f].getBegin(),
- features[f].getEnd(), null);
-
- 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());
- entry.setType(ids[p].getType());
- al.getSequenceAt(i).getDatasetSequence().addPDBId(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, "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.getColour(al, groups[i].getColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(groups[i].getPidThreshold(), true);
- }
-
- }
-
- Vector seqs = new Vector();
- int[] ids = groups[i].getSeq();
-
- for (int s = 0; s < ids.length; s++)
- {
- seqs.addElement((jalview.datamodel.SequenceI) 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.setOutlineColour(new java.awt.Color(groups[i].getOutlineColour()));
-
- if (groups[i].getConsThreshold() != 0)
- {
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(
- "All", ResidueProperties.propHash, 3,
- 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.setStartRes(view.getStartRes());
- af.viewport.setStartSeq(view.getStartSeq());
- 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()));
- af.alignPanel.fontChanged();
-
- af.viewport.setRenderGaps(view.getRenderGaps());
- af.viewport.setWrapAlignment(view.getWrapAlignment());
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());
- af.viewport.setShowAnnotation(view.getShowAnnotation());
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
- 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.getColour(al, view.getBgColour());
- }
-
- if (cs != null)
- {
- cs.setThreshold(view.getPidThreshold(), true);
- cs.setConsensus(af.viewport.getSequenceConsensusHash());
- }
- }
-
- af.viewport.setGlobalColourScheme(cs);
- af.viewport.setColourAppliesToAllGroups(false);
- af.changeColour(cs);
- if (view.getConservationSelected() && cs != null)
- {
- cs.setConservationInc(view.getConsThreshold());
- }
-
- af.viewport.setColourAppliesToAllGroups(true);
- af.viewport.showSequenceFeatures = view.getShowSequenceFeatures();
-
- if (jms.getFeatureSettings() != null)
- {
- af.viewport.featuresDisplayed = new Hashtable();
- String[] renderOrder = new String[jms.getFeatureSettings()
- .getSettingCount()];
- 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()));
-
- renderOrder[fs] = setting.getType();
-
- if (setting.getDisplay())
- {
- af.viewport.featuresDisplayed.put(setting.getType(), new Integer(
- setting.getColour()));
- }
- }
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
- }
-
- 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;
- }
-}
+/*
+ * 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.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.getTreeCanvas().setThreshold(tree.getThreshold());
+
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+
+ return af;
+ }
+}