-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.schemes.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import java.io.*;\r
-\r
-import java.net.*;\r
-\r
-import java.util.*;\r
-\r
-import java.util.jar.*;\r
-\r
-import javax.swing.*;\r
-\r
-import org.exolab.castor.xml.*;\r
-\r
-import jalview.binding.*;\r
-\r
-\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Jalview2XML_V1\r
-{\r
- jalview.schemes.UserColourScheme GetUserColourScheme(\r
- JalviewModelSequence jms, String id)\r
- {\r
- UserColours[] uc = jms.getUserColours();\r
- UserColours colours = null;\r
-\r
- for (int i = 0; i < uc.length; i++)\r
- {\r
- if (uc[i].getId().equals(id))\r
- {\r
- colours = uc[i];\r
-\r
- break;\r
- }\r
- }\r
-\r
- int csize = colours.getUserColourScheme().getColourCount();\r
- java.awt.Color[] newColours = new java.awt.Color[csize];\r
-\r
- for (int i = 0; i < csize; i++)\r
- {\r
- newColours[i] = new java.awt.Color(Integer.parseInt(\r
- colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
- }\r
-\r
- return new jalview.schemes.UserColourScheme(newColours);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- */\r
- public AlignFrame LoadJalviewAlign(String file)\r
- {\r
-\r
- jalview.gui.AlignFrame af = null;\r
-\r
- try\r
- {\r
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
- URL url = null;\r
-\r
- if (file.startsWith("http://"))\r
- {\r
- url = new URL(file);\r
- }\r
-\r
- JarInputStream jin = null;\r
- JarEntry jarentry = null;\r
- int entryCount = 1;\r
-\r
- do\r
- {\r
- if (url != null)\r
- {\r
- jin = new JarInputStream(url.openStream());\r
- }\r
- else\r
- {\r
- jin = new JarInputStream(new FileInputStream(file));\r
- }\r
-\r
- for (int i = 0; i < entryCount; i++)\r
- {\r
- jarentry = jin.getNextJarEntry();\r
- }\r
-\r
- class NoDescIDResolver implements IDResolver\r
- {\r
- public Object resolve(String idref)\r
- {\r
- System.out.println(idref+" used");\r
- return null;\r
- }\r
- }\r
-\r
-\r
- if (jarentry != null)\r
- {\r
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
- JalviewModel object = new JalviewModel();\r
-\r
- object = (JalviewModel) object.unmarshal(in);\r
-\r
- af = LoadFromObject(object);\r
- entryCount++;\r
- }\r
- }\r
- while (jarentry != null);\r
- }\r
- catch(java.net.UnknownHostException ex)\r
- {\r
- ex.printStackTrace();\r
- System.err.println("Couldn't locate Jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + file,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- System.err.println("Exception whilst loading jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Error loading " + file,\r
- "Error loading Jalview file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
-\r
- return af;\r
- }\r
-\r
- AlignFrame LoadFromObject(JalviewModel object)\r
- {\r
- Vector seqids = new Vector();\r
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
- Sequence[] vamsasSeq = vamsasSet.getSequence();\r
-\r
- JalviewModelSequence jms = object.getJalviewModelSequence();\r
-\r
- //////////////////////////////////\r
- //LOAD SEQUENCES\r
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
- for (int i = 0; i < vamsasSeq.length; i++)\r
- {\r
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
- vamsasSeq[i].getSequence());\r
- jseqs[i].setStart(JSEQ[i].getStart());\r
- jseqs[i].setEnd(JSEQ[i].getEnd());\r
- jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
- seqids.add(jseqs[i]);\r
- }\r
-\r
- ///SequenceFeatures are added to the DatasetSequence,\r
- // so we must create the dataset before loading features\r
- /////////////////////////////////\r
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
- al.setDataset(null);\r
- /////////////////////////////////\r
-\r
- for (int i = 0; i < vamsasSeq.length; i++)\r
- {\r
- if (JSEQ[i].getFeaturesCount() > 0)\r
- {\r
- Features[] features = JSEQ[i].getFeatures();\r
- for (int f = 0; f < features.length; f++)\r
- {\r
- jalview.datamodel.SequenceFeature sf\r
- = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
- features[f].getDescription(), features[f].getStatus(),\r
- features[f].getBegin(), features[f].getEnd(),\r
- null);\r
-\r
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
- }\r
- }\r
- if (JSEQ[i].getPdbidsCount() > 0)\r
- {\r
- Pdbids[] ids = JSEQ[i].getPdbids();\r
- for (int p = 0; p < ids.length; p++)\r
- {\r
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
- entry.setId(ids[p].getId());\r
- entry.setType(ids[p].getType());\r
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
- }\r
-\r
- }\r
- }\r
-\r
- /////////////////////////////////\r
- //////////////////////////////////\r
- //LOAD ANNOTATIONS\r
- if (vamsasSet.getAnnotation() != null)\r
- {\r
- Annotation[] an = vamsasSet.getAnnotation();\r
-\r
- for (int i = 0; i < an.length; i++)\r
- {\r
- AnnotationElement[] ae = an[i].getAnnotationElement();\r
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
-\r
- for (int aa = 0; aa < ae.length; aa++)\r
- {\r
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
- ae[aa].getDescription(),\r
- ae[aa].getSecondaryStructure().charAt(0),\r
- ae[aa].getValue());\r
- }\r
-\r
- jalview.datamodel.AlignmentAnnotation jaa = null;\r
-\r
- if (an[i].getGraph())\r
- {\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot, 0, 0,\r
- jalview.datamodel.AlignmentAnnotation.BAR_GRAPH);\r
- }\r
- else\r
- {\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot);\r
- }\r
-\r
- al.addAnnotation(jaa);\r
- }\r
- }\r
-\r
-\r
- /////////////////////////////////\r
- // LOAD VIEWPORT\r
- Viewport[] views = jms.getViewport();\r
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
-\r
- AlignFrame af = new AlignFrame(al);\r
-\r
-\r
- // af.changeColour() );\r
- /////////////////////////\r
- //LOAD GROUPS\r
- if (jms.getJGroupCount() > 0)\r
- {\r
- JGroup[] groups = jms.getJGroup();\r
-\r
- for (int i = 0; i < groups.length; i++)\r
- {\r
- ColourSchemeI cs = null;\r
-\r
- if (groups[i].getColour() != null)\r
- {\r
- if (groups[i].getColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, groups[i].getColour());\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al,\r
- groups[i].getColour());\r
- }\r
-\r
- if(cs!=null)\r
- cs.setThreshold(groups[i].getPidThreshold(), true);\r
-\r
- }\r
-\r
- Vector seqs = new Vector();\r
- int[] ids = groups[i].getSeq();\r
-\r
- for (int s = 0; s < ids.length; s++)\r
- {\r
- seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
- ids[s]));\r
- }\r
-\r
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
- groups[i].getDisplayText(), groups[i].getColourText(),\r
- groups[i].getStart(), groups[i].getEnd());\r
-\r
- sg.setOutlineColour(new java.awt.Color(\r
- groups[i].getOutlineColour()));\r
-\r
- if (groups[i].getConsThreshold() != 0)\r
- {\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
- ResidueProperties.propHash, 3, sg.getSequences(false), 0,\r
- sg.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, 25);\r
- sg.cs.setConservation(c);\r
- }\r
-\r
- al.addGroup(sg);\r
- }\r
- }\r
-\r
-\r
-\r
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
- view.getHeight());\r
- af.viewport.setStartRes(view.getStartRes());\r
- af.viewport.setStartSeq(view.getStartSeq());\r
- af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.viewport.showConservation = view.getShowConservation();\r
- af.viewport.showQuality = view.getShowQuality();\r
- af.viewport.showIdentity = view.getShowIdentity();\r
- af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
- af.abovePIDThreshold.setSelected(view.getPidSelected());\r
- af.viewport.setColourText(view.getShowColourText());\r
- af.colourTextMenuItem.setSelected(view.getShowColourText());\r
- af.viewport.setConservationSelected(view.getConservationSelected());\r
- af.conservationMenuItem.setSelected(view.getConservationSelected());\r
-\r
- af.viewport.setShowJVSuffix(view.getShowFullId());\r
- af.seqLimits.setSelected(view.getShowFullId());\r
-\r
- af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(), view.getFontSize()));\r
- af.alignPanel.fontChanged();\r
-\r
- af.viewport.setRenderGaps(view.getRenderGaps());\r
- af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
-\r
- af.viewport.setWrapAlignment(view.getWrapAlignment());\r
- af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
-\r
-\r
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
-\r
- af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
- af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
-\r
-\r
- af.viewport.setShowBoxes(view.getShowBoxes());\r
- af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
- af.viewport.setShowText(view.getShowText());\r
- af.viewTextMenuItem.setSelected(view.getShowText());\r
-\r
- ColourSchemeI cs = null;\r
-\r
- if (view.getBgColour() != null)\r
- {\r
- if (view.getBgColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, view.getBgColour());\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
- }\r
-\r
- if(cs!=null)\r
- {\r
- cs.setThreshold(view.getPidThreshold(), true);\r
- cs.setConsensus(af.viewport.vconsensus);\r
- }\r
- }\r
-\r
- af.setColourSelected(view.getBgColour());\r
- af.viewport.setGlobalColourScheme(cs);\r
- af.viewport.setColourAppliesToAllGroups(false);\r
- af.changeColour(cs);\r
- if (view.getConservationSelected() && cs!=null)\r
- {\r
- cs.setConservationInc(view.getConsThreshold());\r
- }\r
-\r
- af.viewport.setColourAppliesToAllGroups(true);\r
-\r
- if (view.getShowSequenceFeatures())\r
- {\r
- af.viewport.showSequenceFeatures = true;\r
- af.showSeqFeatures.setSelected(true);\r
- }\r
-\r
- if(jms.getFeatureSettings()!=null)\r
- {\r
- af.viewport.featuresDisplayed = new Hashtable();\r
- String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
- for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
- {\r
- Setting setting = jms.getFeatureSettings().getSetting(fs);\r
-\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
- new java.awt.Color(setting.getColour()));\r
-\r
- renderOrder[fs] = setting.getType();\r
-\r
- if(setting.getDisplay())\r
- af.viewport.featuresDisplayed.put(\r
- setting.getType(), new Integer(setting.getColour()));\r
- }\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
- }\r
-\r
-\r
- Desktop.addInternalFrame(af, view.getTitle(),\r
- view.getWidth(), view.getHeight());\r
-\r
- //LOAD TREES\r
- ///////////////////////////////////////\r
- if (jms.getTreeCount() > 0)\r
- {\r
- try\r
- {\r
- for (int t = 0; t < jms.getTreeCount(); t++)\r
- {\r
-\r
- Tree tree = jms.getTree(t);\r
-\r
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
- tree.getNewick()), tree.getTitle(),\r
- tree.getWidth(), tree.getHeight(),\r
- tree.getXpos(), tree.getYpos());\r
-\r
- tp.fitToWindow.setState(tree.getFitToWindow());\r
- tp.fitToWindow_actionPerformed(null);\r
-\r
- if(tree.getFontName()!=null)\r
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
- tree.getFontStyle(),\r
- tree.getFontSize()));\r
- else\r
- tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(),\r
- tree.getFontSize()));\r
-\r
- tp.showPlaceholders(tree.getMarkUnlinked());\r
- tp.showBootstrap(tree.getShowBootstrap());\r
- tp.showDistances(tree.getShowDistances());\r
-\r
- tp.treeCanvas.threshold = tree.getThreshold();\r
-\r
- if (tree.getCurrentTree())\r
- af.viewport.setCurrentTree(tp.getTree());\r
- }\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- }\r
-\r
- return af;\r
- }\r
-}\r
-\r
+/*
+ * 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.getTreeCanvas().setThreshold(tree.getThreshold());
+
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
+
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+
+ return af;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff