X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=f0551e89fa6f4a7f7ed9701b036d470be54aeffa;hb=6951479b7dc56bd022ce2c370b7f88b5571004fd;hp=c06e8058af844c5ca21751c8ec223d16224d0881;hpb=beee04ddbd33c3d9c847719e67ddadaf1707cbbc;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index c06e805..f0551e8 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -1,947 +1,1931 @@ -/* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2005 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 - */ -package jalview.gui; - -import jalview.io.*; - -import jalview.schemes.*; - -import java.io.*; - -import java.net.*; - -import java.util.*; - -import java.util.jar.*; - -import javax.swing.*; - -import jalview.binding.*; - - -/** - * DOCUMENT ME! - * - * @author $author$ - * @version $Revision$ - */ -public class Jalview2XML -{ - // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE - public static void SaveState(File statefile) - { - long creation = System.currentTimeMillis(); - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - if (frames == null) - { - return; - } - - try - { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); - - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); - - Vector shortNames = new Vector(); - - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) - { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; - - String shortName = af.getTitle(); - - if (shortName.indexOf(File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - File.separatorChar) + 1); - } - - int count = 1; - - while (shortNames.contains(shortName)) - { - if (shortName.endsWith("_" + (count - 1))) - { - shortName = shortName.substring(0, - shortName.lastIndexOf("_")); - } - - shortName = shortName.concat("_" + count); - count++; - } - - shortNames.addElement(shortName); - - if (!shortName.endsWith(".xml")) - { - shortName = shortName + ".xml"; - } - - SaveState(af, creation, shortName, jout, out); - } - } - - out.close(); - jout.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public static void SaveAlignment(AlignFrame af, String jarFile, - String fileName) - { - try - { - FileOutputStream fos = new FileOutputStream(jarFile); - JarOutputStream jout = new JarOutputStream(fos); - - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); - - SaveState(af, System.currentTimeMillis(), fileName, jout, out); - out.close(); - jout.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - /** - * DOCUMENT ME! - * - * @param af DOCUMENT ME! - * @param timeStamp DOCUMENT ME! - * @param fileName DOCUMENT ME! - * @param jout DOCUMENT ME! - * @param out DOCUMENT ME! - */ - public static void SaveState(AlignFrame af, long timeStamp, - String fileName, JarOutputStream jout, PrintWriter out) - { - Vector seqids = new Vector(); - Vector userColours = new Vector(); - - AlignViewport av = af.viewport; - - JalviewModel object = new JalviewModel(); - object.setVamsasModel(new jalview.binding.VamsasModel()); - - object.setCreationDate(new java.util.Date(timeStamp)); - object.setVersion(jalview.bin.Cache.getProperty("VERSION")); - - jalview.datamodel.AlignmentI jal = af.viewport.alignment; - - SequenceSet vamsasSet = new SequenceSet(); - Sequence vamsasSeq; - JalviewModelSequence jms = new JalviewModelSequence(); - - vamsasSet.setGapChar(jal.getGapCharacter() + ""); - - JSeq jseq; - - //SAVE SEQUENCES - int id = 0; - - for (int i = 0; i < jal.getHeight(); i++) - { - seqids.add(jal.getSequenceAt(i)); - - vamsasSeq = new Sequence(); - vamsasSeq.setId(id + ""); - vamsasSeq.setName(jal.getSequenceAt(i).getName()); - vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); - - jseq = new JSeq(); - jseq.setStart(jal.getSequenceAt(i).getStart()); - jseq.setEnd(jal.getSequenceAt(i).getEnd()); - - jseq.setColour(jal.getSequenceAt(i).getColor().getRGB()); - - jseq.setId(id); - - if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null) - { - Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements(); - while(en.hasMoreElements()) - { - Features features = new Features(); - jalview.datamodel.SequenceFeature sf - = (jalview.datamodel.SequenceFeature)en.nextElement(); - - features.setBegin(sf.getBegin()); - features.setEnd(sf.getEnd()); - features.setDescription(sf.getDescription()); - features.setStatus(sf.getStatus()); - features.setType(sf.getType()); - jseq.addFeatures(features); - } - } - - if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null) - { - Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements(); - while(en.hasMoreElements()) - { - Pdbids pdb = new Pdbids(); - jalview.datamodel.PDBEntry entry - = (jalview.datamodel.PDBEntry)en.nextElement(); - - pdb.setId(entry.getId()); - pdb.setType(entry.getType()); - - if(entry.getProperty()!=null) - { - PdbentryItem item = new PdbentryItem(); - Hashtable properties = entry.getProperty(); - Enumeration en2 = properties.keys(); - while(en2.hasMoreElements()) - { - Property prop = new Property(); - String key = en2.nextElement().toString(); - prop.setName(key); - prop.setValue( properties.get(key).toString() ); - item.addProperty(prop); - } - pdb.addPdbentryItem(item); - } - - jseq.addPdbids(pdb); - } - } - - jms.addJSeq(jseq); - vamsasSet.addSequence(vamsasSeq); - id++; - } - - //SAVE TREES - /////////////////////////////////// - if (af.viewport.currentTree != null) - { - // FIND ANY ASSOCIATED TREES - // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT - if (Desktop.desktop != null) - { - JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - - for (int t = 0; t < frames.length; t++) - { - if (frames[t] instanceof TreePanel) - { - TreePanel tp = (TreePanel) frames[t]; - - if (tp.treeCanvas.av.alignment == jal) - { - Tree tree = new Tree(); - tree.setTitle(tp.getTitle()); - tree.setCurrentTree( (af.viewport.currentTree == tp.getTree())); - tree.setNewick(tp.getTree().toString()); - tree.setThreshold(tp.treeCanvas.threshold); - - tree.setFitToWindow(tp.fitToWindow.getState()); - tree.setFontName(tp.getTreeFont().getName()); - tree.setFontSize(tp.getTreeFont().getSize()); - tree.setFontStyle(tp.getTreeFont().getStyle()); - tree.setMarkUnlinked(tp.placeholdersMenu.getState()); - - tree.setShowBootstrap(tp.bootstrapMenu.getState()); - tree.setShowDistances(tp.distanceMenu.getState()); - - tree.setHeight(tp.getHeight()); - tree.setWidth(tp.getWidth()); - tree.setXpos(tp.getX()); - tree.setYpos(tp.getY()); - - jms.addTree(tree); - } - } - } - } - } - - //SAVE ANNOTATIONS - if (jal.getAlignmentAnnotation() != null) - { - jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); - - for (int i = 0; i < aa.length; i++) - { - if (aa[i].label.equals("Quality") || - aa[i].label.equals("Conservation") || - aa[i].label.equals("Consensus")) - { - continue; - } - - Annotation an = new Annotation(); - an.setDescription(aa[i].description); - an.setGraph(aa[i].isGraph); - an.setLabel(aa[i].label); - - AnnotationElement ae; - - for (int a = 0; a < aa[i].annotations.length; a++) - { - if ((aa[i] == null) || (aa[i].annotations[a] == null)) - { - continue; - } - - ae = new AnnotationElement(); - ae.setDescription(aa[i].annotations[a].description); - ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); - ae.setValue(aa[i].annotations[a].value); - ae.setPosition(a); - ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + - ""); - an.addAnnotationElement(ae); - } - - vamsasSet.addAnnotation(an); - } - } - - //SAVE GROUPS - if (jal.getGroups() != null) - { - JGroup[] groups = new JGroup[jal.getGroups().size()]; - - for (int i = 0; i < groups.length; i++) - { - groups[i] = new JGroup(); - - jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups() - .elementAt(i); - groups[i].setStart(sg.getStartRes()); - groups[i].setEnd(sg.getEndRes()); - groups[i].setName(sg.getName()); - if(sg.cs!=null) - { - if (sg.cs.conservationApplied()) - { - groups[i].setConsThreshold(sg.cs.getConservationInc()); - - if (sg.cs instanceof jalview.schemes.UserColourScheme) - { - groups[i].setColour(SetUserColourScheme(sg.cs, - userColours, - jms)); - } - else - { - groups[i].setColour(ColourSchemeProperty.getColourName(sg. - cs)); - } - } - else if (sg.cs instanceof jalview.schemes.UserColourScheme) - { - groups[i].setColour(SetUserColourScheme(sg.cs, userColours, - jms)); - } - else - { - groups[i].setColour(ColourSchemeProperty.getColourName( - sg.cs)); - } - - groups[i].setPidThreshold(sg.cs.getThreshold()); - } - - groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); - groups[i].setDisplayBoxes(sg.getDisplayBoxes()); - groups[i].setDisplayText(sg.getDisplayText()); - groups[i].setColourText(sg.getColourText()); - - for (int s = 0; s < sg.getSize(); s++) - { - jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s); - int index = seqids.indexOf(seq); - groups[i].addSeq(index); - } - } - - jms.setJGroup(groups); - } - - - ///////////SAVE VIEWPORT - Viewport view = new Viewport(); - view.setTitle(af.getTitle()); - view.setXpos(af.getX()); - view.setYpos(af.getY()); - view.setWidth(af.getWidth()); - view.setHeight(af.getHeight()); - view.setStartRes(av.startRes); - view.setStartSeq(av.startSeq); - - if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) - { - view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), - userColours, jms)); - } - else - { - view.setBgColour(ColourSchemeProperty.getColourName( - av.getGlobalColourScheme())); - } - - ColourSchemeI cs = av.getGlobalColourScheme(); - - if(cs!=null) - { - if (cs.conservationApplied()) - { - view.setConsThreshold(cs.getConservationInc()); - if (cs instanceof jalview.schemes.UserColourScheme) - view.setBgColour(SetUserColourScheme(cs, userColours, jms)); - } - - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold(cs.getThreshold()); - } - } - - view.setConservationSelected(av.getConservationSelected()); - view.setPidSelected(av.getAbovePIDThreshold()); - view.setFontName(av.font.getName()); - view.setFontSize(av.font.getSize()); - view.setFontStyle(av.font.getStyle()); - view.setRenderGaps(av.renderGaps); - view.setShowAnnotation(av.getShowAnnotation()); - view.setShowBoxes(av.getShowBoxes()); - view.setShowColourText(av.getColourText()); - view.setShowConservation(av.showConservation); - view.setShowFullId(av.getShowJVSuffix()); - view.setShowIdentity(av.showIdentity); - view.setShowQuality(av.showQuality); - view.setShowSequenceFeatures(av.showSequenceFeatures); - view.setShowText(av.getShowText()); - view.setWrapAlignment(av.getWrapAlignment()); - - if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null) - { - jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings(); - - Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys(); - while (e.hasMoreElements()) - { - String type = e.nextElement().toString(); - Setting setting = new Setting(); - setting.setType(type); - setting.setColour( - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB() - ); - setting.setDisplay( - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type) - ); - - fs.addSetting(setting); - - } - jms.setFeatureSettings(fs); - - } - - jms.addViewport(view); - - - object.setJalviewModelSequence(jms); - object.getVamsasModel().addSequenceSet(vamsasSet); - - try - { - if (!fileName.endsWith(".xml")) - { - fileName = fileName + ".xml"; - } - - JarEntry entry = new JarEntry(fileName); - jout.putNextEntry(entry); - - object.marshal(out); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } - - static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, - Vector userColours, JalviewModelSequence jms) - { - String id = null; - jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; - - if (!userColours.contains(ucs)) - { - userColours.add(ucs); - - java.awt.Color[] colours = ucs.getColours(); - jalview.binding.UserColours uc = new jalview.binding.UserColours(); - jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme(); - - for (int i = 0; i < colours.length; i++) - { - jalview.binding.Colour col = new jalview.binding.Colour(); - col.setRGB(jalview.util.Format.getHexString(colours[i])); - jbucs.addColour(col); - } - - id = "ucs" + userColours.indexOf(ucs); - uc.setId(id); - uc.setUserColourScheme(jbucs); - jms.addUserColours(uc); - } - - return id; - } - - static 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 static AlignFrame LoadJalviewAlign(String file) - { - JalviewModel object = new JalviewModel(); - jalview.gui.AlignFrame af = null; - - try - { - //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING - URL url = null; - - if (file.startsWith("http://")) - { - url = new URL(file); - } - - 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)); - } - - for (int i = 0; i < entryCount; i++) - { - jarentry = jin.getNextJarEntry(); - } - - if (jarentry != null) - { - InputStreamReader in = new InputStreamReader(jin, "UTF-8"); - object = (JalviewModel) object.unmarshal(in); - af = LoadFromObject(object); - entryCount++; - } - } - while (jarentry != null); - } - catch(java.net.UnknownHostException ex) - { - ex.printStackTrace(); - 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) - { - ex.printStackTrace(); - System.err.println("Exception whilst loading jalview XML file : " + - ex + "\n"); - JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Error loading " + file, - "Error loading Jalview file", - JOptionPane.WARNING_MESSAGE); - - } - - return af; - } - - static AlignFrame LoadFromObject(JalviewModel object) - { - 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()); - jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour())); - 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++) - { - //features[f].getBegin() - jalview.datamodel.SequenceFeature sf - = new jalview.datamodel.SequenceFeature(features[f].getType(), - features[f].getDescription(), features[f].getStatus(), - features[f].getBegin(), features[f].getEnd()); - 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, 1); - } - 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); - - - // 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()); - } - - 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.sequences, 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.showConservation = view.getShowConservation(); - af.viewport.showQuality = view.getShowQuality(); - af.viewport.showIdentity = view.getShowIdentity(); - af.viewport.setAbovePIDThreshold(view.getPidSelected()); - af.abovePIDThreshold.setSelected(view.getPidSelected()); - af.viewport.setColourText(view.getShowColourText()); - af.colourTextMenuItem.setSelected(view.getShowColourText()); - af.viewport.setConservationSelected(view.getConservationSelected()); - af.conservationMenuItem.setSelected(view.getConservationSelected()); - - af.viewport.setShowJVSuffix(view.getShowFullId()); - af.seqLimits.setSelected(view.getShowFullId()); - - af.viewport.setFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), view.getFontSize())); - af.alignPanel.fontChanged(); - - af.viewport.setRenderGaps(view.getRenderGaps()); - af.renderGapsMenuItem.setSelected(view.getRenderGaps()); - - af.viewport.setWrapAlignment(view.getWrapAlignment()); - af.wrapMenuItem.setSelected(view.getWrapAlignment()); - - if (view.getWrapAlignment()) - { - af.alignPanel.setWrapAlignment(view.getWrapAlignment()); - } - else - { - af.annotationPanelMenuItem.setState(view.getShowAnnotation()); - af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); - } - - af.viewport.setShowBoxes(view.getShowBoxes()); - af.viewBoxesMenuItem.setSelected(view.getShowBoxes()); - af.viewport.setShowText(view.getShowText()); - af.viewTextMenuItem.setSelected(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.vconsensus); - } - } - - af.setColourSelected(view.getBgColour()); - af.viewport.setGlobalColourScheme(cs); - af.viewport.setColourAppliesToAllGroups(false); - af.changeColour(cs); - if (view.getConservationSelected() && cs!=null) - { - cs.setConservationInc(view.getConsThreshold()); - } - - af.viewport.setColourAppliesToAllGroups(true); - - if (view.getShowSequenceFeatures()) - { - af.featureSettings.setEnabled(true); - af.viewport.showSequenceFeatures = true; - af.sequenceFeatures.setSelected(true); - } - - if(jms.getFeatureSettings()!=null) - { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector(); - // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null) - // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings(); - for(int fs=0; fs 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 + * 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 + */ +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.schemabinding.version2.*; +import jalview.schemes.*; +import jalview.structure.StructureSelectionManager; + +/** + * DOCUMENT ME! + * + * @author $author$ + * @version $Revision$ + */ +public class Jalview2XML +{ + + Hashtable seqRefIds; + + /** + * This maintains a list of viewports, the key being the + * seqSetId. Important to set historyItem and redoList + * for multiple views + */ + Hashtable viewportsAdded; + + Hashtable annotationIds = new Hashtable(); + + String uniqueSetSuffix = ""; + /** + * List of pdbfiles added to Jar + */ + Vector pdbfiles = null; + + // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE + public void SaveState(File statefile) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + + if (frames == null) + { + return; + } + + try + { + FileOutputStream fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); + + //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS + //////////////////////////////////////////////////// + PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, + "UTF-8")); + + Vector shortNames = new Vector(); + + //REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) + { + AlignFrame af = (AlignFrame) frames[i]; + + String shortName = af.getTitle(); + + if (shortName.indexOf(File.separatorChar) > -1) + { + shortName = shortName.substring(shortName.lastIndexOf( + File.separatorChar) + 1); + } + + int count = 1; + + while (shortNames.contains(shortName)) + { + if (shortName.endsWith("_" + (count - 1))) + { + shortName = shortName.substring(0, + shortName.lastIndexOf("_")); + } + + shortName = shortName.concat("_" + count); + count++; + } + + shortNames.addElement(shortName); + + if (!shortName.endsWith(".xml")) + { + shortName = shortName + ".xml"; + } + + int ap, apSize = af.alignPanels.size(); + for (ap = 0; ap < apSize; ap++) + { + AlignmentPanel apanel = (AlignmentPanel) af.alignPanels. + elementAt(ap); + + SaveState(apanel, + apSize == 1 ? shortName : ap + shortName, + jout, out); + } + } + } + + out.close(); + jout.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW + public boolean SaveAlignment(AlignFrame af, String jarFile, + String fileName) + { + try + { + int ap, apSize = af.alignPanels.size(); + FileOutputStream fos = new FileOutputStream(jarFile); + JarOutputStream jout = new JarOutputStream(fos); + PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, + "UTF-8")); + for (ap = 0; ap < apSize; ap++) + { + AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap); + + SaveState(apanel, + apSize == 1 ? fileName : fileName + ap, + jout, out); + } + + out.close(); + jout.close(); + return true; + } + catch (Exception ex) + { + ex.printStackTrace(); + return false; + } + } + + /** + * DOCUMENT ME! + * + * @param af DOCUMENT ME! + * @param timeStamp DOCUMENT ME! + * @param fileName DOCUMENT ME! + * @param jout DOCUMENT ME! + * @param out DOCUMENT ME! + */ + public JalviewModel SaveState(AlignmentPanel ap, + String fileName, + JarOutputStream jout, + PrintWriter out) + { + if (seqRefIds == null) + { + seqRefIds = new Hashtable(); + } + + Vector userColours = new Vector(); + + AlignViewport av = ap.av; + + JalviewModel object = new JalviewModel(); + object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); + + object.setCreationDate(new java.util.Date(System.currentTimeMillis())); + object.setVersion(jalview.bin.Cache.getProperty("VERSION")); + + jalview.datamodel.AlignmentI jal = av.alignment; + + if (av.hasHiddenRows) + { + jal = jal.getHiddenSequences().getFullAlignment(); + } + + SequenceSet vamsasSet = new SequenceSet(); + Sequence vamsasSeq; + JalviewModelSequence jms = new JalviewModelSequence(); + + vamsasSet.setGapChar(jal.getGapCharacter() + ""); + + JSeq jseq; + + //SAVE SEQUENCES + int id = 0; + jalview.datamodel.SequenceI jds; + for (int i = 0; i < jal.getHeight(); i++) + { + jds = jal.getSequenceAt(i); + id = jds.hashCode(); + + if (seqRefIds.get(id + "") != null) + { + + } + else + { + vamsasSeq = new Sequence(); + vamsasSeq.setId(id + ""); + vamsasSeq.setName(jds.getName()); + vamsasSeq.setSequence(jds.getSequenceAsString()); + vamsasSeq.setDescription(jds.getDescription()); + + if (jds.getDatasetSequence().getDBRef() != null) + { + jalview.datamodel.DBRefEntry[] dbrefs = + jds.getDatasetSequence().getDBRef(); + + for (int d = 0; d < dbrefs.length; d++) + { + DBRef dbref = new DBRef(); + dbref.setSource(dbrefs[d].getSource()); + dbref.setVersion(dbrefs[d].getVersion()); + dbref.setAccessionId(dbrefs[d].getAccessionId()); + vamsasSeq.addDBRef(dbref); + } + } + + vamsasSet.addSequence(vamsasSeq); + seqRefIds.put(id + "", jal.getSequenceAt(i)); + } + + jseq = new JSeq(); + jseq.setStart(jds.getStart()); + jseq.setEnd(jds.getEnd()); + jseq.setColour(av.getSequenceColour(jds).getRGB()); + + jseq.setId(id); + + if (av.hasHiddenRows) + { + jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds)); + + if (av.hiddenRepSequences != null + && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i))) + { + jalview.datamodel.SequenceI[] reps = + ( (jalview.datamodel.SequenceGroup) + av.hiddenRepSequences.get( + jal.getSequenceAt(i))).getSequencesInOrder(jal); + + for (int h = 0; h < reps.length; h++) + { + if (reps[h] != jal.getSequenceAt(i)) + { + jseq.addHiddenSequences( + jal.findIndex(reps[h]) + ); + } + } + } + } + + if (jds.getDatasetSequence().getSequenceFeatures() != null) + { + jalview.datamodel.SequenceFeature[] sf + = jds.getDatasetSequence().getSequenceFeatures(); + int index = 0; + while (index < sf.length) + { + Features features = new Features(); + + features.setBegin(sf[index].getBegin()); + features.setEnd(sf[index].getEnd()); + features.setDescription(sf[index].getDescription()); + features.setType(sf[index].getType()); + features.setFeatureGroup(sf[index].getFeatureGroup()); + features.setScore(sf[index].getScore()); + if (sf[index].links != null) + { + for (int l = 0; l < sf[index].links.size(); l++) + { + OtherData keyValue = new OtherData(); + keyValue.setKey("LINK_" + l); + keyValue.setValue(sf[index].links.elementAt(l).toString()); + features.addOtherData(keyValue); + } + } + if (sf[index].otherDetails != null) + { + String key; + Enumeration keys = sf[index].otherDetails.keys(); + while (keys.hasMoreElements()) + { + key = keys.nextElement().toString(); + OtherData keyValue = new OtherData(); + keyValue.setKey(key); + keyValue.setValue( + sf[index].otherDetails.get(key).toString()); + features.addOtherData(keyValue); + } + } + + jseq.addFeatures(features); + index++; + } + } + + if (jds.getDatasetSequence().getPDBId() != null) + { + Enumeration en = jds.getDatasetSequence().getPDBId().elements(); + while (en.hasMoreElements()) + { + Pdbids pdb = new Pdbids(); + jalview.datamodel.PDBEntry entry + = (jalview.datamodel.PDBEntry) en.nextElement(); + + pdb.setId(entry.getId()); + pdb.setType(entry.getType()); + + AppJMol jmol; + //This must have been loaded, is it still visible? + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + for (int f = frames.length - 1; f > -1; f--) + { + if (frames[f] instanceof AppJMol) + { + 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()); + + state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", "")); + + for (int s = 0; s < jmol.sequence.length; s++) + { + if (jal.findIndex(jmol.sequence[s]) > -1) + { + pdb.addStructureState(state); + } + } + } + } + + + if (entry.getFile() != null) + { + pdb.setFile(entry.getFile()); + if (pdbfiles == null) + { + pdbfiles = new Vector(); + } + + if (!pdbfiles.contains(entry.getId())) + { + pdbfiles.addElement(entry.getId()); + try + { + File file = new File(entry.getFile()); + if (file.exists() && jout != null) + { + byte[] data = new byte[ (int) file.length()]; + jout.putNextEntry(new JarEntry(entry.getId())); + DataInputStream dis = new DataInputStream(new + FileInputStream(file)); + dis.readFully(data); + + DataOutputStream dout = new DataOutputStream(jout); + dout.write(data, 0, data.length); + jout.closeEntry(); + } + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + } + } + + if (entry.getProperty() != null) + { + PdbentryItem item = new PdbentryItem(); + Hashtable properties = entry.getProperty(); + Enumeration en2 = properties.keys(); + while (en2.hasMoreElements()) + { + Property prop = new Property(); + String key = en2.nextElement().toString(); + prop.setName(key); + prop.setValue(properties.get(key).toString()); + item.addProperty(prop); + } + pdb.addPdbentryItem(item); + } + + jseq.addPdbids(pdb); + } + } + + jms.addJSeq(jseq); + } + + if (av.hasHiddenRows) + { + jal = av.alignment; + } + + //SAVE TREES + /////////////////////////////////// + if (av.currentTree != null) + { + // FIND ANY ASSOCIATED TREES + // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT + if (Desktop.desktop != null) + { + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); + + for (int t = 0; t < frames.length; t++) + { + if (frames[t] instanceof TreePanel) + { + TreePanel tp = (TreePanel) frames[t]; + + if (tp.treeCanvas.av.alignment == jal) + { + Tree tree = new Tree(); + tree.setTitle(tp.getTitle()); + tree.setCurrentTree( (av.currentTree == tp.getTree())); + tree.setNewick(tp.getTree().toString()); + tree.setThreshold(tp.treeCanvas.threshold); + + tree.setFitToWindow(tp.fitToWindow.getState()); + tree.setFontName(tp.getTreeFont().getName()); + tree.setFontSize(tp.getTreeFont().getSize()); + tree.setFontStyle(tp.getTreeFont().getStyle()); + tree.setMarkUnlinked(tp.placeholdersMenu.getState()); + + tree.setShowBootstrap(tp.bootstrapMenu.getState()); + tree.setShowDistances(tp.distanceMenu.getState()); + + tree.setHeight(tp.getHeight()); + tree.setWidth(tp.getWidth()); + tree.setXpos(tp.getX()); + tree.setYpos(tp.getY()); + + jms.addTree(tree); + } + } + } + } + } + + //SAVE ANNOTATIONS + if (jal.getAlignmentAnnotation() != null) + { + jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); + + for (int i = 0; i < aa.length; i++) + { + Annotation an = new Annotation(); + + if (aa[i].annotationId != null) + { + annotationIds.put(aa[i].annotationId, aa[i]); + } + + 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.setDescription(aa[i].description); + + if (aa[i].sequenceRef != null) + { + an.setSequenceRef(aa[i].sequenceRef.getName()); + } + + if (aa[i].graph > 0) + { + an.setGraph(true); + an.setGraphType(aa[i].graph); + an.setGraphGroup(aa[i].graphGroup); + if (aa[i].getThreshold() != null) + { + ThresholdLine line = new ThresholdLine(); + line.setLabel(aa[i].getThreshold().label); + line.setValue(aa[i].getThreshold().value); + line.setColour(aa[i].getThreshold().colour.getRGB()); + an.setThresholdLine(line); + } + } + else + { + an.setGraph(false); + } + + an.setLabel(aa[i].label); + if (aa[i].hasScore()) + { + an.setScore(aa[i].getScore()); + } + AnnotationElement ae; + if (aa[i].annotations!=null) + { + an.setScoreOnly(false); + for (int a = 0; a < aa[i].annotations.length; a++) + { + if ((aa[i] == null) || (aa[i].annotations[a] == null)) + { + continue; + } + + ae = new AnnotationElement(); + ae.setDescription(aa[i].annotations[a].description); + ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter); + ae.setValue(aa[i].annotations[a].value); + ae.setPosition(a); + ae + .setSecondaryStructure(aa[i].annotations[a].secondaryStructure + + ""); + + if (aa[i].annotations[a].colour != java.awt.Color.black) + { + ae.setColour(aa[i].annotations[a].colour.getRGB()); + } + + an.addAnnotationElement(ae); + } + } else { + an.setScoreOnly(true); + } + vamsasSet.addAnnotation(an); + } + } + + //SAVE GROUPS + if (jal.getGroups() != null) + { + JGroup[] groups = new JGroup[jal.getGroups().size()]; + + for (int i = 0; i < groups.length; i++) + { + groups[i] = new JGroup(); + + jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) + jal.getGroups() + .elementAt(i); + groups[i].setStart(sg.getStartRes()); + groups[i].setEnd(sg.getEndRes()); + groups[i].setName(sg.getName()); + if (sg.cs != null) + { + if (sg.cs.conservationApplied()) + { + groups[i].setConsThreshold(sg.cs.getConservationInc()); + + if (sg.cs instanceof jalview.schemes.UserColourScheme) + { + groups[i].setColour(SetUserColourScheme(sg.cs, + userColours, + jms)); + } + else + { + groups[i].setColour(ColourSchemeProperty.getColourName(sg. + cs)); + } + } + else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient) + { + groups[i].setColour( + ColourSchemeProperty.getColourName( + ( (jalview.schemes.AnnotationColourGradient) sg.cs). + getBaseColour())); + } + else if (sg.cs instanceof jalview.schemes.UserColourScheme) + { + groups[i].setColour(SetUserColourScheme(sg.cs, userColours, + jms)); + } + else + { + groups[i].setColour(ColourSchemeProperty.getColourName( + sg.cs)); + } + + groups[i].setPidThreshold(sg.cs.getThreshold()); + } + + groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); + groups[i].setDisplayBoxes(sg.getDisplayBoxes()); + groups[i].setDisplayText(sg.getDisplayText()); + groups[i].setColourText(sg.getColourText()); + groups[i].setTextCol1(sg.textColour.getRGB()); + groups[i].setTextCol2(sg.textColour2.getRGB()); + groups[i].setTextColThreshold(sg.thresholdTextColour); + + for (int s = 0; s < sg.getSize(); s++) + { + jalview.datamodel.Sequence seq = + (jalview.datamodel.Sequence) sg.getSequenceAt(s); + groups[i].addSeq(seq.hashCode()); + } + } + + jms.setJGroup(groups); + } + + ///////////SAVE VIEWPORT + Viewport view = new Viewport(); + view.setTitle(ap.alignFrame.getTitle()); + view.setSequenceSetId(av.getSequenceSetId()); + view.setViewName(av.viewName); + view.setGatheredViews(av.gatherViewsHere); + + + + if (ap.av.explodedPosition != null) + { + view.setXpos(av.explodedPosition.x); + view.setYpos(av.explodedPosition.y); + view.setWidth(av.explodedPosition.width); + view.setHeight(av.explodedPosition.height); + } + else + { + view.setXpos(ap.alignFrame.getBounds().x); + view.setYpos(ap.alignFrame.getBounds().y); + view.setWidth(ap.alignFrame.getBounds().width); + view.setHeight(ap.alignFrame.getBounds().height); + } + + view.setStartRes(av.startRes); + view.setStartSeq(av.startSeq); + + if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme) + { + view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), + userColours, jms)); + } + else if (av.getGlobalColourScheme() instanceof jalview.schemes. + AnnotationColourGradient) + { + jalview.schemes.AnnotationColourGradient acg + = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme(); + + AnnotationColours ac = new AnnotationColours(); + ac.setAboveThreshold(acg.getAboveThreshold()); + ac.setThreshold(acg.getAnnotationThreshold()); + ac.setAnnotation(acg.getAnnotation()); + if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme) + { + ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(), + userColours, jms)); + } + else + { + ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour())); + } + + ac.setMaxColour(acg.getMaxColour().getRGB()); + ac.setMinColour(acg.getMinColour().getRGB()); + view.setAnnotationColours(ac); + view.setBgColour("AnnotationColourGradient"); + } + else + { + view.setBgColour(ColourSchemeProperty.getColourName( + av.getGlobalColourScheme())); + } + + ColourSchemeI cs = av.getGlobalColourScheme(); + + if (cs != null) + { + if (cs.conservationApplied()) + { + view.setConsThreshold(cs.getConservationInc()); + if (cs instanceof jalview.schemes.UserColourScheme) + { + view.setBgColour(SetUserColourScheme(cs, userColours, jms)); + } + } + + if (cs instanceof ResidueColourScheme) + { + view.setPidThreshold(cs.getThreshold()); + } + } + + view.setConservationSelected(av.getConservationSelected()); + view.setPidSelected(av.getAbovePIDThreshold()); + view.setFontName(av.font.getName()); + view.setFontSize(av.font.getSize()); + view.setFontStyle(av.font.getStyle()); + view.setRenderGaps(av.renderGaps); + view.setShowAnnotation(av.getShowAnnotation()); + view.setShowBoxes(av.getShowBoxes()); + view.setShowColourText(av.getColourText()); + view.setShowFullId(av.getShowJVSuffix()); + view.setRightAlignIds(av.rightAlignIds); + view.setShowSequenceFeatures(av.showSequenceFeatures); + view.setShowText(av.getShowText()); + view.setWrapAlignment(av.getWrapAlignment()); + view.setTextCol1(av.textColour.getRGB()); + view.setTextCol2(av.textColour2.getRGB()); + view.setTextColThreshold(av.thresholdTextColour); + + 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(); + for (int ro = 0; ro < renderOrder.length; ro++) + { + Setting setting = new Setting(); + setting.setType(renderOrder[ro]); + setting.setColour( + ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]). + getRGB() + ); + + setting.setDisplay( + av.featuresDisplayed.containsKey(renderOrder[ro]) + ); + float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]); + if (rorder>-1) { + setting.setOrder(rorder); + } + fs.addSetting(setting); + settingsAdded.addElement(renderOrder[ro]); + } + + //Make sure we save none displayed feature settings + Enumeration en = + ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys(); + while (en.hasMoreElements()) + { + String key = en.nextElement().toString(); + if (settingsAdded.contains(key)) + { + continue; + } + + Setting setting = new Setting(); + setting.setType(key); + setting.setColour( + ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB() + ); + + setting.setDisplay(false); + float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key); + if (rorder>-1) + { + setting.setOrder(rorder); + } + fs.addSetting(setting); + settingsAdded.addElement(key); + } + en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys(); + Vector groupsAdded=new Vector(); + while (en.hasMoreElements()) + { + String grp = en.nextElement().toString(); + if (groupsAdded.contains(grp)) + { + continue; + } + Group g = new Group(); + g.setName(grp); + g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue()); + fs.addGroup(g); + groupsAdded.addElement(grp); + } + jms.setFeatureSettings(fs); + + } + + if (av.hasHiddenColumns) + { + 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); + } + } + + jms.addViewport(view); + + object.setJalviewModelSequence(jms); + object.getVamsasModel().addSequenceSet(vamsasSet); + + if (out != null) + { + //We may not want to right the object to disk, + //eg we can copy the alignViewport to a new view object + //using save and then load + try + { + if (!fileName.endsWith(".xml")) + { + fileName = fileName + ".xml"; + } + + JarEntry entry = new JarEntry(fileName); + jout.putNextEntry(entry); + + object.marshal(out); + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + return object; + } + + String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, + Vector userColours, JalviewModelSequence jms) + { + String id = null; + jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) + cs; + + if (!userColours.contains(ucs)) + { + userColours.add(ucs); + + 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(); + + for (int i = 0; i < colours.length; i++) + { + jalview.schemabinding.version2.Colour col = new jalview.schemabinding. + version2.Colour(); + col.setName(ResidueProperties.aa[i]); + col.setRGB(jalview.util.Format.getHexString(colours[i])); + jbucs.addColour(col); + } + if (ucs.getLowerCaseColours() != null) + { + colours = ucs.getLowerCaseColours(); + for (int i = 0; i < colours.length; i++) + { + jalview.schemabinding.version2.Colour col = new jalview.schemabinding. + version2.Colour(); + col.setName(ResidueProperties.aa[i].toLowerCase()); + col.setRGB(jalview.util.Format.getHexString(colours[i])); + jbucs.addColour(col); + } + } + + id = "ucs" + userColours.indexOf(ucs); + uc.setId(id); + uc.setUserColourScheme(jbucs); + jms.addUserColours(uc); + } + + return id; + } + + 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; + } + } + + java.awt.Color[] newColours = new java.awt.Color[24]; + + for (int i = 0; i < 24; i++) + { + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i).getRGB(), 16)); + } + + jalview.schemes.UserColourScheme ucs = + new jalview.schemes.UserColourScheme(newColours); + + if (colours.getUserColourScheme().getColourCount() > 24) + { + newColours = new java.awt.Color[23]; + for (int i = 0; i < 23; i++) + { + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i + 24).getRGB(), 16)); + } + ucs.setLowerCaseColours(newColours); + } + + return ucs; + } + + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + */ + public AlignFrame LoadJalviewAlign(final String file) + { + uniqueSetSuffix = System.currentTimeMillis() % 100000 + ""; + + jalview.gui.AlignFrame af = null; + + seqRefIds = new Hashtable(); + viewportsAdded = new Hashtable(); + + Hashtable gatherToThisFrame = new Hashtable(); + + try + { + //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING + URL url = null; + + if (file.startsWith("http://")) + { + url = new URL(file); + } + + 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)); + } + + for (int i = 0; i < entryCount; i++) + { + jarentry = jin.getNextJarEntry(); + } + + if (jarentry != null && jarentry.getName().endsWith(".xml")) + { + InputStreamReader in = new InputStreamReader(jin, "UTF-8"); + JalviewModel object = new JalviewModel(); + + Unmarshaller unmar = new Unmarshaller(object); + unmar.setValidation(false); + object = (JalviewModel) unmar.unmarshal(in); + + af = LoadFromObject(object, file, true); + if (af.viewport.gatherViewsHere) + { + gatherToThisFrame.put(af.viewport.getSequenceSetId(), af); + } + entryCount++; + } + else if (jarentry != null) + { + //Some other file here. + entryCount++; + } + } + while (jarentry != null); + } + catch (java.net.UnknownHostException ex) + { + ex.printStackTrace(); + System.err.println("Couldn't locate Jalview XML file : " + + ex + "\n"); + + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Couldn't locate " + file, + "URL not found", + JOptionPane.WARNING_MESSAGE); + } + }); + } + catch (Exception ex) + { + //Is Version 1 Jar file? + af = new Jalview2XML_V1().LoadJalviewAlign(file); + + if (af != null) + { + System.out.println("Successfully loaded archive file"); + return af; + } + ex.printStackTrace(); + + System.err.println("Exception whilst loading jalview XML file : " + + ex + "\n"); + javax.swing.SwingUtilities.invokeLater(new Runnable() + { + public void run() + { + + JOptionPane.showInternalMessageDialog(Desktop.desktop, + "Error loading " + file, + "Error loading Jalview file", + JOptionPane.WARNING_MESSAGE); + } + }); + } + + if (Desktop.instance != null) + { + Desktop.instance.stopLoading(); + } + + Enumeration en = gatherToThisFrame.elements(); + while(en.hasMoreElements()) + { + Desktop.instance.gatherViews( + (AlignFrame) en.nextElement()); + } + + return af; + } + + Hashtable alreadyLoadedPDB; + String loadPDBFile(String file, String pdbId) + { + if (alreadyLoadedPDB == null) + alreadyLoadedPDB = new Hashtable(); + + if (alreadyLoadedPDB.containsKey(pdbId)) + return alreadyLoadedPDB.get(pdbId).toString(); + + try + { + JarInputStream jin = null; + + if (file.startsWith("http://")) + { + jin = new JarInputStream(new URL(file).openStream()); + } + else + { + jin = new JarInputStream(new FileInputStream(file)); + } + + JarEntry entry = null; + do + { + entry = jin.getNextJarEntry(); + } + while (!entry.getName().equals(pdbId)); + + 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); + } + out.close(); + + alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath()); + return outFile.getAbsolutePath(); + + } + catch (Exception ex) + { + ex.printStackTrace(); + } + + return null; + } + + AlignFrame LoadFromObject(JalviewModel object, + String file, + boolean loadTreesAndStructures) + { + SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); + Sequence[] vamsasSeq = vamsasSet.getSequence(); + + JalviewModelSequence jms = object.getJalviewModelSequence(); + + Viewport view = jms.getViewport(0); + + ////////////////////////////////// + //LOAD SEQUENCES + + Vector hiddenSeqs = null; + jalview.datamodel.Sequence jseq; + + ArrayList tmpseqs = new ArrayList(); + + boolean multipleView = false; + + JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); + for (int i = 0; i < JSEQ.length; i++) + { + String seqId = JSEQ[i].getId() + ""; + + if (seqRefIds.get(seqId) != null) + { + tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId)); + multipleView = true; + } + else + { + jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), + vamsasSeq[i].getSequence()); + jseq.setDescription(vamsasSeq[i].getDescription()); + jseq.setStart(JSEQ[i].getStart()); + jseq.setEnd(JSEQ[i].getEnd()); + seqRefIds.put(vamsasSeq[i].getId(), jseq); + tmpseqs.add(jseq); + } + + if (JSEQ[i].getHidden()) + { + if (hiddenSeqs == null) + { + hiddenSeqs = new Vector(); + } + + hiddenSeqs.addElement( + (jalview.datamodel.Sequence) seqRefIds.get(seqId)); + } + + } + + ///SequenceFeatures are added to the DatasetSequence, + // so we must create the dataset before loading features + ///////////////////////////////// + + + jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[ + tmpseqs.size()]; + + tmpseqs.toArray(orderedSeqs); + + jalview.datamodel.Alignment al = + new jalview.datamodel.Alignment(orderedSeqs); + + al.setDataset(null); + ///////////////////////////////// + + + Hashtable pdbloaded = new Hashtable(); + + if (!multipleView) + { + 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(), + features[f].getFeatureGroup()); + + sf.setScore(features[f].getScore()); + for (int od = 0; od < features[f].getOtherDataCount(); od++) + { + OtherData keyValue = features[f].getOtherData(od); + if (keyValue.getKey().startsWith("LINK")) + { + sf.addLink(keyValue.getValue()); + } + else + { + sf.setValue(keyValue.getKey(), keyValue.getValue()); + } + + } + + 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()); + if (ids[p].getFile() != null) + { + if (!pdbloaded.containsKey(ids[p].getFile())) + { + entry.setFile(loadPDBFile(file, ids[p].getId())); + } + else + { + entry.setFile(pdbloaded.get(ids[p].getId()).toString()); + } + } + + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + } + if (vamsasSeq[i].getDBRefCount() > 0) + { + for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++) + { + jalview.datamodel.DBRefEntry entry = + new jalview.datamodel.DBRefEntry( + vamsasSeq[i].getDBRef(d).getSource(), + vamsasSeq[i].getDBRef(d).getVersion(), + vamsasSeq[i].getDBRef(d).getAccessionId() + ); + al.getSequenceAt(i).getDatasetSequence().addDBRef(entry); + } + + } + } + } + + ///////////////////////////////// + ////////////////////////////////// + //LOAD ANNOTATIONS + boolean hideQuality = true, + hideConservation = true, + hideConsensus = true; + + if (vamsasSet.getAnnotationCount() > 0) + { + Annotation[] an = vamsasSet.getAnnotation(); + + for (int i = 0; i < an.length; i++) + { + if (an[i].getLabel().equals("Quality")) + { + hideQuality = false; + continue; + } + else if (an[i].getLabel().equals("Conservation")) + { + hideConservation = false; + continue; + } + else if (an[i].getLabel().equals("Consensus")) + { + hideConsensus = false; + continue; + } + + if (an[i].getId() != null + && annotationIds.containsKey(an[i].getId())) + { + al.addAnnotation( + (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i]. + getId()) + ); + + continue; + } + + AnnotationElement[] ae = an[i].getAnnotationElement(); + jalview.datamodel.Annotation[] anot = null; + if (!an[i].getScoreOnly()) + { + anot = new jalview.datamodel.Annotation[ + al.getWidth()]; + + for (int aa = 0; aa < ae.length && aa < anot.length; aa++) + { + anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa]. + getDisplayCharacter(), + ae[aa].getDescription(), + ae[aa].getSecondaryStructure().length() == 0 ? ' ' : + ae[aa].getSecondaryStructure().charAt(0), + ae[aa].getValue()); + anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa]. + getColour()); + } + } + jalview.datamodel.AlignmentAnnotation jaa = null; + + if (an[i].getGraph()) + { + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot, 0, 0, + an[i].getGraphType()); + + jaa.graphGroup = an[i].getGraphGroup(); + + if (an[i].getThresholdLine() != null) + { + jaa.setThreshold(new jalview.datamodel.GraphLine( + an[i].getThresholdLine().getValue(), + an[i].getThresholdLine().getLabel(), + new java.awt.Color(an[i].getThresholdLine().getColour())) + ); + + } + + } + else + { + jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), + an[i].getDescription(), anot); + } + + if (an[i].getId() != null) + { + annotationIds.put(an[i].getId(), jaa); + jaa.annotationId = an[i].getId(); + } + + if (an[i].getSequenceRef() != null) + { + jaa.createSequenceMapping( + al.findName(an[i].getSequenceRef()), 1, true + ); + al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa); + } + if (an[i].hasScore()) + { + jaa.setScore(an[i].getScore()); + } + al.addAnnotation(jaa); + } + } + + ///////////////////////// + //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(); + + for (int s = 0; s < groups[i].getSeqCount(); s++) + { + String seqId = groups[i].getSeq(s) + ""; + jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI) + seqRefIds.get(seqId); + + if (ts != null) + { + seqs.addElement(ts); + } + } + + if (seqs.size() < 1) + { + continue; + } + + 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())); + + sg.textColour = new java.awt.Color(groups[i].getTextCol1()); + sg.textColour2 = new java.awt.Color(groups[i].getTextCol2()); + sg.thresholdTextColour = groups[i].getTextColThreshold(); + + 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); + } + } + + ///////////////////////////////// + // LOAD VIEWPORT + + 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.alignment.getSequenceAt(i), + 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) + { + jalview.gui.AlignViewport av = + (jalview.gui.AlignViewport) + viewportsAdded.get(uniqueSeqSetId); + + af.viewport.sequenceSetID = uniqueSeqSetId; + if (av != null) + { + + af.viewport.historyList = av.historyList; + af.viewport.redoList = av.redoList; + } + else + { + viewportsAdded.put(uniqueSeqSetId, af.viewport); + } + + PaintRefresher.Register(af.alignPanel, uniqueSeqSetId); + } + if (hiddenSeqs != null) + { + for (int s = 0; s < JSEQ.length; s++) + { + jalview.datamodel.SequenceGroup hidden = + new jalview.datamodel.SequenceGroup(); + + for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++) + { + hidden.addSequence( + al.getSequenceAt(JSEQ[s].getHiddenSequences(r)) + , false + ); + } + af.viewport.hideRepSequences(al.getSequenceAt(s), hidden); + } + + jalview.datamodel.SequenceI[] hseqs = new + jalview.datamodel.SequenceI[hiddenSeqs.size()]; + + for (int s = 0; s < hiddenSeqs.size(); s++) + { + hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s); + } + + af.viewport.hideSequence(hseqs); + + } + + if ( (hideConsensus || hideQuality || hideConservation) + && al.getAlignmentAnnotation() != null) + { + int hSize = al.getAlignmentAnnotation().length; + for (int h = 0; h < hSize; h++) + { + if ( + (hideConsensus && + al.getAlignmentAnnotation()[h].label.equals("Consensus")) + || + (hideQuality && + al.getAlignmentAnnotation()[h].label.equals("Quality")) + || + (hideConservation && + al.getAlignmentAnnotation()[h].label.equals("Conservation"))) + { + al.deleteAnnotation(al.getAlignmentAnnotation()[h]); + hSize--; + h--; + } + } + af.alignPanel.adjustAnnotationHeight(); + } + + if (view.getViewName() != null) + { + af.viewport.viewName = view.getViewName(); + af.setInitialTabVisible(); + } + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), + view.getHeight()); + + 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.rightAlignIds = view.getRightAlignIds(); + 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()); + + 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.setStartRes(view.getStartRes()); + af.viewport.setStartSeq(view.getStartSeq()); + + ColourSchemeI cs = null; + + if (view.getBgColour() != null) + { + if (view.getBgColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, view.getBgColour()); + } + else if (view.getBgColour().startsWith("Annotation")) + { + //int find annotation + for (int i = 0; + i < af.viewport.alignment.getAlignmentAnnotation().length; i++) + { + if (af.viewport.alignment.getAlignmentAnnotation()[i].label. + equals(view.getAnnotationColours().getAnnotation())) + { + 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++) + { + jalview.datamodel.SequenceGroup sg + = (jalview.datamodel.SequenceGroup) al.getGroups(). + elementAt(g); + + 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; + } + + } + } + else + { + cs = ColourSchemeProperty.getColour(al, view.getBgColour()); + } + + if (cs != null) + { + cs.setThreshold(view.getPidThreshold(), true); + cs.setConsensus(af.viewport.hconsensus); + } + } + + af.viewport.setGlobalColourScheme(cs); + af.viewport.setColourAppliesToAllGroups(false); + + if (view.getConservationSelected() && cs != null) + { + cs.setConservationInc(view.getConsThreshold()); + } + + af.changeColour(cs); + + af.viewport.setColourAppliesToAllGroups(true); + + if (view.getShowSequenceFeatures()) + { + af.viewport.showSequenceFeatures = true; + } + + 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.hasOrder()) + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder()); + else + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount()); + if (setting.getDisplay()) + { + af.viewport.featuresDisplayed.put( + setting.getType(), new Integer(setting.getColour())); + } + } + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = + renderOrder; + Hashtable fgtable; + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable(); + for (int gs=0;gs 0) + { + for (int c = 0; c < view.getHiddenColumnsCount(); c++) + { + af.viewport.hideColumns( + view.getHiddenColumns(c).getStart(), + view.getHiddenColumns(c).getEnd() //+1 + ); + } + } + + af.setMenusFromViewport(af.viewport); + + 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(); + + if (tree.getCurrentTree()) + { + af.viewport.setCurrentTree(tp.getTree()); + } + } + + } + catch (Exception ex) + { + ex.printStackTrace(); + } + } + + ////LOAD STRUCTURES + if(loadTreesAndStructures) + { + 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 = Desktop.desktop.getComponentAt(x, y); + + String pdbFile = loadPDBFile(file, ids[p].getId()); + + jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[] + { + al.getSequenceAt(i)}; + + if (comp == null || + (comp.getWidth() != width && comp.getHeight() != height)) + { + 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, pdbFile, + jalview.io.AppletFormatAdapter.FILE); + + ( (AppJMol) comp).addSequence(seq); + } + } + } + } + } + } + + return af; + } + + public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap, + boolean keepSeqRefs) + { + jalview.schemabinding.version2.JalviewModel jm + = SaveState(ap, null, null, null); + + if (!keepSeqRefs) + { + seqRefIds.clear(); + jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null); + } + else + { + uniqueSetSuffix = ""; + } + + viewportsAdded = new Hashtable(); + + AlignFrame af = LoadFromObject(jm, null, false); + af.alignPanels.clear(); + af.closeMenuItem_actionPerformed(true); + + /* if(ap.av.alignment.getAlignmentAnnotation()!=null) + { + for(int i=0; i