X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=bbe338944252658a2e31bf40f855c07f6eaa8d52;hb=eacce9627f059fc2f9e880c81d8d1bdfbe7fe5b3;hp=bfd97f03b7c0ec5235a91b091db2231dc6286780;hpb=588042b69abf8e60bcc950b24c283933c7dd422f;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index bfd97f0..bbe3389 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -18,694 +18,887 @@ */ 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.*; -import jalview.io.*; -import jalview.schemes.*; + +/** + * 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) + // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE + public static void SaveState(File statefile) { - return; - } + long creation = System.currentTimeMillis(); + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - try - { - FileOutputStream fos = new FileOutputStream(statefile); - JarOutputStream jout = new JarOutputStream(fos); + if (frames == null) + { + return; + } - //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS - //////////////////////////////////////////////////// - PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, - "UTF-8")); + try + { + FileOutputStream fos = new FileOutputStream(statefile); + JarOutputStream jout = new JarOutputStream(fos); - Vector shortNames = new Vector(); + //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS + //////////////////////////////////////////////////// + PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, + "UTF-8")); - //REVERSE ORDER - for (int i = frames.length - 1; i > -1; i--) - { - if (frames[i] instanceof AlignFrame) - { - AlignFrame af = (AlignFrame) frames[i]; + Vector shortNames = new Vector(); - String shortName = af.getTitle(); + //REVERSE ORDER + for (int i = frames.length - 1; i > -1; i--) + { + if (frames[i] instanceof AlignFrame) + { + AlignFrame af = (AlignFrame) frames[i]; - if (shortName.indexOf(File.separatorChar) > -1) - { - shortName = shortName.substring(shortName.lastIndexOf( - File.separatorChar) + 1); - } + String shortName = af.getTitle(); - int count = 1; + if (shortName.indexOf(File.separatorChar) > -1) + { + shortName = shortName.substring(shortName.lastIndexOf( + File.separatorChar) + 1); + } - while (shortNames.contains(shortName)) - { - if (shortName.endsWith("_" + (count - 1))) - { - shortName = shortName.substring(0, - shortName.lastIndexOf("_")); - } + int count = 1; - shortName = shortName.concat("_" + count); - count++; - } + while (shortNames.contains(shortName)) + { + if (shortName.endsWith("_" + (count - 1))) + { + shortName = shortName.substring(0, + shortName.lastIndexOf("_")); + } - shortNames.addElement(shortName); + shortName = shortName.concat("_" + count); + count++; + } - if (!shortName.endsWith(".xml")) - { - shortName = shortName + ".xml"; - } + shortNames.addElement(shortName); - SaveState(af, creation, shortName, jout, out); - } - } + if (!shortName.endsWith(".xml")) + { + shortName = shortName + ".xml"; + } - out.close(); - jout.close(); - } - catch (Exception ex) - { - ex.printStackTrace(); + 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 SaveState(AlignFrame af, String jarFile, String fileName) - { - try + // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW + public static void SaveAlignment(AlignFrame af, String jarFile, + String fileName) { - FileOutputStream fos = new FileOutputStream(jarFile); - JarOutputStream jout = new JarOutputStream(fos); + 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")); + //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) - { + SaveState(af, System.currentTimeMillis(), fileName, jout, out); + out.close(); + jout.close(); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } - } - 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; + /** + * 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(); - JalviewModel object = new JalviewModel(); - object.setVamsasModel(new VamsasModel()); + AlignViewport av = af.viewport; - object.setCreationDate(new java.util.Date(timeStamp)); + JalviewModel object = new JalviewModel(); + object.setVamsasModel(new jalview.binding.VamsasModel()); - jalview.datamodel.AlignmentI jal = af.viewport.alignment; + object.setCreationDate(new java.util.Date(timeStamp)); + object.setVersion(jalview.bin.Cache.getProperty("VERSION")); - SequenceSet vamsasSet = new SequenceSet(); - Sequence vamsasSeq; - JalviewModelSequence jms = new JalviewModelSequence(); + jalview.datamodel.AlignmentI jal = af.viewport.alignment; - vamsasSet.setGapChar(jal.getGapCharacter() + ""); + SequenceSet vamsasSet = new SequenceSet(); + Sequence vamsasSeq; + JalviewModelSequence jms = new JalviewModelSequence(); - JSeq jseq; + vamsasSet.setGapChar(jal.getGapCharacter() + ""); - //SAVE SEQUENCES - int id = 0; + JSeq jseq; - for (int i = 0; i < jal.getHeight(); i++) - { - seqids.add(jal.getSequenceAt(i)); + //SAVE SEQUENCES + int id = 0; - vamsasSeq = new Sequence(); - vamsasSeq.setId(id + ""); - vamsasSeq.setName(jal.getSequenceAt(i).getName()); - vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); + for (int i = 0; i < jal.getHeight(); i++) + { + seqids.add(jal.getSequenceAt(i)); - jseq = new JSeq(); - jseq.setStart(jal.getSequenceAt(i).getStart()); - jseq.setEnd(jal.getSequenceAt(i).getEnd()); + vamsasSeq = new Sequence(); + vamsasSeq.setId(id + ""); + vamsasSeq.setName(jal.getSequenceAt(i).getName()); + vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); - jseq.setColour(jal.getSequenceAt(i).getColor().getRGB()); + jseq = new JSeq(); + jseq.setStart(jal.getSequenceAt(i).getStart()); + jseq.setEnd(jal.getSequenceAt(i).getEnd()); - jseq.setId(id); + jseq.setColour(jal.getSequenceAt(i).getColor().getRGB()); - jms.addJSeq(jseq); - vamsasSet.addSequence(vamsasSeq); - id++; - } + jseq.setId(id); - //SAVE TREES - if (af.viewport.currentTree != null) - { - object.getVamsasModel().addTree(af.viewport.currentTree.toString()); - } + 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); + } + } - //SAVE ANNOTATIONS - if (jal.getAlignmentAnnotation() != null) - { - jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); + 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); + } + } - 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; + jms.addJSeq(jseq); + vamsasSet.addSequence(vamsasSeq); + id++; } - 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++) + //SAVE TREES + /////////////////////////////////// + if (af.viewport.currentTree != null) { - if ( (aa[i] == null) || (aa[i].annotations[a] == null)) + // FIND ANY ASSOCIATED TREES + // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT + if (Desktop.desktop != null) { - continue; - } + JInternalFrame[] frames = Desktop.desktop.getAllFrames(); - 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); + 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); + } + } + } + } } - vamsasSet.addAnnotation(an); - } - } + //SAVE ANNOTATIONS + if (jal.getAlignmentAnnotation() != null) + { + jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation(); - //SAVE GROUPS - if (jal.getGroups() != null) - { - JGroup[] groups = new JGroup[jal.getGroups().size()]; + 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); + } + } - for (int i = 0; i < groups.length; i++) - { - groups[i] = new JGroup(); + //SAVE GROUPS + if (jal.getGroups() != null) + { + JGroup[] groups = new JGroup[jal.getGroups().size()]; - 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()); + 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); + } + } - if (sg.cs instanceof ConservationColourScheme) - { - groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc); + jms.setJGroup(groups); } - if (sg.cs instanceof ResidueColourScheme) - { - groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs). - getThreshold()); - } - else if (sg.cs instanceof ScoreColourScheme) - { - groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold()); - } - if (sg.cs instanceof jalview.schemes.UserColourScheme) + ///////////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) { - groups[i].setColour(SetUserColourScheme(sg.cs, userColours, - jms)); + view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(), + userColours, jms)); } else { - groups[i].setColour(ColourSchemeProperty.getColourName( - sg.cs)); + view.setBgColour(ColourSchemeProperty.getColourName( + av.getGlobalColourScheme())); } - groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); - groups[i].setDisplayBoxes(sg.getDisplayBoxes()); - groups[i].setDisplayText(sg.getDisplayText()); - groups[i].setColourText(sg.getColourText()); + ColourSchemeI cs = av.getGlobalColourScheme(); - for (int s = 0; s < sg.getSize(); s++) + if(cs!=null) { - jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg. - getSequenceAt(s); - int index = seqids.indexOf(seq); - groups[i].addSeq(index); - } - } + if (cs.conservationApplied()) + { + view.setConsThreshold(cs.getConservationInc()); + if (cs instanceof jalview.schemes.UserColourScheme) + view.setBgColour(SetUserColourScheme(cs, userColours, jms)); + } - jms.setJGroup(groups); - } + if (cs instanceof ResidueColourScheme) + { + view.setPidThreshold(cs.getThreshold()); + } + } - ///////////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())); - } + 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()); + + jms.addViewport(view); + + object.setJalviewModelSequence(jms); + object.getVamsasModel().addSequenceSet(vamsasSet); + + try + { + if (!fileName.endsWith(".xml")) + { + fileName = fileName + ".xml"; + } - ColourSchemeI cs = av.getGlobalColourScheme(); + JarEntry entry = new JarEntry(fileName); + jout.putNextEntry(entry); - if (cs instanceof ConservationColourScheme) - { - view.setConsThreshold( ( (ConservationColourScheme) cs).inc); + object.marshal(out); + } + catch (Exception ex) + { + ex.printStackTrace(); + } } - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold()); - } - else if (cs instanceof ScoreColourScheme) + static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, + Vector userColours, JalviewModelSequence jms) { - view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold()); - } + String id = null; + jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs; - view.setConservationSelected(av.getConservationSelected()); - view.setPidSelected(av.getAbovePIDThreshold()); - view.setFontName(av.font.getFontName()); - 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.getShowFullId()); - view.setShowIdentity(av.showIdentity); - view.setShowQuality(av.showQuality); - view.setShowSequenceFeatures(av.showSequenceFeatures); - view.setShowText(av.getShowText()); - view.setWrapAlignment(av.getWrapAlignment()); - - jms.addViewport(view); - - object.setJalviewModelSequence(jms); - object.getVamsasModel().addSequenceSet(vamsasSet); - - try - { - if (!fileName.endsWith(".xml")) - { - fileName = fileName + ".xml"; - } + if (!userColours.contains(ucs)) + { + userColours.add(ucs); - JarEntry entry = new JarEntry(fileName); - jout.putNextEntry(entry); + java.awt.Color[] colours = ucs.getColours(); + jalview.binding.UserColours uc = new jalview.binding.UserColours(); + jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme(); - object.marshal(out); - } - catch (Exception ex) - { - ex.printStackTrace(); - } - } + 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); + } - static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, - Vector userColours, - JalviewModelSequence jms) - { - String id = null; - jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) - cs; + id = "ucs" + userColours.indexOf(ucs); + uc.setId(id); + uc.setUserColourScheme(jbucs); + jms.addUserColours(uc); + } - 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; } - 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++) + static jalview.schemes.UserColourScheme GetUserColourScheme( + JalviewModelSequence jms, String id) { - if (uc[i].getId().equals(id)) - { - colours = uc[i]; + UserColours[] uc = jms.getUserColours(); + UserColours colours = null; - break; - } - } + for (int i = 0; i < uc.length; i++) + { + if (uc[i].getId().equals(id)) + { + colours = uc[i]; - int csize = colours.getUserColourScheme().getColourCount(); - java.awt.Color[] newColours = new java.awt.Color[csize]; + break; + } + } - for (int i = 0; i < csize; i++) - { - newColours[i] = new java.awt.Color(Integer.parseInt( - colours.getUserColourScheme().getColour(i).getRGB(), 16)); - } + int csize = colours.getUserColourScheme().getColourCount(); + java.awt.Color[] newColours = new java.awt.Color[csize]; - return new jalview.schemes.UserColourScheme(newColours); - } + for (int i = 0; i < csize; i++) + { + newColours[i] = new java.awt.Color(Integer.parseInt( + colours.getUserColourScheme().getColour(i).getRGB(), 16)); + } - public static void LoadJalviewAlign(String file) - { - JalviewModel object = new JalviewModel(); + return new jalview.schemes.UserColourScheme(newColours); + } - try + /** + * DOCUMENT ME! + * + * @param file DOCUMENT ME! + */ + public static AlignFrame LoadJalviewAlign(String file) { - //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING - URL url = null; + JalviewModel object = new JalviewModel(); + jalview.gui.AlignFrame af = null; - if (file.startsWith("http://")) - { - url = new URL(file); - } + try + { + //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING + URL url = null; - JarInputStream jin = null; - JarEntry jarentry = null; - int entryCount = 1; + if (file.startsWith("http://")) + { + url = new URL(file); + } - do - { - if (url != null) - { - jin = new JarInputStream(url.openStream()); + 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); } - else + catch(java.net.UnknownHostException ex) { - jin = new JarInputStream(new FileInputStream(file)); - } + 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); - for (int i = 0; i < entryCount; i++) - { - jarentry = jin.getNextJarEntry(); } - - if (jarentry != null) + catch (Exception ex) { - InputStreamReader in = new InputStreamReader(jin, "UTF-8"); - object = (JalviewModel) object.unmarshal(in); - LoadFromObject(object); - entryCount++; + 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); + } - } - while (jarentry != null); + + return af; } - catch (Exception ex) + + static AlignFrame LoadFromObject(JalviewModel object) { - System.err.println("Exception whilst loading jalview XML file : " + - ex + "\n"); - ex.printStackTrace(); + Vector seqids = new Vector(); + SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); + Sequence[] vamsasSeq = vamsasSet.getSequence(); - return; - } - } + JalviewModelSequence jms = object.getJalviewModelSequence(); - static void LoadFromObject(JalviewModel object) - { - Vector seqids = new Vector(); - SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); - Sequence[] vamsasSeq = vamsasSet.getSequence(); + ////////////////////////////////// + //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()); - JalviewModelSequence jms = object.getJalviewModelSequence(); + 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]); + } - ////////////////////////////////// - //LOAD SEQUENCES - jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[ - vamsasSeq.length]; - JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); + ///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++) - { - jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), - vamsasSeq[i].getSequence()); + 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); + } - 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]); - } + } + } + ///////////////////////////////// + ////////////////////////////////// + //LOAD ANNOTATIONS + if (vamsasSet.getAnnotation() != null) + { + Annotation[] an = vamsasSet.getAnnotation(); - ///////////////////////////////// - jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); + 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 ANNOTATIONS - if (vamsasSet.getAnnotation() != null) - { - Annotation[] an = vamsasSet.getAnnotation(); + ///////////////////////////////// + // LOAD VIEWPORT + Viewport[] views = jms.getViewport(); + Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER - for (int i = 0; i < an.length; i++) - { - AnnotationElement[] ae = an[i].getAnnotationElement(); - jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[ - al.getWidth()]; + AlignFrame af = new AlignFrame(al); - for (int aa = 0; aa < ae.length; aa++) + // af.changeColour() ); + ///////////////////////// + //LOAD GROUPS + if (jms.getJGroupCount() > 0) { - anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa]. - getDisplayCharacter(), - ae[aa].getDescription(), - ae[aa].getSecondaryStructure().charAt(0), - ae[aa].getValue()); + 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); + } } - jalview.datamodel.AlignmentAnnotation jaa = null; - if (an[i].getGraph()) + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), + view.getHeight()); + af.viewport.setStartRes(view.getStartRes()); + af.viewport.setStartSeq(view.getStartSeq()); + 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()) { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, 0, 0, 1); + af.alignPanel.setWrapAlignment(view.getWrapAlignment()); } else { - jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot); + af.annotationPanelMenuItem.setState(view.getShowAnnotation()); + af.viewport.setShowAnnotation(view.getShowAnnotation()); + af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); } - 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(); + af.viewport.setShowBoxes(view.getShowBoxes()); + af.viewBoxesMenuItem.setSelected(view.getShowBoxes()); + af.viewport.setShowText(view.getShowText()); + af.viewTextMenuItem.setSelected(view.getShowText()); - for (int i = 0; i < groups.length; i++) - { ColourSchemeI cs = null; - if (groups[i].getColour() != null) + if (view.getBgColour() != null) { - if (groups[i].getColour().startsWith("ucs")) - { - cs = GetUserColourScheme(jms, groups[i].getColour()); - } - else - { - cs = ColourSchemeProperty.getColour(al, - groups[i].getColour()); - } + if (view.getBgColour().startsWith("ucs")) + { + cs = GetUserColourScheme(jms, view.getBgColour()); + } + else + { + cs = ColourSchemeProperty.getColour(al, view.getBgColour()); + } - if (cs instanceof ResidueColourScheme) - { - ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold()); - } - else if (cs instanceof ScoreColourScheme) - { - ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold()); - } + if(cs!=null) + { + cs.setThreshold(view.getPidThreshold(), true); + cs.setConsensus(af.viewport.vconsensus); + } } - jalview.datamodel.SequenceGroup sg = new jalview.datamodel. - SequenceGroup(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())); - - int[] ids = groups[i].getSeq(); - - for (int s = 0; s < ids.length; s++) + af.setColourSelected(view.getBgColour()); + af.viewport.setGlobalColourScheme(cs); + af.viewport.setColourAppliesToAllGroups(false); + af.changeColour(cs); + if (view.getConservationSelected() && cs!=null) { - sg.addSequence( (jalview.datamodel.SequenceI) seqids.elementAt( - ids[s])); + cs.setConservationInc(view.getConsThreshold()); } - if (groups[i].getConsThreshold() != 0) + af.viewport.setColourAppliesToAllGroups(true); + + if (view.getShowSequenceFeatures()) { - jalview.analysis.Conservation c = new jalview.analysis.Conservation( - "All", - ResidueProperties.propHash, 3, sg.sequences, 0, - sg.getWidth() - 1); - c.calculate(); - c.verdict(false, 25); - cs = new ConservationColourScheme(c, cs); - sg.cs = cs; + af.featureSettings.setEnabled(true); + af.viewport.showSequenceFeatures = true; + af.sequenceFeatures.setSelected(true); } - al.addGroup(sg); - } - } + Desktop.addInternalFrame(af, view.getTitle(), + view.getWidth(), view.getHeight()); - Desktop.addInternalFrame(af, view.getTitle(), - AlignFrame.NEW_WINDOW_WIDTH, - AlignFrame.NEW_WINDOW_HEIGHT); - af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), - view.getHeight()); - af.viewport.setStartRes(view.getStartRes()); - af.viewport.setStartSeq(view.getStartSeq()); - af.viewport.showConservation = view.getShowConservation(); - af.viewport.showQuality = view.getShowQuality(); - af.viewport.showIdentity = view.getShowIdentity(); - af.viewport.setAbovePIDThreshold(view.getPidSelected()); - af.viewport.setColourText(view.getShowColourText()); - af.viewport.setConservationSelected(view.getConservationSelected()); - af.viewport.setShowFullId(view.getShowFullId()); - af.viewport.setFont(new java.awt.Font(view.getFontName(), - view.getFontStyle(), view.getFontSize())); - af.alignPanel.fontChanged(); - - af.sequenceFeatures_actionPerformed(null); - af.viewport.setRenderGaps(view.getRenderGaps()); - - af.viewport.setWrapAlignment(view.getWrapAlignment()); - - if (view.getWrapAlignment()) - { - af.alignPanel.setWrapAlignment(view.getWrapAlignment()); - } - else - { - af.viewport.setShowAnnotation(view.getShowAnnotation()); - af.alignPanel.setAnnotationVisible(view.getShowAnnotation()); - } + //LOAD TREES + /////////////////////////////////////// + if (jms.getTreeCount() > 0) + { + try + { + for (int t = 0; t < jms.getTreeCount(); t++) + { - af.viewport.setShowBoxes(view.getShowBoxes()); - af.viewport.setShowText(view.getShowText()); + Tree tree = jms.getTree(t); - ColourSchemeI cs = null; + TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile( + tree.getNewick()), tree.getTitle(), + tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); - if (view.getBgColour() != null) - { - if (view.getBgColour().startsWith("ucs")) - { - cs = GetUserColourScheme(jms, view.getBgColour()); - } - else - { - cs = ColourSchemeProperty.getColour(al, view.getBgColour()); - } - - if (cs instanceof ConservationColourScheme) - { - ( (ConservationColourScheme) cs).inc = view.getConsThreshold(); - } - - if (cs instanceof ResidueColourScheme) - { - ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold()); - } - else if (cs instanceof ScoreColourScheme) - { - ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold()); - } - } + tp.fitToWindow.setState(tree.getFitToWindow()); + tp.fitToWindow_actionPerformed(null); - af.viewport.setGlobalColourScheme(cs); + 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())); - af.viewport.setColourAppliesToAllGroups(false); - af.changeColour(af.viewport.getGlobalColourScheme()); - af.viewport.setColourAppliesToAllGroups(true); + tp.showPlaceholders(tree.getMarkUnlinked()); + tp.showBootstrap(tree.getShowBootstrap()); + tp.showDistances(tree.getShowDistances()); - System.out.println(view.getShowSequenceFeatures()); + tp.treeCanvas.threshold = tree.getThreshold(); - if (view.getShowSequenceFeatures()) - { - ; - } + if (tree.getCurrentTree()) + af.viewport.setCurrentTree(tp.getTree()); + } - { - SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, - af.alignPanel); - } + } + catch (Exception ex) + { + ex.printStackTrace(); + } - //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE - if (object.getVamsasModel().getTreeCount() > 0) - { - try - { - af.ShowNewickTree(new jalview.io.NewickFile( - (String) object.getVamsasModel().getTree(0)), "Tree"); - } - catch (Exception ex) - { - ex.printStackTrace(); - } + } + + return af; } - } }