X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=5a4b03a0fea1e94adb5932ac33649b2d988f64e2;hb=b2319fcc38be5c500ed7cafc014cf9da96a4ce98;hp=44ff2ad943e9f19309353e4ef169091faa69c293;hpb=1ee8b306b296ea2724e128f66486675bdaac7a3d;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 44ff2ad..5a4b03a 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -18,21 +18,27 @@ */ package jalview.gui; -import jalview.binding.*; - -import jalview.io.*; import jalview.schemes.*; +import 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.*; + + + /** * DOCUMENT ME! @@ -43,7 +49,7 @@ import javax.swing.*; public class Jalview2XML { // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE - public static void SaveState(File statefile) + public void SaveState(File statefile) { long creation = System.currentTimeMillis(); JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -115,7 +121,7 @@ public class Jalview2XML } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public static void SaveAlignment(AlignFrame af, String jarFile, + public void SaveAlignment(AlignFrame af, String jarFile, String fileName) { try @@ -134,6 +140,7 @@ public class Jalview2XML } catch (Exception ex) { + ex.printStackTrace(); } } @@ -146,7 +153,7 @@ public class Jalview2XML * @param jout DOCUMENT ME! * @param out DOCUMENT ME! */ - public static void SaveState(AlignFrame af, long timeStamp, + public void SaveState(AlignFrame af, long timeStamp, String fileName, JarOutputStream jout, PrintWriter out) { Vector seqids = new Vector(); @@ -155,7 +162,7 @@ public class Jalview2XML AlignViewport av = af.viewport; JalviewModel object = new JalviewModel(); - object.setVamsasModel(new VamsasModel()); + object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); object.setCreationDate(new java.util.Date(timeStamp)); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); @@ -181,6 +188,7 @@ public class Jalview2XML vamsasSeq.setId(id + ""); vamsasSeq.setName(jal.getSequenceAt(i).getName()); vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); + vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription()); jseq = new JSeq(); jseq.setStart(jal.getSequenceAt(i).getStart()); @@ -190,6 +198,58 @@ public class Jalview2XML jseq.setId(id); + if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null) + { + jalview.datamodel.SequenceFeature[] sf + = jal.getSequenceAt(i).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.setStatus(sf[index].getStatus()); + features.setType(sf[index].getType()); + features.setFeatureGroup(sf[index].getFeatureGroup()); + jseq.addFeatures(features); + index ++; + } + } + + 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++; @@ -199,38 +259,45 @@ public class Jalview2XML /////////////////////////////////// if (af.viewport.currentTree != null) { - // FIND ANY ASSOCIATED TREES + // 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 (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.setFontSize(tp.treeCanvas.fontSize); - 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); - } + 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 @@ -249,7 +316,14 @@ public class Jalview2XML Annotation an = new Annotation(); an.setDescription(aa[i].description); - an.setGraph(aa[i].isGraph); + if(aa[i].graph>0) + { + an.setGraph(true); + an.setGraphType(aa[i].graph); + } + else + an.setGraph(false); + an.setLabel(aa[i].label); AnnotationElement ae; @@ -289,30 +363,36 @@ public class Jalview2XML groups[i].setStart(sg.getStartRes()); groups[i].setEnd(sg.getEndRes()); groups[i].setName(sg.getName()); - - if (sg.cs instanceof ConservationColourScheme) - { - groups[i].setConsThreshold(((ConservationColourScheme) sg.cs).inc); - } - - if (sg.cs instanceof ResidueColourScheme) + if(sg.cs!=null) { - groups[i].setPidThreshold(((ResidueColourScheme) sg.cs).getThreshold()); - } - else if (sg.cs instanceof ScoreColourScheme) - { - groups[i].setPidThreshold(((ScoreColourScheme) sg.cs).getThreshold()); - } + if (sg.cs.conservationApplied()) + { + groups[i].setConsThreshold(sg.cs.getConservationInc()); - if (sg.cs instanceof jalview.schemes.UserColourScheme) - { + 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 - { + jms)); + } + else + { groups[i].setColour(ColourSchemeProperty.getColourName( - sg.cs)); + sg.cs)); + } + + groups[i].setPidThreshold(sg.cs.getThreshold()); } groups[i].setOutlineColour(sg.getOutlineColour().getRGB()); @@ -331,6 +411,7 @@ public class Jalview2XML jms.setJGroup(groups); } + ///////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(af.getTitle()); @@ -354,23 +435,24 @@ public class Jalview2XML ColourSchemeI cs = av.getGlobalColourScheme(); - if (cs instanceof ConservationColourScheme) - { - view.setConsThreshold(((ConservationColourScheme) cs).inc); - } - - if (cs instanceof ResidueColourScheme) - { - view.setPidThreshold(((ResidueColourScheme) cs).getThreshold()); - } - else if (cs instanceof ScoreColourScheme) + if(cs!=null) { - view.setPidThreshold(((ScoreColourScheme) cs).getThreshold()); + 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.getFontName()); + view.setFontName(av.font.getName()); view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); view.setRenderGaps(av.renderGaps); @@ -378,15 +460,42 @@ public class Jalview2XML view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowConservation(av.showConservation); - view.setShowFullId(av.getShowFullId()); + 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(av.featuresDisplayed!=null) + { + jalview.schemabinding.version2.FeatureSettings fs + = new jalview.schemabinding.version2.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( + av.featuresDisplayed.containsKey(type) + ); + + fs.addSetting(setting); + + } + jms.setFeatureSettings(fs); + + } + jms.addViewport(view); + object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); @@ -408,7 +517,7 @@ public class Jalview2XML } } - static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, + String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, Vector userColours, JalviewModelSequence jms) { String id = null; @@ -419,12 +528,12 @@ public class Jalview2XML 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(); + 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.binding.Colour col = new jalview.binding.Colour(); + jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setRGB(jalview.util.Format.getHexString(colours[i])); jbucs.addColour(col); } @@ -438,7 +547,7 @@ public class Jalview2XML return id; } - static jalview.schemes.UserColourScheme GetUserColourScheme( + jalview.schemes.UserColourScheme GetUserColourScheme( JalviewModelSequence jms, String id) { UserColours[] uc = jms.getUserColours(); @@ -471,9 +580,9 @@ public class Jalview2XML * * @param file DOCUMENT ME! */ - public static AlignFrame LoadJalviewAlign(String file) + public AlignFrame LoadJalviewAlign(String file) { - JalviewModel object = new JalviewModel(); + jalview.gui.AlignFrame af = null; try @@ -504,25 +613,61 @@ public class Jalview2XML for (int i = 0; i < entryCount; i++) { jarentry = jin.getNextJarEntry(); - } + + } + + + class NoDescIDResolver implements IDResolver + { + public Object resolve(String idref) + { + System.out.println(idref+" used"); + return null; + } + } + if (jarentry != null) { InputStreamReader in = new InputStreamReader(jin, "UTF-8"); - object = (JalviewModel) object.unmarshal(in); + JalviewModel object = new JalviewModel(); + + Unmarshaller unmar = new Unmarshaller(object); + object = (JalviewModel) unmar.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) { + //Is Version 1 Jar file? + af = new Jalview2XML_V1().LoadJalviewAlign(file); + + if(af!=null) + { + System.out.println("Successfuly loaded archive file"); + return af; + } + ex.printStackTrace(); System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); JOptionPane.showInternalMessageDialog(Desktop.desktop, - "Couldn't locate " + file, - "URL not found", + "Error loading " + file, + "Error loading Jalview file", JOptionPane.WARNING_MESSAGE); } @@ -530,7 +675,7 @@ public class Jalview2XML return af; } - static AlignFrame LoadFromObject(JalviewModel object) + AlignFrame LoadFromObject(JalviewModel object) { Vector seqids = new Vector(); SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); @@ -542,11 +687,11 @@ public class Jalview2XML //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].setDescription( vamsasSeq[i].getDescription() ); jseqs[i].setStart(JSEQ[i].getStart()); jseqs[i].setEnd(JSEQ[i].getEnd()); @@ -554,10 +699,44 @@ public class Jalview2XML seqids.add(jseqs[i]); } + ///SequenceFeatures are added to the DatasetSequence, + // so we must create the dataset before loading features ///////////////////////////////// jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); - + al.setDataset(null); ///////////////////////////////// + + for (int i = 0; i < vamsasSeq.length; i++) + { + if (JSEQ[i].getFeaturesCount() > 0) + { + Features[] features = JSEQ[i].getFeatures(); + for (int f = 0; f < features.length; f++) + { + jalview.datamodel.SequenceFeature sf + = new jalview.datamodel.SequenceFeature(features[f].getType(), + features[f].getDescription(), features[f].getStatus(), + features[f].getBegin(), features[f].getEnd(), + features[f].getFeatureGroup()); + + 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) @@ -582,7 +761,8 @@ public class Jalview2XML if (an[i].getGraph()) { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, 0, 0, 1); + an[i].getDescription(), anot, 0, 0, + an[i].getGraphType()); } else { @@ -594,6 +774,7 @@ public class Jalview2XML } } + ///////////////////////////////// // LOAD VIEWPORT Viewport[] views = jms.getViewport(); @@ -601,6 +782,7 @@ public class Jalview2XML AlignFrame af = new AlignFrame(al); + // af.changeColour() ); ///////////////////////// //LOAD GROUPS @@ -624,14 +806,7 @@ public class Jalview2XML groups[i].getColour()); } - if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold()); - } - else if (cs instanceof ScoreColourScheme) - { - ((ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold()); - } + cs.setThreshold(groups[i].getPidThreshold(), true); } Vector seqs = new Vector(); @@ -658,20 +833,20 @@ public class Jalview2XML sg.getWidth() - 1); c.calculate(); c.verdict(false, 25); - cs = new ConservationColourScheme(c, cs); - sg.cs = cs; + sg.cs.setConservation(c); } al.addGroup(sg); } } - 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.setShowAnnotation(view.getShowAnnotation()); af.viewport.showConservation = view.getShowConservation(); af.viewport.showQuality = view.getShowQuality(); af.viewport.showIdentity = view.getShowIdentity(); @@ -682,8 +857,8 @@ public class Jalview2XML af.viewport.setConservationSelected(view.getConservationSelected()); af.conservationMenuItem.setSelected(view.getConservationSelected()); - af.viewport.setShowFullId(view.getShowFullId()); - af.fullSeqId.setSelected(view.getShowFullId()); + af.viewport.setShowJVSuffix(view.getShowFullId()); + af.seqLimits.setSelected(view.getShowFullId()); af.viewport.setFont(new java.awt.Font(view.getFontName(), view.getFontStyle(), view.getFontSize())); @@ -724,35 +899,54 @@ public class Jalview2XML cs = ColourSchemeProperty.getColour(al, view.getBgColour()); } - if (cs instanceof ConservationColourScheme) + if(cs!=null) { - ((ConservationColourScheme) cs).inc = view.getConsThreshold(); - } - - if (cs instanceof ResidueColourScheme) - { - ((ResidueColourScheme) cs).setThreshold(view.getPidThreshold()); - } - else if (cs instanceof ScoreColourScheme) - { - ((ScoreColourScheme) cs).setThreshold(view.getPidThreshold()); + cs.setThreshold(view.getPidThreshold(), true); + cs.setConsensus(af.viewport.vconsensus); } } + af.setColourSelected(view.getBgColour()); af.viewport.setGlobalColourScheme(cs); - af.viewport.setColourAppliesToAllGroups(false); - af.changeColour(af.viewport.getGlobalColourScheme()); + af.changeColour(cs); + if (view.getConservationSelected() && cs!=null) + { + cs.setConservationInc(view.getConsThreshold()); + } + af.viewport.setColourAppliesToAllGroups(true); if (view.getShowSequenceFeatures()) { - af.viewport.showSequenceFeatures = true; - af.sequenceFeatures.setSelected(true); - new SequenceFeatureFetcher(al, af.alignPanel); - al.featuresAdded = true; + af.viewport.showSequenceFeatures = true; + af.showSeqFeatures.setSelected(true); } + if(jms.getFeatureSettings()!=null) + { + af.viewport.featuresDisplayed = new Hashtable(); + String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()]; + for(int fs=0; fs 0) @@ -761,35 +955,45 @@ public class Jalview2XML { 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()); - - tp.setBounds(tree.getXpos(), tree.getYpos(), - tree.getWidth(), tree.getHeight()); + tree.getNewick()), tree.getTitle(), + tree.getWidth(), tree.getHeight(), + tree.getXpos(), tree.getYpos()); tp.fitToWindow.setState(tree.getFitToWindow()); tp.fitToWindow_actionPerformed(null); - tp.treeCanvas.fontSize = tree.getFontSize(); - tp.fontSize.setText("Font Size - " + tree.getFontSize()); - tp.placeholdersMenu.setState(tree.getMarkUnlinked()); - tp.placeholdersMenu_actionPerformed(null); - tp.bootstrapMenu.setState(tree.getShowBootstrap()); - tp.bootstrapMenu_actionPerformed(null); - tp.distanceMenu.setState(tree.getShowDistances()); - tp.distanceMenu_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; } } +