-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-\r
-import jalview.schemes.*;\r
-\r
-import jalview.gui.*;\r
-\r
-import java.io.*;\r
-\r
-import java.net.*;\r
-\r
-import java.util.*;\r
-\r
-import java.util.jar.*;\r
-\r
-import javax.swing.*;\r
-\r
-import org.exolab.castor.xml.*;\r
-\r
-import jalview.schemabinding.version2.*;\r
-\r
-\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class Jalview2XML\r
-{\r
- // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
- public void SaveState(File statefile)\r
- {\r
- long creation = System.currentTimeMillis();\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
-\r
- if (frames == null)\r
- {\r
- return;\r
- }\r
-\r
- try\r
- {\r
- FileOutputStream fos = new FileOutputStream(statefile);\r
- JarOutputStream jout = new JarOutputStream(fos);\r
-\r
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
- ////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
- "UTF-8"));\r
-\r
- Vector shortNames = new Vector();\r
-\r
- //REVERSE ORDER\r
- for (int i = frames.length - 1; i > -1; i--)\r
- {\r
- if (frames[i] instanceof AlignFrame)\r
- {\r
- AlignFrame af = (AlignFrame) frames[i];\r
-\r
- String shortName = af.getTitle();\r
-\r
- if (shortName.indexOf(File.separatorChar) > -1)\r
- {\r
- shortName = shortName.substring(shortName.lastIndexOf(\r
- File.separatorChar) + 1);\r
- }\r
-\r
- int count = 1;\r
-\r
- while (shortNames.contains(shortName))\r
- {\r
- if (shortName.endsWith("_" + (count - 1)))\r
- {\r
- shortName = shortName.substring(0,\r
- shortName.lastIndexOf("_"));\r
- }\r
-\r
- shortName = shortName.concat("_" + count);\r
- count++;\r
- }\r
-\r
- shortNames.addElement(shortName);\r
-\r
- if (!shortName.endsWith(".xml"))\r
- {\r
- shortName = shortName + ".xml";\r
- }\r
-\r
- SaveState(af, creation, shortName, jout, out);\r
- }\r
- }\r
-\r
- out.close();\r
- jout.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
- public void SaveAlignment(AlignFrame af, String jarFile,\r
- String fileName)\r
- {\r
- try\r
- {\r
- FileOutputStream fos = new FileOutputStream(jarFile);\r
- JarOutputStream jout = new JarOutputStream(fos);\r
-\r
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
- ////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
- "UTF-8"));\r
-\r
- SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
- out.close();\r
- jout.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param af DOCUMENT ME!\r
- * @param timeStamp DOCUMENT ME!\r
- * @param fileName DOCUMENT ME!\r
- * @param jout DOCUMENT ME!\r
- * @param out DOCUMENT ME!\r
- */\r
- public void SaveState(AlignFrame af, long timeStamp,\r
- String fileName, JarOutputStream jout, PrintWriter out)\r
- {\r
- Vector seqids = new Vector();\r
- Vector userColours = new Vector();\r
-\r
- AlignViewport av = af.viewport;\r
-\r
- JalviewModel object = new JalviewModel();\r
- object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
-\r
- object.setCreationDate(new java.util.Date(timeStamp));\r
- object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
-\r
- jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
-\r
- SequenceSet vamsasSet = new SequenceSet();\r
- Sequence vamsasSeq;\r
- JalviewModelSequence jms = new JalviewModelSequence();\r
-\r
- vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
-\r
- JSeq jseq;\r
-\r
- //SAVE SEQUENCES\r
- int id = 0;\r
-\r
- for (int i = 0; i < jal.getHeight(); i++)\r
- {\r
- seqids.add(jal.getSequenceAt(i));\r
-\r
- vamsasSeq = new Sequence();\r
- vamsasSeq.setId(id + "");\r
- vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
- vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
- vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
-\r
- jseq = new JSeq();\r
- jseq.setStart(jal.getSequenceAt(i).getStart());\r
- jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
-\r
- jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
-\r
- jseq.setId(id);\r
-\r
- if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
- {\r
- jalview.datamodel.SequenceFeature[] sf\r
- = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
- int index = 0;\r
- while(index < sf.length)\r
- {\r
- Features features = new Features();\r
-\r
- features.setBegin(sf[index].getBegin());\r
- features.setEnd(sf[index].getEnd());\r
- features.setDescription(sf[index].getDescription());\r
- features.setType(sf[index].getType());\r
- features.setFeatureGroup(sf[index].getFeatureGroup());\r
- jseq.addFeatures(features);\r
- index ++;\r
- }\r
- }\r
-\r
- if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
- {\r
- Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
- while(en.hasMoreElements())\r
- {\r
- Pdbids pdb = new Pdbids();\r
- jalview.datamodel.PDBEntry entry\r
- = (jalview.datamodel.PDBEntry)en.nextElement();\r
-\r
- pdb.setId(entry.getId());\r
- pdb.setType(entry.getType());\r
-\r
- if(entry.getProperty()!=null)\r
- {\r
- PdbentryItem item = new PdbentryItem();\r
- Hashtable properties = entry.getProperty();\r
- Enumeration en2 = properties.keys();\r
- while(en2.hasMoreElements())\r
- {\r
- Property prop = new Property();\r
- String key = en2.nextElement().toString();\r
- prop.setName(key);\r
- prop.setValue( properties.get(key).toString() );\r
- item.addProperty(prop);\r
- }\r
- pdb.addPdbentryItem(item);\r
- }\r
-\r
- jseq.addPdbids(pdb);\r
- }\r
- }\r
-\r
- jms.addJSeq(jseq);\r
- vamsasSet.addSequence(vamsasSeq);\r
- id++;\r
- }\r
-\r
- //SAVE TREES\r
- ///////////////////////////////////\r
- if (af.viewport.currentTree != null)\r
- {\r
- // FIND ANY ASSOCIATED TREES\r
- // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
- if (Desktop.desktop != null)\r
- {\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
-\r
- for (int t = 0; t < frames.length; t++)\r
- {\r
- if (frames[t] instanceof TreePanel)\r
- {\r
- TreePanel tp = (TreePanel) frames[t];\r
-\r
- if (tp.treeCanvas.av.alignment == jal)\r
- {\r
- Tree tree = new Tree();\r
- tree.setTitle(tp.getTitle());\r
- tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
- tree.setNewick(tp.getTree().toString());\r
- tree.setThreshold(tp.treeCanvas.threshold);\r
-\r
- tree.setFitToWindow(tp.fitToWindow.getState());\r
- tree.setFontName(tp.getTreeFont().getName());\r
- tree.setFontSize(tp.getTreeFont().getSize());\r
- tree.setFontStyle(tp.getTreeFont().getStyle());\r
- tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
-\r
- tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
- tree.setShowDistances(tp.distanceMenu.getState());\r
-\r
- tree.setHeight(tp.getHeight());\r
- tree.setWidth(tp.getWidth());\r
- tree.setXpos(tp.getX());\r
- tree.setYpos(tp.getY());\r
-\r
- jms.addTree(tree);\r
- }\r
- }\r
- }\r
- }\r
- }\r
-\r
- //SAVE ANNOTATIONS\r
- if (jal.getAlignmentAnnotation() != null)\r
- {\r
- jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
-\r
- for (int i = 0; i < aa.length; i++)\r
- {\r
- Annotation an = new Annotation();\r
-\r
- if (aa[i].label.equals("Quality") ||\r
- aa[i].label.equals("Conservation") ||\r
- aa[i].label.equals("Consensus"))\r
- {\r
- an.setLabel(aa[i].label);\r
- an.setGraph(true);\r
- vamsasSet.addAnnotation(an);\r
- continue;\r
- }\r
-\r
-\r
- an.setDescription(aa[i].description);\r
-\r
- if(aa[i].sequenceRef!=null)\r
- {\r
- an.setSequenceRef(aa[i].sequenceRef.getName());\r
- }\r
-\r
- if(aa[i].graph>0)\r
- {\r
- an.setGraph(true);\r
- an.setGraphType(aa[i].graph);\r
- an.setGraphGroup(aa[i].graphGroup);\r
- if(aa[i].getThreshold()!=null)\r
- {\r
- ThresholdLine line = new ThresholdLine();\r
- line.setLabel(aa[i].getThreshold().label);\r
- line.setValue(aa[i].getThreshold().value);\r
- line.setColour(aa[i].getThreshold().colour.getRGB());\r
- an.setThresholdLine(line);\r
- }\r
- }\r
- else\r
- an.setGraph(false);\r
-\r
- an.setLabel(aa[i].label);\r
-\r
- AnnotationElement ae;\r
-\r
- for (int a = 0; a < aa[i].annotations.length; a++)\r
- {\r
- if ((aa[i] == null) || (aa[i].annotations[a] == null))\r
- {\r
- continue;\r
- }\r
-\r
- ae = new AnnotationElement();\r
- ae.setDescription(aa[i].annotations[a].description);\r
- ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);\r
- ae.setValue(aa[i].annotations[a].value);\r
- ae.setPosition(a);\r
- ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +\r
- "");\r
-\r
- if(aa[i].annotations[a].colour!=java.awt.Color.black)\r
- ae.setColour(aa[i].annotations[a].colour.getRGB());\r
-\r
- an.addAnnotationElement(ae);\r
- }\r
-\r
- vamsasSet.addAnnotation(an);\r
- }\r
- }\r
-\r
- //SAVE GROUPS\r
- if (jal.getGroups() != null)\r
- {\r
- JGroup[] groups = new JGroup[jal.getGroups().size()];\r
-\r
- for (int i = 0; i < groups.length; i++)\r
- {\r
- groups[i] = new JGroup();\r
-\r
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
- .elementAt(i);\r
- groups[i].setStart(sg.getStartRes());\r
- groups[i].setEnd(sg.getEndRes());\r
- groups[i].setName(sg.getName());\r
- if(sg.cs!=null)\r
- {\r
- if (sg.cs.conservationApplied())\r
- {\r
- groups[i].setConsThreshold(sg.cs.getConservationInc());\r
-\r
- if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
- {\r
- groups[i].setColour(SetUserColourScheme(sg.cs,\r
- userColours,\r
- jms));\r
- }\r
- else\r
- {\r
- groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
- cs));\r
- }\r
- }\r
- else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
- {\r
- groups[i].setColour(\r
- ColourSchemeProperty.getColourName(\r
- ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
- }\r
- else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
- {\r
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
- jms));\r
- }\r
- else\r
- {\r
- groups[i].setColour(ColourSchemeProperty.getColourName(\r
- sg.cs));\r
- }\r
-\r
- groups[i].setPidThreshold(sg.cs.getThreshold());\r
- }\r
-\r
- groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
- groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
- groups[i].setDisplayText(sg.getDisplayText());\r
- groups[i].setColourText(sg.getColourText());\r
-\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
- int index = seqids.indexOf(seq);\r
- groups[i].addSeq(index);\r
- }\r
- }\r
-\r
- jms.setJGroup(groups);\r
- }\r
-\r
-\r
- ///////////SAVE VIEWPORT\r
- Viewport view = new Viewport();\r
- view.setTitle(af.getTitle());\r
- view.setXpos(af.getX());\r
- view.setYpos(af.getY());\r
- view.setWidth(af.getWidth());\r
- view.setHeight(af.getHeight());\r
- view.setStartRes(av.startRes);\r
- view.setStartSeq(av.startSeq);\r
-\r
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
- {\r
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
- userColours, jms));\r
- }\r
- else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
- {\r
- jalview.schemes.AnnotationColourGradient acg\r
- = (jalview.schemes.AnnotationColourGradient)av.getGlobalColourScheme();\r
-\r
- AnnotationColours ac = new AnnotationColours();\r
- ac.setAboveThreshold(acg.getAboveThreshold());\r
- ac.setThreshold(acg.getAnnotationThreshold());\r
- ac.setAnnotation(acg.getAnnotation());\r
- if(acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)\r
- ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),\r
- userColours, jms));\r
- else\r
- ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));\r
-\r
- ac.setMaxColour(acg.getMaxColour().getRGB());\r
- ac.setMinColour(acg.getMinColour().getRGB());\r
- view.setAnnotationColours(ac);\r
- view.setBgColour("AnnotationColourGradient");\r
- }\r
- else\r
- {\r
- view.setBgColour(ColourSchemeProperty.getColourName(\r
- av.getGlobalColourScheme()));\r
- }\r
-\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
-\r
- if(cs!=null)\r
- {\r
- if (cs.conservationApplied())\r
- {\r
- view.setConsThreshold(cs.getConservationInc());\r
- if (cs instanceof jalview.schemes.UserColourScheme)\r
- view.setBgColour(SetUserColourScheme(cs, userColours, jms));\r
- }\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- view.setPidThreshold(cs.getThreshold());\r
- }\r
- }\r
-\r
- view.setConservationSelected(av.getConservationSelected());\r
- view.setPidSelected(av.getAbovePIDThreshold());\r
- view.setFontName(av.font.getName());\r
- view.setFontSize(av.font.getSize());\r
- view.setFontStyle(av.font.getStyle());\r
- view.setRenderGaps(av.renderGaps);\r
- view.setShowAnnotation(av.getShowAnnotation());\r
- view.setShowBoxes(av.getShowBoxes());\r
- view.setShowColourText(av.getColourText());\r
- view.setShowConservation(av.showConservation);\r
- view.setShowFullId(av.getShowJVSuffix());\r
- view.setShowIdentity(av.showIdentity);\r
- view.setShowQuality(av.showQuality);\r
- view.setShowSequenceFeatures(av.showSequenceFeatures);\r
- view.setShowText(av.getShowText());\r
- view.setWrapAlignment(av.getWrapAlignment());\r
-\r
- if(av.featuresDisplayed!=null)\r
- {\r
- jalview.schemabinding.version2.FeatureSettings fs\r
- = new jalview.schemabinding.version2.FeatureSettings();\r
-\r
- String [] renderOrder =\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
- for(int ro=0; ro<renderOrder.length; ro++)\r
- {\r
- Setting setting = new Setting();\r
- setting.setType(renderOrder[ro]);\r
- setting.setColour(\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
- );\r
-\r
- setting.setDisplay(\r
- av.featuresDisplayed.containsKey(renderOrder[ro])\r
- );\r
-\r
- fs.addSetting(setting);\r
-\r
- }\r
- jms.setFeatureSettings(fs);\r
-\r
- }\r
-\r
- jms.addViewport(view);\r
-\r
-\r
- object.setJalviewModelSequence(jms);\r
- object.getVamsasModel().addSequenceSet(vamsasSet);\r
-\r
- try\r
- {\r
- if (!fileName.endsWith(".xml"))\r
- {\r
- fileName = fileName + ".xml";\r
- }\r
-\r
- JarEntry entry = new JarEntry(fileName);\r
- jout.putNextEntry(entry);\r
-\r
- object.marshal(out);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
- Vector userColours, JalviewModelSequence jms)\r
- {\r
- String id = null;\r
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
-\r
- if (!userColours.contains(ucs))\r
- {\r
- userColours.add(ucs);\r
-\r
- java.awt.Color[] colours = ucs.getColours();\r
- jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
- jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
-\r
- for (int i = 0; i < colours.length; i++)\r
- {\r
- jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour();\r
- col.setRGB(jalview.util.Format.getHexString(colours[i]));\r
- jbucs.addColour(col);\r
- }\r
-\r
- id = "ucs" + userColours.indexOf(ucs);\r
- uc.setId(id);\r
- uc.setUserColourScheme(jbucs);\r
- jms.addUserColours(uc);\r
- }\r
-\r
- return id;\r
- }\r
-\r
- jalview.schemes.UserColourScheme GetUserColourScheme(\r
- JalviewModelSequence jms, String id)\r
- {\r
- UserColours[] uc = jms.getUserColours();\r
- UserColours colours = null;\r
-\r
- for (int i = 0; i < uc.length; i++)\r
- {\r
- if (uc[i].getId().equals(id))\r
- {\r
- colours = uc[i];\r
-\r
- break;\r
- }\r
- }\r
-\r
- int csize = colours.getUserColourScheme().getColourCount();\r
- java.awt.Color[] newColours = new java.awt.Color[csize];\r
-\r
- for (int i = 0; i < csize; i++)\r
- {\r
- newColours[i] = new java.awt.Color(Integer.parseInt(\r
- colours.getUserColourScheme().getColour(i).getRGB(), 16));\r
- }\r
-\r
- return new jalview.schemes.UserColourScheme(newColours);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param file DOCUMENT ME!\r
- */\r
- public AlignFrame LoadJalviewAlign(String file)\r
- {\r
-\r
- jalview.gui.AlignFrame af = null;\r
-\r
- try\r
- {\r
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
- URL url = null;\r
-\r
- if (file.startsWith("http://"))\r
- {\r
- url = new URL(file);\r
- }\r
-\r
- JarInputStream jin = null;\r
- JarEntry jarentry = null;\r
- int entryCount = 1;\r
-\r
- do\r
- {\r
- if (url != null)\r
- {\r
- jin = new JarInputStream(url.openStream());\r
- }\r
- else\r
- {\r
- jin = new JarInputStream(new FileInputStream(file));\r
- }\r
-\r
- for (int i = 0; i < entryCount; i++)\r
- {\r
- jarentry = jin.getNextJarEntry();\r
-\r
- }\r
-\r
-\r
- class NoDescIDResolver implements IDResolver\r
- {\r
- public Object resolve(String idref)\r
- {\r
- System.out.println(idref+" used");\r
- return null;\r
- }\r
- }\r
-\r
-\r
- if (jarentry != null)\r
- {\r
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
- JalviewModel object = new JalviewModel();\r
-\r
- Unmarshaller unmar = new Unmarshaller(object);\r
- unmar.setValidation(false);\r
- object = (JalviewModel) unmar.unmarshal( in );\r
-\r
- af = LoadFromObject(object);\r
- entryCount++;\r
- }\r
- }\r
- while (jarentry != null);\r
- }\r
- catch(java.net.UnknownHostException ex)\r
- {\r
- ex.printStackTrace();\r
- System.err.println("Couldn't locate Jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Couldn't locate " + file,\r
- "URL not found",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- //Is Version 1 Jar file?\r
- af = new Jalview2XML_V1().LoadJalviewAlign(file);\r
-\r
- if(af!=null)\r
- {\r
- System.out.println("Successfully loaded archive file");\r
- return af;\r
- }\r
- ex.printStackTrace();\r
- System.err.println("Exception whilst loading jalview XML file : " +\r
- ex + "\n");\r
- JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
- "Error loading " + file,\r
- "Error loading Jalview file",\r
- JOptionPane.WARNING_MESSAGE);\r
-\r
- }\r
-\r
- return af;\r
- }\r
-\r
- AlignFrame LoadFromObject(JalviewModel object)\r
- {\r
- Vector seqids = new Vector();\r
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
- Sequence[] vamsasSeq = vamsasSet.getSequence();\r
-\r
- JalviewModelSequence jms = object.getJalviewModelSequence();\r
-\r
- //////////////////////////////////\r
- //LOAD SEQUENCES\r
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
- for (int i = 0; i < vamsasSeq.length; i++)\r
- {\r
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
- vamsasSeq[i].getSequence());\r
- jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
-\r
- jseqs[i].setStart(JSEQ[i].getStart());\r
- jseqs[i].setEnd(JSEQ[i].getEnd());\r
- jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
- seqids.add(jseqs[i]);\r
- }\r
-\r
- ///SequenceFeatures are added to the DatasetSequence,\r
- // so we must create the dataset before loading features\r
- /////////////////////////////////\r
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
- al.setDataset(null);\r
- /////////////////////////////////\r
-\r
- for (int i = 0; i < vamsasSeq.length; i++)\r
- {\r
- if (JSEQ[i].getFeaturesCount() > 0)\r
- {\r
- Features[] features = JSEQ[i].getFeatures();\r
- for (int f = 0; f < features.length; f++)\r
- {\r
- jalview.datamodel.SequenceFeature sf\r
- = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
- features[f].getDescription(), features[f].getStatus(),\r
- features[f].getBegin(), features[f].getEnd(),\r
- features[f].getFeatureGroup());\r
-\r
- al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
- }\r
- }\r
- if (JSEQ[i].getPdbidsCount() > 0)\r
- {\r
- Pdbids[] ids = JSEQ[i].getPdbids();\r
- for (int p = 0; p < ids.length; p++)\r
- {\r
- jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
- entry.setId(ids[p].getId());\r
- entry.setType(ids[p].getType());\r
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
- }\r
-\r
- }\r
- }\r
-\r
-\r
- /////////////////////////////////\r
- //////////////////////////////////\r
- //LOAD ANNOTATIONS\r
- boolean hideQuality = true,\r
- hideConservation = true,\r
- hideConsensus = true;\r
-\r
- if (vamsasSet.getAnnotation() != null)\r
- {\r
- Annotation[] an = vamsasSet.getAnnotation();\r
-\r
- for (int i = 0; i < an.length; i++)\r
- {\r
- if (an[i].getLabel().equals("Quality"))\r
- {\r
- hideQuality = false;\r
- continue;\r
- }\r
- else if(an[i].getLabel().equals("Conservation"))\r
- {\r
- hideConservation = false;\r
- continue;\r
- }\r
- else if(an[i].getLabel().equals("Consensus"))\r
- {\r
- hideConsensus = false;\r
- continue;\r
- }\r
-\r
- AnnotationElement[] ae = an[i].getAnnotationElement();\r
- jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];\r
-\r
- for (int aa = 0; aa < ae.length; aa++)\r
- {\r
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),\r
- ae[aa].getDescription(),\r
- ae[aa].getSecondaryStructure().length()==0?' ':ae[aa].getSecondaryStructure().charAt(0),\r
- ae[aa].getValue());\r
- anot[ae[aa].getPosition()].colour = new java.awt.Color( ae[aa].getColour() );\r
- }\r
-\r
- jalview.datamodel.AlignmentAnnotation jaa = null;\r
-\r
- if (an[i].getGraph())\r
- {\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot, 0, 0,\r
- an[i].getGraphType());\r
-\r
- jaa.graphGroup = an[i].getGraphGroup();\r
-\r
- if (an[i].getThresholdLine() != null)\r
- {\r
- jaa.setThreshold(new jalview.datamodel.GraphLine(\r
- an[i].getThresholdLine().getValue(),\r
- an[i].getThresholdLine().getLabel(),\r
- new java.awt.Color(an[i].getThresholdLine().getColour()))\r
- );\r
-\r
- }\r
-\r
- }\r
- else\r
- {\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot);\r
- }\r
-\r
- if(an[i].getSequenceRef()!=null)\r
- {\r
- jaa.createSequenceMapping(\r
- al.findName(an[i].getSequenceRef()), 1\r
- );\r
- al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);\r
- }\r
-\r
- al.addAnnotation(jaa);\r
- }\r
- }\r
-\r
-\r
- // af.changeColour() );\r
- /////////////////////////\r
- //LOAD GROUPS\r
- if (jms.getJGroupCount() > 0)\r
- {\r
- JGroup[] groups = jms.getJGroup();\r
-\r
- for (int i = 0; i < groups.length; i++)\r
- {\r
- ColourSchemeI cs = null;\r
-\r
- if (groups[i].getColour() != null)\r
- {\r
- if (groups[i].getColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, groups[i].getColour());\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al,\r
- groups[i].getColour());\r
- }\r
-\r
- if(cs!=null)\r
- cs.setThreshold(groups[i].getPidThreshold(), true);\r
- }\r
-\r
- Vector seqs = new Vector();\r
- int[] ids = groups[i].getSeq();\r
-\r
- for (int s = 0; s < ids.length; s++)\r
- {\r
- seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
- ids[s]));\r
- }\r
-\r
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
- groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
- groups[i].getDisplayText(), groups[i].getColourText(),\r
- groups[i].getStart(), groups[i].getEnd());\r
-\r
- sg.setOutlineColour(new java.awt.Color(\r
- groups[i].getOutlineColour()));\r
-\r
- if (groups[i].getConsThreshold() != 0)\r
- {\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
- ResidueProperties.propHash, 3, sg.sequences, 0,\r
- sg.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, 25);\r
- sg.cs.setConservation(c);\r
- }\r
-\r
- al.addGroup(sg);\r
- }\r
- }\r
-\r
-\r
- /////////////////////////////////\r
- // LOAD VIEWPORT\r
- Viewport[] views = jms.getViewport();\r
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
-\r
- AlignFrame af = new AlignFrame(al);\r
- if(hideConsensus || hideQuality || hideConservation)\r
- {\r
- int hSize = al.getAlignmentAnnotation().length;\r
- for (int h = 0; h < hSize; h++)\r
- {\r
- if (\r
- (hideConsensus &&\r
- al.getAlignmentAnnotation()[h].label.equals("Consensus"))\r
- ||\r
- (hideQuality &&\r
- al.getAlignmentAnnotation()[h].label.equals("Quality"))\r
- ||\r
- (hideConservation &&\r
- al.getAlignmentAnnotation()[h].label.equals("Conservation")))\r
- {\r
- al.deleteAnnotation(al.getAlignmentAnnotation()[h]);\r
- hSize--;\r
- h--;\r
- }\r
- }\r
- af.alignPanel.adjustAnnotationHeight();\r
- }\r
-\r
- af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
- view.getHeight());\r
- af.viewport.setStartRes(view.getStartRes());\r
- af.viewport.setStartSeq(view.getStartSeq());\r
- af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.viewport.showConservation = view.getShowConservation();\r
- af.viewport.showQuality = view.getShowQuality();\r
- af.viewport.showIdentity = view.getShowIdentity();\r
- af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
- af.abovePIDThreshold.setSelected(view.getPidSelected());\r
- af.viewport.setColourText(view.getShowColourText());\r
- af.colourTextMenuItem.setSelected(view.getShowColourText());\r
- af.viewport.setConservationSelected(view.getConservationSelected());\r
- af.conservationMenuItem.setSelected(view.getConservationSelected());\r
-\r
- af.viewport.setShowJVSuffix(view.getShowFullId());\r
- af.seqLimits.setSelected(view.getShowFullId());\r
-\r
- af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(), view.getFontSize()));\r
- af.alignPanel.fontChanged();\r
-\r
- af.viewport.setRenderGaps(view.getRenderGaps());\r
- af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
-\r
- af.viewport.setWrapAlignment(view.getWrapAlignment());\r
- af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
-\r
- if (view.getWrapAlignment())\r
- {\r
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
- }\r
- else\r
- {\r
- af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
- af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
- }\r
-\r
- af.viewport.setShowBoxes(view.getShowBoxes());\r
- af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
- af.viewport.setShowText(view.getShowText());\r
- af.viewTextMenuItem.setSelected(view.getShowText());\r
-\r
- ColourSchemeI cs = null;\r
-\r
- if (view.getBgColour() != null)\r
- {\r
- if (view.getBgColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, view.getBgColour());\r
- }\r
- else if(view.getBgColour().startsWith("Annotation"))\r
- {\r
- //int find annotation\r
- for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
- {\r
- if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
- equals(view.getAnnotationColours().getAnnotation()))\r
- {\r
- if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
- getThreshold() == null)\r
- {\r
- af.viewport.alignment.getAlignmentAnnotation()[i].\r
- setThreshold(\r
- new jalview.datamodel.GraphLine(\r
- view.getAnnotationColours().getThreshold(),\r
- "Threshold", java.awt.Color.black)\r
-\r
- );\r
- }\r
-\r
-\r
- if (view.getAnnotationColours().getColourScheme().equals(\r
- "None"))\r
- {\r
- cs = new AnnotationColourGradient(\r
- af.viewport.alignment.getAlignmentAnnotation()[i],\r
- new java.awt.Color(view.getAnnotationColours().\r
- getMinColour()),\r
- new java.awt.Color(view.getAnnotationColours().\r
- getMaxColour()),\r
- view.getAnnotationColours().getAboveThreshold());\r
- }\r
- else if (view.getAnnotationColours().getColourScheme().\r
- startsWith("ucs"))\r
- {\r
- cs = new AnnotationColourGradient(\r
- af.viewport.alignment.getAlignmentAnnotation()[i],\r
- GetUserColourScheme(jms, view.getAnnotationColours().\r
- getColourScheme()),\r
- view.getAnnotationColours().getAboveThreshold()\r
- );\r
- }\r
- else\r
- {\r
- cs = new AnnotationColourGradient(\r
- af.viewport.alignment.getAlignmentAnnotation()[i],\r
- ColourSchemeProperty.getColour(al,\r
- view.getAnnotationColours().getColourScheme()),\r
- view.getAnnotationColours().getAboveThreshold()\r
- );\r
- }\r
-\r
- // Also use these settings for all the groups\r
- if (al.getGroups() != null)\r
- for (int g = 0; g < al.getGroups().size(); g++)\r
- {\r
- jalview.datamodel.SequenceGroup sg\r
- = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
-\r
- if(sg.cs == null)\r
- continue;\r
-\r
-\r
- /* if (view.getAnnotationColours().getColourScheme().equals("None"))\r
- {\r
- sg.cs = new AnnotationColourGradient(\r
- af.viewport.alignment.getAlignmentAnnotation()[i],\r
- new java.awt.Color(view.getAnnotationColours().\r
- getMinColour()),\r
- new java.awt.Color(view.getAnnotationColours().\r
- getMaxColour()),\r
- view.getAnnotationColours().getAboveThreshold());\r
- }\r
- else*/\r
- {\r
- sg.cs = new AnnotationColourGradient(\r
- af.viewport.alignment.getAlignmentAnnotation()[i],\r
- sg.cs,\r
- view.getAnnotationColours().getAboveThreshold()\r
- );\r
- }\r
-\r
- }\r
-\r
-\r
- break;\r
- }\r
-\r
- }\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
- }\r
-\r
- if(cs!=null)\r
- {\r
- cs.setThreshold(view.getPidThreshold(), true);\r
- cs.setConsensus(af.viewport.vconsensus);\r
- }\r
- }\r
-\r
- af.setColourSelected(view.getBgColour());\r
- af.viewport.setGlobalColourScheme(cs);\r
- af.viewport.setColourAppliesToAllGroups(false);\r
- af.changeColour(cs);\r
- if (view.getConservationSelected() && cs!=null)\r
- {\r
- cs.setConservationInc(view.getConsThreshold());\r
- }\r
-\r
- af.viewport.setColourAppliesToAllGroups(true);\r
-\r
- if (view.getShowSequenceFeatures())\r
- {\r
- af.viewport.showSequenceFeatures = true;\r
- af.showSeqFeatures.setSelected(true);\r
- }\r
-\r
- if(jms.getFeatureSettings()!=null)\r
- {\r
- af.viewport.featuresDisplayed = new Hashtable();\r
- String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
- for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
- {\r
- Setting setting = jms.getFeatureSettings().getSetting(fs);\r
-\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
- new java.awt.Color(setting.getColour()));\r
-\r
- renderOrder[fs] = setting.getType();\r
-\r
- if(setting.getDisplay())\r
- af.viewport.featuresDisplayed.put(\r
- setting.getType(), new Integer(setting.getColour()));\r
- }\r
- af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
- }\r
-\r
-\r
- Desktop.addInternalFrame(af, view.getTitle(),\r
- view.getWidth(), view.getHeight());\r
-\r
- //LOAD TREES\r
- ///////////////////////////////////////\r
- if (jms.getTreeCount() > 0)\r
- {\r
- try\r
- {\r
- for (int t = 0; t < jms.getTreeCount(); t++)\r
- {\r
-\r
- Tree tree = jms.getTree(t);\r
-\r
- TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(\r
- tree.getNewick()), tree.getTitle(),\r
- tree.getWidth(), tree.getHeight(),\r
- tree.getXpos(), tree.getYpos());\r
-\r
- tp.fitToWindow.setState(tree.getFitToWindow());\r
- tp.fitToWindow_actionPerformed(null);\r
-\r
- if(tree.getFontName()!=null)\r
- tp.setTreeFont(new java.awt.Font(tree.getFontName(),\r
- tree.getFontStyle(),\r
- tree.getFontSize()));\r
- else\r
- tp.setTreeFont(new java.awt.Font(view.getFontName(),\r
- view.getFontStyle(),\r
- tree.getFontSize()));\r
-\r
- tp.showPlaceholders(tree.getMarkUnlinked());\r
- tp.showBootstrap(tree.getShowBootstrap());\r
- tp.showDistances(tree.getShowDistances());\r
-\r
- tp.treeCanvas.threshold = tree.getThreshold();\r
-\r
- if (tree.getCurrentTree())\r
- af.viewport.setCurrentTree(tp.getTree());\r
- }\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- }\r
-\r
- return af;\r
- }\r
-}\r
-\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ *
+ * This file is part of Jalview.
+ *
+ * Jalview is free software: you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
+ *
+ * Jalview is distributed in the hope that it will be useful, but
+ * WITHOUT ANY WARRANTY; without even the implied warranty
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
+ * PURPOSE. See the GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.gui;
+
+import java.awt.Rectangle;
+import java.io.*;
+import java.lang.reflect.InvocationTargetException;
+import java.net.*;
+import java.util.*;
+import java.util.Map.Entry;
+import java.util.jar.*;
+
+import javax.swing.*;
+
+import org.exolab.castor.xml.*;
+
+import uk.ac.vamsas.objects.utils.MapList;
+import jalview.bin.Cache;
+import jalview.datamodel.Alignment;
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.SequenceI;
+import jalview.schemabinding.version2.*;
+import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
+import jalview.util.jarInputStreamProvider;
+
+/**
+ * Write out the current jalview desktop state as a Jalview XML stream.
+ *
+ * Note: the vamsas objects referred to here are primitive versions of the
+ * VAMSAS project schema elements - they are not the same and most likely never
+ * will be :)
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview2XML
+{
+ /**
+ * create/return unique hash string for sq
+ *
+ * @param sq
+ * @return new or existing unique string for sq
+ */
+ String seqHash(SequenceI sq)
+ {
+ if (seqsToIds == null)
+ {
+ initSeqRefs();
+ }
+ if (seqsToIds.containsKey(sq))
+ {
+ return (String) seqsToIds.get(sq);
+ }
+ else
+ {
+ // create sequential key
+ String key = "sq" + (seqsToIds.size() + 1);
+ key = makeHashCode(sq, key); // check we don't have an external reference
+ // for it already.
+ seqsToIds.put(sq, key);
+ return key;
+ }
+ }
+
+ void clearSeqRefs()
+ {
+ if (_cleartables)
+ {
+ if (seqRefIds != null)
+ {
+ seqRefIds.clear();
+ }
+ if (seqsToIds != null)
+ {
+ seqsToIds.clear();
+ }
+ // seqRefIds = null;
+ // seqsToIds = null;
+ }
+ else
+ {
+ // do nothing
+ warn("clearSeqRefs called when _cleartables was not set. Doing nothing.");
+ // seqRefIds = new Hashtable();
+ // seqsToIds = new IdentityHashMap();
+ }
+ }
+
+ void initSeqRefs()
+ {
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap();
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ }
+
+ /**
+ * SequenceI reference -> XML ID string in jalview XML. Populated as XML reps
+ * of sequence objects are created.
+ */
+ java.util.IdentityHashMap seqsToIds = null;
+
+ /**
+ * jalview XML Sequence ID to jalview sequence object reference (both dataset
+ * and alignment sequences. Populated as XML reps of sequence objects are
+ * created.)
+ */
+ java.util.Hashtable seqRefIds = null; // key->SequenceI resolution
+
+ Vector frefedSequence = null;
+
+ boolean raiseGUI = true; // whether errors are raised in dialog boxes or not
+
+ public Jalview2XML()
+ {
+ }
+
+ public Jalview2XML(boolean raiseGUI)
+ {
+ this.raiseGUI = raiseGUI;
+ }
+
+ public void resolveFrefedSequences()
+ {
+ if (frefedSequence.size() > 0)
+ {
+ int r = 0, rSize = frefedSequence.size();
+ while (r < rSize)
+ {
+ Object[] ref = (Object[]) frefedSequence.elementAt(r);
+ if (ref != null)
+ {
+ String sref = (String) ref[0];
+ if (seqRefIds.containsKey(sref))
+ {
+ if (ref[1] instanceof jalview.datamodel.Mapping)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ ((jalview.datamodel.Mapping) ref[1]).setTo(seq);
+ }
+ else
+ {
+ if (ref[1] instanceof jalview.datamodel.AlignedCodonFrame)
+ {
+ SequenceI seq = (SequenceI) seqRefIds.get(sref);
+ while (seq.getDatasetSequence() != null)
+ {
+ seq = seq.getDatasetSequence();
+ }
+ if (ref[2] != null
+ && ref[2] instanceof jalview.datamodel.Mapping)
+ {
+ jalview.datamodel.Mapping mp = (jalview.datamodel.Mapping) ref[2];
+ ((jalview.datamodel.AlignedCodonFrame) ref[1]).addMap(
+ seq, mp.getTo(), mp.getMap());
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for AlcodonFrames involving "
+ + ref[2].getClass() + " type objects.");
+ }
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION ERROR: Unimplemented forward sequence references for "
+ + ref[1].getClass() + " type objects.");
+ }
+ }
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ else
+ {
+ System.err
+ .println("IMPLEMENTATION WARNING: Unresolved forward reference for hash string "
+ + ref[0]
+ + " with objecttype "
+ + ref[1].getClass());
+ r++;
+ }
+ }
+ else
+ {
+ // empty reference
+ frefedSequence.remove(r);
+ rSize--;
+ }
+ }
+ }
+ }
+
+ /**
+ * 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)
+ {
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ SaveState(jout);
+
+ } catch (Exception e)
+ {
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive to output file '"
+ + statefile + "' - See console error log for details";
+ }
+ else
+ {
+ errorMessage += "(output file was '" + statefile + "')";
+ }
+ e.printStackTrace();
+ }
+ reportErrors();
+ }
+
+ /**
+ * Writes a jalview project archive to the given Jar output stream.
+ *
+ * @param jout
+ */
+ public void SaveState(JarOutputStream jout)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+
+ try
+ {
+
+ // NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+ // //////////////////////////////////////////////////
+ // NOTE ALSO new PrintWriter must be used for each new JarEntry
+ PrintWriter out = null;
+
+ 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];
+ // skip ?
+ if (skipList != null
+ && skipList.containsKey(af.getViewport()
+ .getSequenceSetId()))
+ {
+ continue;
+ }
+
+ 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);
+ String fileName = apSize == 1 ? shortName : ap + shortName;
+ if (!fileName.endsWith(".xml"))
+ {
+ fileName = fileName + ".xml";
+ }
+
+ SaveState(apanel, fileName, jout);
+ }
+ }
+ }
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ jout.close();
+ } catch (Exception ex)
+ {
+ // TODO: inform user of the problem - they need to know if their data was
+ // not saved !
+ if (errorMessage == null)
+ {
+ errorMessage = "Couldn't write Jalview Archive - see error output for details";
+ }
+ 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);
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels
+ .elementAt(ap);
+ String jfileName = apSize == 1 ? fileName : fileName + ap;
+ if (!jfileName.endsWith(".xml"))
+ {
+ jfileName = jfileName + ".xml";
+ }
+ SaveState(apanel, jfileName, jout);
+ }
+
+ try
+ {
+ jout.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ jout.close();
+ return true;
+ } catch (Exception ex)
+ {
+ errorMessage = "Couldn't Write alignment view to Jalview Archive - see error output for details";
+ ex.printStackTrace();
+ return false;
+ }
+ }
+
+ /**
+ * create a JalviewModel from an algnment view and marshall it to a
+ * JarOutputStream
+ *
+ * @param ap
+ * panel to create jalview model for
+ * @param fileName
+ * name of alignment panel written to output stream
+ * @param jout
+ * jar output stream
+ * @param out
+ * jar entry name
+ */
+ public JalviewModel SaveState(AlignmentPanel ap, String fileName,
+ JarOutputStream jout)
+ {
+ initSeqRefs();
+ Vector jmolViewIds = new Vector(); //
+ 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() + "");
+
+ if (jal.getDataset() != null)
+ {
+ // dataset id is the dataset's hashcode
+ vamsasSet.setDatasetId(getDatasetIdRef(jal.getDataset()));
+ }
+ if (jal.getProperties() != null)
+ {
+ Enumeration en = jal.getProperties().keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ SequenceSetProperties ssp = new SequenceSetProperties();
+ ssp.setKey(key);
+ ssp.setValue(jal.getProperties().get(key).toString());
+ vamsasSet.addSequenceSetProperties(ssp);
+ }
+ }
+
+ JSeq jseq;
+
+ // SAVE SEQUENCES
+ String id = "";
+ jalview.datamodel.SequenceI jds;
+ for (int i = 0; i < jal.getHeight(); i++)
+ {
+ jds = jal.getSequenceAt(i);
+ id = seqHash(jds);
+
+ if (seqRefIds.get(id) != null)
+ {
+ // This happens for two reasons: 1. multiple views are being serialised.
+ // 2. the hashCode has collided with another sequence's code. This DOES
+ // HAPPEN! (PF00072.15.stk does this)
+ // JBPNote: Uncomment to debug writing out of files that do not read
+ // back in due to ArrayOutOfBoundExceptions.
+ // System.err.println("vamsasSeq backref: "+id+"");
+ // System.err.println(jds.getName()+"
+ // "+jds.getStart()+"-"+jds.getEnd()+" "+jds.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(jds));
+ // SequenceI rsq = (SequenceI) seqRefIds.get(id + "");
+ // System.err.println(rsq.getName()+"
+ // "+rsq.getStart()+"-"+rsq.getEnd()+" "+rsq.getSequenceAsString());
+ // System.err.println("Hashcode: "+seqHash(rsq));
+ }
+ else
+ {
+ vamsasSeq = createVamsasSequence(id, jds);
+ vamsasSet.addSequence(vamsasSeq);
+ seqRefIds.put(id, jds);
+ }
+
+ jseq = new JSeq();
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour(av.getSequenceColour(jds).getRGB());
+
+ jseq.setId(id); // jseq id should be a string not a number
+
+ 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();
+ String matchedFile = null;
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof AppJmol)
+ {
+ // TODO: revise schema to allow many:one PDB id binding to viewer
+ jmol = (AppJmol) frames[f];
+ for (int peid = 0; peid < jmol.jmb.pdbentry.length; peid++)
+ {
+ if (!jmol.jmb.pdbentry[peid].getId().equals(entry.getId())
+ && !(entry.getId().length() > 4 && entry
+ .getId()
+ .toLowerCase()
+ .startsWith(
+ jmol.jmb.pdbentry[peid].getId()
+ .toLowerCase())))
+ continue;
+ if (matchedFile == null)
+ {
+ matchedFile = jmol.jmb.pdbentry[peid].getFile();
+ }
+ else if (!matchedFile.equals(jmol.jmb.pdbentry[peid]
+ .getFile()))
+ {
+ Cache.log
+ .warn("Probably lost some PDB-Sequence mappings for this structure file (which apparently has same PDB Entry code): "
+ + jmol.jmb.pdbentry[peid].getFile());
+ ; // record the
+ }
+ // file so we
+ // can get at it if the ID
+ // match is ambiguous (e.g.
+ // 1QIP==1qipA)
+ String statestring = jmol.jmb.viewer.getStateInfo();
+
+ for (int smap = 0; smap < jmol.jmb.sequence[peid].length; smap++)
+ {
+ if (jal.findIndex(jmol.jmb.sequence[peid][smap]) > -1)
+ {
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(jmol.getX());
+ state.setYpos(jmol.getY());
+ state.setWidth(jmol.getWidth());
+ state.setHeight(jmol.getHeight());
+ state.setViewId(jmol.getViewId());
+ if (!jmolViewIds.contains(state.getViewId()))
+ {
+ // Make sure we only store a Jmol state once in each XML
+ // document.
+ jmolViewIds.addElement(state.getViewId());
+ state.setContent(statestring.replaceAll("\n", ""));
+ }
+ else
+ {
+ state.setContent("# duplicate state");
+ }
+ pdb.addStructureState(state);
+ }
+ }
+ }
+ }
+ }
+
+ if (matchedFile != null || entry.getFile() != null)
+ {
+ if (entry.getFile() != null)
+ {
+ // use entry's file
+ matchedFile = entry.getFile();
+ }
+ pdb.setFile(matchedFile); // entry.getFile());
+ if (pdbfiles == null)
+ {
+ pdbfiles = new Vector();
+ }
+
+ if (!pdbfiles.contains(entry.getId()))
+ {
+ pdbfiles.addElement(entry.getId());
+ try
+ {
+ File file = new File(matchedFile);
+ 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);
+ dout.flush();
+ 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 MAPPINGS
+ if (jal.getCodonFrames() != null && jal.getCodonFrames().length > 0)
+ {
+ jalview.datamodel.AlignedCodonFrame[] jac = jal.getCodonFrames();
+ for (int i = 0; i < jac.length; i++)
+ {
+ AlcodonFrame alc = new AlcodonFrame();
+ vamsasSet.addAlcodonFrame(alc);
+ for (int p = 0; p < jac[i].aaWidth; p++)
+ {
+ Alcodon cmap = new Alcodon();
+ if (jac[i].codons[p] != null)
+ {
+ // Null codons indicate a gapped column in the translated peptide
+ // alignment.
+ cmap.setPos1(jac[i].codons[p][0]);
+ cmap.setPos2(jac[i].codons[p][1]);
+ cmap.setPos3(jac[i].codons[p][2]);
+ }
+ alc.addAlcodon(cmap);
+ }
+ if (jac[i].getProtMappings() != null
+ && jac[i].getProtMappings().length > 0)
+ {
+ SequenceI[] dnas = jac[i].getdnaSeqs();
+ jalview.datamodel.Mapping[] pmaps = jac[i].getProtMappings();
+ for (int m = 0; m < pmaps.length; m++)
+ {
+ AlcodMap alcmap = new AlcodMap();
+ alcmap.setDnasq(seqHash(dnas[m]));
+ alcmap.setMapping(createVamsasMapping(pmaps[m], dnas[m], null,
+ false));
+ alc.addAlcodMap(alcmap);
+ }
+ }
+ }
+ }
+
+ // 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());
+ tree.setId(makeHashCode(tp, null));
+ jms.addTree(tree);
+ }
+ }
+ }
+ }
+ }
+
+ // SAVE ANNOTATIONS
+ /**
+ * store forward refs from an annotationRow to any groups
+ */
+ IdentityHashMap groupRefs = new IdentityHashMap();
+ 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);
+
+ an.setVisible(aa[i].visible);
+
+ an.setDescription(aa[i].description);
+
+ if (aa[i].sequenceRef != null)
+ {
+ // TODO later annotation sequenceRef should be the XML ID of the
+ // sequence rather than its display name
+ an.setSequenceRef(aa[i].sequenceRef.getName());
+ }
+ if (aa[i].groupRef != null)
+ {
+ Object groupIdr = groupRefs.get(aa[i].groupRef);
+ if (groupIdr == null)
+ {
+ // make a locally unique String
+ groupRefs.put(aa[i].groupRef,
+ groupIdr = ("" + System.currentTimeMillis()
+ + aa[i].groupRef.getName() + groupRefs.size()));
+ }
+ an.setGroupRef(groupIdr.toString());
+ }
+ if (aa[i] == av.quality || aa[i] == av.conservation
+ || aa[i] == av.consensus || aa[i].autoCalculated)
+ {
+ // new way of indicating autocalculated annotation -
+ an.setAutoCalculated(aa[i].autoCalculated);
+ // write a stub for this annotation - indicate presence of autocalc
+ // rows
+ an.setLabel(aa[i].label);
+ an.setGraph(true);
+ vamsasSet.addAnnotation(an);
+ continue;
+ }
+
+ 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();
+ if (aa[i].annotations[a].description != null)
+ ae.setDescription(aa[i].annotations[a].description);
+ if (aa[i].annotations[a].displayCharacter != null)
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+
+ if (!Float.isNaN(aa[i].annotations[a].value))
+ ae.setValue(aa[i].annotations[a].value);
+
+ ae.setPosition(a);
+ if (aa[i].annotations[a].secondaryStructure != ' '
+ && aa[i].annotations[a].secondaryStructure != '\0')
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+
+ if (aa[i].annotations[a].colour != null
+ && 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 (groupRefs.containsKey(sg))
+ {
+ // group has references so set it's ID field
+ groups[i].setId(groupRefs.get(sg).toString());
+ }
+ 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);
+ groups[i].setShowUnconserved(sg.getShowNonconserved());
+ groups[i].setIgnoreGapsinConsensus(sg.getIgnoreGapsConsensus());
+ groups[i].setShowConsensusHistogram(sg.isShowConsensusHistogram());
+ groups[i].setShowSequenceLogo(sg.isShowSequenceLogo());
+ for (int s = 0; s < sg.getSize(); s++)
+ {
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg
+ .getSequenceAt(s);
+ groups[i].addSeq(seqHash(seq));
+ }
+ }
+
+ jms.setJGroup(groups);
+ }
+
+ // /////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(makeHashCode(av.getSequenceSetId(),
+ av.getSequenceSetId()));
+ view.setId(av.getViewId());
+ 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.setShowUnconserved(av.getShowUnconserved());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.textColour.getRGB());
+ view.setTextCol2(av.textColour2.getRGB());
+ view.setTextColThreshold(av.thresholdTextColour);
+ view.setShowConsensusHistogram(av.isShowConsensusHistogram());
+ view.setShowSequenceLogo(av.isShowSequenceLogo());
+ view.setShowGroupConsensus(av.isShowGroupConsensus());
+ view.setShowGroupConservation(av.isShowGroupConservation());
+ view.setShowNPfeatureTooltip(av.isShowNpFeats());
+ view.setShowDbRefTooltip(av.isShowDbRefs());
+ view.setFollowHighlight(av.followHighlight);
+ view.setFollowSelection(av.followSelection);
+ view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus());
+ 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();
+ Object gstyle = null;
+ GraduatedColor gcol = null;
+ for (int ro = 0; ro < renderOrder.length; ro++)
+ {
+ gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer()
+ .getFeatureStyle(renderOrder[ro]);
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ if (gstyle instanceof GraduatedColor)
+ {
+ gcol = (GraduatedColor) gstyle;
+ setting.setColour(gcol.getMaxColor().getRGB());
+ setting.setMincolour(gcol.getMinColor().getRGB());
+ setting.setMin(gcol.getMin());
+ setting.setMax(gcol.getMax());
+ setting.setColourByLabel(gcol.isColourByLabel());
+ setting.setAutoScale(gcol.isAutoScale());
+ setting.setThreshold(gcol.getThresh());
+ setting.setThreshstate(gcol.getThreshType());
+ }
+ else
+ {
+ 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)
+ {
+ if (av.getColumnSelection() == null
+ || av.getColumnSelection().getHiddenColumns() == null)
+ {
+ warn("REPORT BUG: avoided null columnselection bug (DMAM reported). Please contact Jim about this.");
+ }
+ else
+ {
+ 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 (jout != null && fileName != null)
+ {
+ // We may not want to write the object to disk,
+ // eg we can copy the alignViewport to a new view object
+ // using save and then load
+ try
+ {
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
+ PrintWriter pout = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+ org.exolab.castor.xml.Marshaller marshaller = new org.exolab.castor.xml.Marshaller(
+ pout);
+ marshaller.marshal(object);
+ pout.flush();
+ jout.closeEntry();
+ } catch (Exception ex)
+ {
+ // TODO: raise error in GUI if marshalling failed.
+ ex.printStackTrace();
+ }
+ }
+ return object;
+ }
+
+ /**
+ * External mapping between jalview objects and objects yielding a valid and
+ * unique object ID string. This is null for normal Jalview project IO, but
+ * non-null when a jalview project is being read or written as part of a
+ * vamsas session.
+ */
+ IdentityHashMap jv2vobj = null;
+
+ /**
+ * Construct a unique ID for jvobj using either existing bindings or if none
+ * exist, the result of the hashcode call for the object.
+ *
+ * @param jvobj
+ * jalview data object
+ * @return unique ID for referring to jvobj
+ */
+ private String makeHashCode(Object jvobj, String altCode)
+ {
+ if (jv2vobj != null)
+ {
+ Object id = jv2vobj.get(jvobj);
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // check string ID mappings
+ if (jvids2vobj != null && jvobj instanceof String)
+ {
+ id = jvids2vobj.get(jvobj);
+ }
+ if (id != null)
+ {
+ return id.toString();
+ }
+ // give up and warn that something has gone wrong
+ warn("Cannot find ID for object in external mapping : " + jvobj);
+ }
+ return altCode;
+ }
+
+ /**
+ * return local jalview object mapped to ID, if it exists
+ *
+ * @param idcode
+ * (may be null)
+ * @return null or object bound to idcode
+ */
+ private Object retrieveExistingObj(String idcode)
+ {
+ if (idcode != null && vobj2jv != null)
+ {
+ return vobj2jv.get(idcode);
+ }
+ return null;
+ }
+
+ /**
+ * binding from ID strings from external mapping table to jalview data model
+ * objects.
+ */
+ private Hashtable vobj2jv;
+
+ private Sequence createVamsasSequence(String id, SequenceI jds)
+ {
+ return createVamsasSequence(true, id, jds, null);
+ }
+
+ private Sequence createVamsasSequence(boolean recurse, String id,
+ SequenceI jds, SequenceI parentseq)
+ {
+ Sequence vamsasSeq = new Sequence();
+ vamsasSeq.setId(id);
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+ jalview.datamodel.DBRefEntry[] dbrefs = null;
+ if (jds.getDatasetSequence() != null)
+ {
+ vamsasSeq.setDsseqid(seqHash(jds.getDatasetSequence()));
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ dbrefs = jds.getDatasetSequence().getDBRef();
+ }
+ }
+ else
+ {
+ vamsasSeq.setDsseqid(id); // so we can tell which sequences really are
+ // dataset sequences only
+ dbrefs = jds.getDBRef();
+ }
+ if (dbrefs != null)
+ {
+ 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());
+ if (dbrefs[d].hasMap())
+ {
+ Mapping mp = createVamsasMapping(dbrefs[d].getMap(), parentseq,
+ jds, recurse);
+ dbref.setMapping(mp);
+ }
+ vamsasSeq.addDBRef(dbref);
+ }
+ }
+ return vamsasSeq;
+ }
+
+ private Mapping createVamsasMapping(jalview.datamodel.Mapping jmp,
+ SequenceI parentseq, SequenceI jds, boolean recurse)
+ {
+ Mapping mp = null;
+ if (jmp.getMap() != null)
+ {
+ mp = new Mapping();
+
+ jalview.util.MapList mlst = jmp.getMap();
+ int r[] = mlst.getFromRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListFrom mfrom = new MapListFrom();
+ mfrom.setStart(r[s]);
+ mfrom.setEnd(r[s + 1]);
+ mp.addMapListFrom(mfrom);
+ }
+ r = mlst.getToRanges();
+ for (int s = 0; s < r.length; s += 2)
+ {
+ MapListTo mto = new MapListTo();
+ mto.setStart(r[s]);
+ mto.setEnd(r[s + 1]);
+ mp.addMapListTo(mto);
+ }
+ mp.setMapFromUnit(mlst.getFromRatio());
+ mp.setMapToUnit(mlst.getToRatio());
+ if (jmp.getTo() != null)
+ {
+ MappingChoice mpc = new MappingChoice();
+ if (recurse
+ && (parentseq != jmp.getTo() || parentseq
+ .getDatasetSequence() != jmp.getTo()))
+ {
+ mpc.setSequence(createVamsasSequence(false, seqHash(jmp.getTo()),
+ jmp.getTo(), jds));
+ }
+ else
+ {
+ String jmpid = "";
+ SequenceI ps = null;
+ if (parentseq != jmp.getTo()
+ && parentseq.getDatasetSequence() != jmp.getTo())
+ {
+ // chaining dbref rather than a handshaking one
+ jmpid = seqHash(ps = jmp.getTo());
+ }
+ else
+ {
+ jmpid = seqHash(ps = parentseq);
+ }
+ mpc.setDseqFor(jmpid);
+ if (!seqRefIds.containsKey(mpc.getDseqFor()))
+ {
+ jalview.bin.Cache.log.debug("creatign new DseqFor ID");
+ seqRefIds.put(mpc.getDseqFor(), ps);
+ }
+ else
+ {
+ jalview.bin.Cache.log.debug("reusing DseqFor ID");
+ }
+ }
+ mp.setMappingChoice(mpc);
+ }
+ }
+ return mp;
+ }
+
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ Vector userColours, JalviewModelSequence jms)
+ {
+ String id = null;
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;
+ boolean newucs = false;
+ if (!userColours.contains(ucs))
+ {
+ userColours.add(ucs);
+ newucs = true;
+ }
+ id = "ucs" + userColours.indexOf(ucs);
+ if (newucs)
+ {
+ // actually create the scheme's entry in the XML model
+ 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);
+ }
+ }
+
+ 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;
+ }
+
+ /**
+ * contains last error message (if any) encountered by XML loader.
+ */
+ String errorMessage = null;
+
+ /**
+ * flag to control whether the Jalview2XML_V1 parser should be deferred to if
+ * exceptions are raised during project XML parsing
+ */
+ public boolean attemptversion1parse = true;
+
+ /**
+ * Load a jalview project archive from a jar file
+ *
+ * @param file
+ * - HTTP URL or filename
+ */
+ public AlignFrame LoadJalviewAlign(final String file)
+ {
+
+ jalview.gui.AlignFrame af = null;
+
+ try
+ {
+ // UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ // Workaround is to make sure caller implements the JarInputStreamProvider
+ // interface
+ // so we can re-open the jar input stream for each entry.
+
+ jarInputStreamProvider jprovider = createjarInputStreamProvider(file);
+ af = LoadJalviewAlign(jprovider);
+ } catch (MalformedURLException e)
+ {
+ errorMessage = "Invalid URL format for '" + file + "'";
+ reportErrors();
+ }
+ return af;
+ }
+
+ private jarInputStreamProvider createjarInputStreamProvider(
+ final String file) throws MalformedURLException
+ {
+ URL url = null;
+ errorMessage = null;
+ uniqueSetSuffix = null;
+ seqRefIds = null;
+ viewportsAdded = null;
+ frefedSequence = null;
+
+ if (file.startsWith("http://"))
+ {
+ url = new URL(file);
+ }
+ final URL _url = url;
+ return new jarInputStreamProvider()
+ {
+
+ public JarInputStream getJarInputStream() throws IOException
+ {
+ if (_url != null)
+ {
+ return new JarInputStream(_url.openStream());
+ }
+ else
+ {
+ return new JarInputStream(new FileInputStream(file));
+ }
+ }
+
+ public String getFilename()
+ {
+ return file;
+ }
+ };
+ }
+
+ /**
+ * Recover jalview session from a jalview project archive. Caller may
+ * initialise uniqueSetSuffix, seqRefIds, viewportsAdded and frefedSequence
+ * themselves. Any null fields will be initialised with default values,
+ * non-null fields are left alone.
+ *
+ * @param jprovider
+ * @return
+ */
+ public AlignFrame LoadJalviewAlign(final jarInputStreamProvider jprovider)
+ {
+ errorMessage = null;
+ if (uniqueSetSuffix == null)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+ }
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ if (viewportsAdded == null)
+ {
+ viewportsAdded = new Hashtable();
+ }
+ if (frefedSequence == null)
+ {
+ frefedSequence = new Vector();
+ }
+
+ jalview.gui.AlignFrame af = null;
+ Hashtable gatherToThisFrame = new Hashtable();
+ final String file = jprovider.getFilename();
+ try
+ {
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
+
+ do
+ {
+ jin = jprovider.getJarInputStream();
+ for (int i = 0; i < entryCount; i++)
+ {
+ jarentry = jin.getNextJarEntry();
+ }
+
+ if (jarentry != null && 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);
+ if (true) // !skipViewport(object))
+ {
+ af = LoadFromObject(object, file, true, jprovider);
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
+ }
+ entryCount++;
+ }
+ else if (jarentry != null)
+ {
+ // Some other file here.
+ entryCount++;
+ }
+ } while (jarentry != null);
+ resolveFrefedSequences();
+ } catch (java.io.FileNotFoundException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (java.net.UnknownHostException ex)
+ {
+ ex.printStackTrace();
+ errorMessage = "Couldn't locate Jalview XML file : " + file;
+ System.err.println("Exception whilst loading jalview XML file : "
+ + ex + "\n");
+ } catch (Exception ex)
+ {
+ System.err.println("Parsing as Jalview Version 2 file failed.");
+ ex.printStackTrace(System.err);
+ if (attemptversion1parse)
+ {
+ // Is Version 1 Jar file?
+ try
+ {
+ af = new Jalview2XML_V1(raiseGUI).LoadJalviewAlign(jprovider);
+ } catch (Exception ex2)
+ {
+ System.err.println("Exception whilst loading as jalviewXMLV1:");
+ ex2.printStackTrace();
+ af = null;
+ }
+ }
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+ 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");
+ } catch (OutOfMemoryError e)
+ {
+ // Don't use the OOM Window here
+ errorMessage = "Out of memory loading jalview XML file";
+ System.err.println("Out of memory whilst loading jalview XML file");
+ e.printStackTrace();
+ }
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
+ Enumeration en = gatherToThisFrame.elements();
+ while (en.hasMoreElements())
+ {
+ Desktop.instance.gatherViews((AlignFrame) en.nextElement());
+ }
+ if (errorMessage != null)
+ {
+ reportErrors();
+ }
+ return af;
+ }
+
+ /**
+ * check errorMessage for a valid error message and raise an error box in the
+ * GUI or write the current errorMessage to stderr and then clear the error
+ * state.
+ */
+ protected void reportErrors()
+ {
+ reportErrors(false);
+ }
+
+ protected void reportErrors(final boolean saving)
+ {
+ if (errorMessage != null)
+ {
+ final String finalErrorMessage = errorMessage;
+ if (raiseGUI)
+ {
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ finalErrorMessage, "Error "
+ + (saving ? "saving" : "loading")
+ + " Jalview file", JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ else
+ {
+ System.err.println("Problem loading Jalview file: " + errorMessage);
+ }
+ }
+ errorMessage = null;
+ }
+
+ Hashtable alreadyLoadedPDB;
+
+ /**
+ * when set, local views will be updated from view stored in JalviewXML
+ * Currently (28th Sep 2008) things will go horribly wrong in vamsas document
+ * sync if this is set to true.
+ */
+ private boolean updateLocalViews = false;
+
+ String loadPDBFile(jarInputStreamProvider jprovider, String pdbId)
+ {
+ if (alreadyLoadedPDB == null)
+ alreadyLoadedPDB = new Hashtable();
+
+ if (alreadyLoadedPDB.containsKey(pdbId))
+ return alreadyLoadedPDB.get(pdbId).toString();
+
+ try
+ {
+ JarInputStream jin = jprovider.getJarInputStream();
+ /*
+ * if (jprovider.startsWith("http://")) { jin = new JarInputStream(new
+ * URL(jprovider).openStream()); } else { jin = new JarInputStream(new
+ * FileInputStream(jprovider)); }
+ */
+
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ } while (entry != null && !entry.getName().equals(pdbId));
+ if (entry != null)
+ {
+ 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);
+ }
+ try
+ {
+ out.flush();
+ } catch (Exception foo)
+ {
+ }
+ ;
+ out.close();
+
+ alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
+ return outFile.getAbsolutePath();
+ }
+ else
+ {
+ warn("Couldn't find PDB file entry in Jalview Jar for " + pdbId);
+ }
+ } catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return null;
+ }
+
+ /**
+ * Load alignment frame from jalview XML DOM object
+ *
+ * @param object
+ * DOM
+ * @param file
+ * filename source string
+ * @param loadTreesAndStructures
+ * when false only create Viewport
+ * @param jprovider
+ * data source provider
+ * @return alignment frame created from view stored in DOM
+ */
+ AlignFrame LoadFromObject(JalviewModel object, String file,
+ boolean loadTreesAndStructures, jarInputStreamProvider jprovider)
+ {
+ 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();
+ int vi = 0; // counter in vamsasSeq array
+ 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[vi].getName(),
+ vamsasSeq[vi].getSequence());
+ jseq.setDescription(vamsasSeq[vi].getDescription());
+ jseq.setStart(JSEQ[i].getStart());
+ jseq.setEnd(JSEQ[i].getEnd());
+ jseq.setVamsasId(uniqueSetSuffix + seqId);
+ seqRefIds.put(vamsasSeq[vi].getId(), jseq);
+ tmpseqs.add(jseq);
+ vi++;
+ }
+
+ if (JSEQ[i].getHidden())
+ {
+ if (hiddenSeqs == null)
+ {
+ hiddenSeqs = new Vector();
+ }
+
+ hiddenSeqs.addElement((jalview.datamodel.Sequence) seqRefIds
+ .get(seqId));
+ }
+
+ }
+
+ // /
+ // Create the alignment object from the sequence set
+ // ///////////////////////////////
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[tmpseqs
+ .size()];
+
+ tmpseqs.toArray(orderedSeqs);
+
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(
+ orderedSeqs);
+
+ // / Add the alignment properties
+ for (int i = 0; i < vamsasSet.getSequenceSetPropertiesCount(); i++)
+ {
+ SequenceSetProperties ssp = vamsasSet.getSequenceSetProperties(i);
+ al.setProperty(ssp.getKey(), ssp.getValue());
+ }
+
+ // /
+ // SequenceFeatures are added to the DatasetSequence,
+ // so we must create or recover the dataset before loading features
+ // ///////////////////////////////
+ if (vamsasSet.getDatasetId() == null || vamsasSet.getDatasetId() == "")
+ {
+ // older jalview projects do not have a dataset id.
+ al.setDataset(null);
+ }
+ else
+ {
+ recoverDatasetFor(vamsasSet, al);
+ }
+ // ///////////////////////////////
+
+ Hashtable pdbloaded = new Hashtable();
+ if (!multipleView)
+ {
+ // load sequence features, database references and any associated PDB
+ // structures for the alignment
+ 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 (vamsasSeq[i].getDBRefCount() > 0)
+ {
+ addDBRefs(al.getSequenceAt(i).getDatasetSequence(), vamsasSeq[i]);
+ }
+ 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(jprovider, ids[p].getId()));
+ }
+ else
+ {
+ entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+ }
+ }
+
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ }
+ }
+ } // end !multipleview
+
+ // ///////////////////////////////
+ // LOAD SEQUENCE MAPPINGS
+
+ if (vamsasSet.getAlcodonFrameCount() > 0)
+ {
+ // TODO Potentially this should only be done once for all views of an
+ // alignment
+ AlcodonFrame[] alc = vamsasSet.getAlcodonFrame();
+ for (int i = 0; i < alc.length; i++)
+ {
+ jalview.datamodel.AlignedCodonFrame cf = new jalview.datamodel.AlignedCodonFrame(
+ alc[i].getAlcodonCount());
+ if (alc[i].getAlcodonCount() > 0)
+ {
+ Alcodon[] alcods = alc[i].getAlcodon();
+ for (int p = 0; p < cf.codons.length; p++)
+ {
+ if (alcods[p].hasPos1() && alcods[p].hasPos2()
+ && alcods[p].hasPos3())
+ {
+ // translated codons require three valid positions
+ cf.codons[p] = new int[3];
+ cf.codons[p][0] = (int) alcods[p].getPos1();
+ cf.codons[p][1] = (int) alcods[p].getPos2();
+ cf.codons[p][2] = (int) alcods[p].getPos3();
+ }
+ else
+ {
+ cf.codons[p] = null;
+ }
+ }
+ }
+ if (alc[i].getAlcodMapCount() > 0)
+ {
+ AlcodMap[] maps = alc[i].getAlcodMap();
+ for (int m = 0; m < maps.length; m++)
+ {
+ SequenceI dnaseq = (SequenceI) seqRefIds
+ .get(maps[m].getDnasq());
+ // Load Mapping
+ jalview.datamodel.Mapping mapping = null;
+ // attach to dna sequence reference.
+ if (maps[m].getMapping() != null)
+ {
+ mapping = addMapping(maps[m].getMapping());
+ }
+ if (dnaseq != null)
+ {
+ cf.addMap(dnaseq, mapping.getTo(), mapping.getMap());
+ }
+ else
+ {
+ // defer to later
+ frefedSequence.add(new Object[]
+ { maps[m].getDnasq(), cf, mapping });
+ }
+ }
+ }
+ al.addCodonFrame(cf);
+ }
+
+ }
+
+ // ////////////////////////////////
+ // LOAD ANNOTATIONS
+ boolean hideQuality = true, hideConservation = true, hideConsensus = true;
+ /**
+ * store any annotations which forward reference a group's ID
+ */
+ Hashtable groupAnnotRefs = new Hashtable();
+
+ if (vamsasSet.getAnnotationCount() > 0)
+ {
+ Annotation[] an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.length; i++)
+ {
+ // set visibility for automatic annotation for this view
+ 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;
+ }
+ // set visiblity for other annotation in this view
+ if (an[i].getId() != null
+ && annotationIds.containsKey(an[i].getId()))
+ {
+ jalview.datamodel.AlignmentAnnotation jda = (jalview.datamodel.AlignmentAnnotation) annotationIds
+ .get(an[i].getId());
+ // in principle Visible should always be true for annotation displayed
+ // in multiple views
+ if (an[i].hasVisible())
+ jda.visible = an[i].getVisible();
+
+ al.addAnnotation(jda);
+
+ continue;
+ }
+ // Construct new annotation from model.
+ 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++)
+ {
+ if (ae[aa].getPosition() >= anot.length)
+ continue;
+
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(
+
+ ae[aa].getDisplayCharacter(), ae[aa].getDescription(),
+ (ae[aa].getSecondaryStructure() == null || ae[aa]
+ .getSecondaryStructure().length() == 0) ? ' '
+ : ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue()
+
+ );
+ // JBPNote: Consider verifying dataflow for IO of secondary
+ // structure annotation read from Stockholm files
+ // this was added to try to ensure that
+ // if (anot[ae[aa].getPosition()].secondaryStructure>' ')
+ // {
+ // anot[ae[aa].getPosition()].displayCharacter = "";
+ // }
+ 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);
+ }
+ // register new annotation
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+ // recover sequence association
+ if (an[i].getSequenceRef() != null)
+ {
+ if (al.findName(an[i].getSequenceRef()) != null)
+ {
+ jaa.createSequenceMapping(al.findName(an[i].getSequenceRef()),
+ 1, true);
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ }
+ }
+ // and make a note of any group association
+ if (an[i].getGroupRef() != null && an[i].getGroupRef().length() > 0)
+ {
+ groupAnnotRefs.put(an[i].getGroupRef(), jaa);
+ }
+
+ if (an[i].hasScore())
+ {
+ jaa.setScore(an[i].getScore());
+ }
+ if (an[i].hasVisible())
+ jaa.visible = an[i].getVisible();
+
+ if (an[i].hasCentreColLabels())
+ jaa.centreColLabels = an[i].getCentreColLabels();
+
+ if (an[i].hasScaleColLabels())
+ {
+ jaa.scaleColLabel = an[i].getScaleColLabels();
+ }
+ if (an[i].hasAutoCalculated() && an[i].isAutoCalculated())
+ {
+ // newer files have an 'autoCalculated' flag and store calculation
+ // state in viewport properties
+ jaa.autoCalculated = true; // means annotation will be marked for
+ // update at end of load.
+ }
+ al.addAnnotation(jaa);
+ }
+ }
+
+ // ///////////////////////
+ // LOAD GROUPS
+ // Create alignment markup and styles for this view
+ 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.setShowNonconserved(groups[i].hasShowUnconserved() ? groups[i]
+ .isShowUnconserved() : false);
+ sg.thresholdTextColour = groups[i].getTextColThreshold();
+ if (groups[i].hasShowConsensusHistogram())
+ {
+ sg.setShowConsensusHistogram(groups[i].isShowConsensusHistogram());
+ }
+ ;
+ if (groups[i].hasShowSequenceLogo())
+ {
+ sg.setshowSequenceLogo(groups[i].isShowSequenceLogo());
+ }
+ if (groups[i].hasIgnoreGapsinConsensus())
+ {
+ sg.setIgnoreGapsConsensus(groups[i].getIgnoreGapsinConsensus());
+ }
+ 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);
+ }
+
+ if (groups[i].getId() != null && groupAnnotRefs.size() > 0)
+ {
+ // re-instate unique group/annotation row reference
+ jalview.datamodel.AlignmentAnnotation jaa = (jalview.datamodel.AlignmentAnnotation) groupAnnotRefs
+ .get(groups[i].getId());
+ if (jaa != null)
+ {
+ jaa.groupRef = sg;
+ }
+ }
+ al.addGroup(sg);
+
+ }
+ }
+
+ // ///////////////////////////////
+ // LOAD VIEWPORT
+
+ // 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;
+ String viewId = (view.getId() == null ? null : view.getId()
+ + uniqueSetSuffix);
+ AlignFrame af = null;
+ AlignViewport av = null;
+ // now check to see if we really need to create a new viewport.
+ if (multipleView && viewportsAdded.size() == 0)
+ {
+ // We recovered an alignment for which a viewport already exists.
+ // TODO: fix up any settings necessary for overlaying stored state onto
+ // state recovered from another document. (may not be necessary).
+ // we may need a binding from a viewport in memory to one recovered from
+ // XML.
+ // and then recover its containing af to allow the settings to be applied.
+ // TODO: fix for vamsas demo
+ System.err
+ .println("About to recover a viewport for existing alignment: Sequence set ID is "
+ + uniqueSeqSetId);
+ Object seqsetobj = retrieveExistingObj(uniqueSeqSetId);
+ if (seqsetobj != null)
+ {
+ if (seqsetobj instanceof String)
+ {
+ uniqueSeqSetId = (String) seqsetobj;
+ System.err
+ .println("Recovered extant sequence set ID mapping for ID : New Sequence set ID is "
+ + uniqueSeqSetId);
+ }
+ else
+ {
+ System.err
+ .println("Warning : Collision between sequence set ID string and existing jalview object mapping.");
+ }
+
+ }
+ }
+ AlignmentPanel ap = null;
+ boolean isnewview = true;
+ if (viewId != null)
+ {
+ // Check to see if this alignment already has a view id == viewId
+ jalview.gui.AlignmentPanel views[] = Desktop
+ .getAlignmentPanels(uniqueSeqSetId);
+ if (views != null && views.length > 0)
+ {
+ for (int v = 0; v < views.length; v++)
+ {
+ if (views[v].av.getViewId().equalsIgnoreCase(viewId))
+ {
+ // recover the existing alignpanel, alignframe, viewport
+ af = views[v].alignFrame;
+ av = views[v].av;
+ ap = views[v];
+ // TODO: could even skip resetting view settings if we don't want to
+ // change the local settings from other jalview processes
+ isnewview = false;
+ }
+ }
+ }
+ }
+
+ if (isnewview)
+ {
+ af = loadViewport(file, JSEQ, hiddenSeqs, al, hideConsensus,
+ hideQuality, hideConservation, jms, view, uniqueSeqSetId,
+ viewId);
+ av = af.viewport;
+ ap = af.alignPanel;
+ }
+ // LOAD TREES
+ // /////////////////////////////////////
+ if (loadTreesAndStructures && jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
+ {
+
+ Tree tree = jms.getTree(t);
+
+ TreePanel tp = (TreePanel) retrieveExistingObj(tree.getId());
+ if (tp == null)
+ {
+ tp = af.ShowNewickTree(
+ new jalview.io.NewickFile(tree.getNewick()),
+ tree.getTitle(), tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
+ if (tree.getId() != null)
+ {
+ // perhaps bind the tree id to something ?
+ }
+ }
+ else
+ {
+ // update local tree attributes ?
+ // TODO: should check if tp has been manipulated by user - if so its
+ // settings shouldn't be modified
+ tp.setTitle(tree.getTitle());
+ tp.setBounds(new Rectangle(tree.getXpos(), tree.getYpos(), tree
+ .getWidth(), tree.getHeight()));
+ tp.av = av; // af.viewport; // TODO: verify 'associate with all
+ // views'
+ // works still
+ tp.treeCanvas.av = av; // af.viewport;
+ tp.treeCanvas.ap = ap; // af.alignPanel;
+
+ }
+ if (tp == null)
+ {
+ warn("There was a problem recovering stored Newick tree: \n"
+ + tree.getNewick());
+ continue;
+ }
+
+ 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)
+ {
+ // run through all PDB ids on the alignment, and collect mappings between
+ // jmol view ids and all sequences referring to it
+ Hashtable<String, Object[]> jmolViewIds = new Hashtable();
+
+ 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++)
+ {
+ // check to see if we haven't already created this structure view
+ String sviewid = (ids[p].getStructureState(s).getViewId() == null) ? null
+ : ids[p].getStructureState(s).getViewId()
+ + uniqueSetSuffix;
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+ // Originally : ids[p].getFile()
+ // : TODO: verify external PDB file recovery still works in normal
+ // jalview project load
+ jpdb.setFile(loadPDBFile(jprovider, 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();
+
+ // Probably don't need to do this anymore...
+ // Desktop.desktop.getComponentAt(x, y);
+ // TODO: NOW: check that this recovers the PDB file correctly.
+ String pdbFile = loadPDBFile(jprovider, ids[p].getId());
+ jalview.datamodel.SequenceI seq = (jalview.datamodel.SequenceI) seqRefIds
+ .get(JSEQ[i].getId() + "");
+ if (sviewid == null)
+ {
+ sviewid = "_jalview_pre2_4_" + x + "," + y + "," + width
+ + "," + height;
+ }
+ if (!jmolViewIds.containsKey(sviewid))
+ {
+ jmolViewIds.put(sviewid, new Object[]
+ { new int[]
+ { x, y, width, height }, "",
+ new Hashtable<String, Object[]>() });
+ }
+ // TODO: assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}} from hash
+ Object[] jmoldat = (Object[]) jmolViewIds.get(sviewid);
+ if (((String) jmoldat[1]).length() < ids[p]
+ .getStructureState(s).getContent().length())
+ {
+ {
+ jmoldat[1] = ids[p].getStructureState(s).getContent();
+ }
+ }
+ Object[] seqstrmaps = (Object[]) ((Hashtable) jmoldat[2])
+ .get(ids[p].getFile());
+ if (seqstrmaps == null)
+ {
+ ((Hashtable) jmoldat[2]).put(
+ new File(ids[p].getFile()).toString(),
+ seqstrmaps = new Object[]
+ { pdbFile, ids[p].getId(), new Vector(),
+ new Vector() });
+ }
+ if (!((Vector) seqstrmaps[2]).contains(seq))
+ {
+ ((Vector) seqstrmaps[2]).addElement(seq);
+ // ((Vector)seqstrmaps[3]).addElement(n) : in principle, chains
+ // should be stored here : do we need to
+ // TODO: store and recover seq/pdb_id : chain mappings
+ }
+ }
+ }
+ }
+ }
+ {
+
+ // Instantiate the associated Jmol views
+ for (Entry<String, Object[]> entry : jmolViewIds.entrySet())
+ {
+ String sviewid = entry.getKey();
+ Object[] svattrib = entry.getValue();
+ int[] geom = (int[]) svattrib[0];
+ String state = (String) svattrib[1];
+ Hashtable<String, Object[]> oldFiles = (Hashtable<String, Object[]>) svattrib[2];
+
+ int x = geom[0], y = geom[1], width = geom[2], height = geom[3];
+ // collate the pdbfile -> sequence mappings from this view
+ Vector<String> pdbfilenames = new Vector<String>();
+ Vector<SequenceI[]> seqmaps = new Vector<SequenceI[]>();
+ Vector<String> pdbids = new Vector<String>();
+
+ // Search to see if we've already created this Jmol view
+ AppJmol comp = null;
+ JInternalFrame[] frames = null;
+ do
+ {
+ try
+ {
+ frames = Desktop.desktop.getAllFrames();
+ } catch (ArrayIndexOutOfBoundsException e)
+ {
+ // occasional No such child exceptions are thrown here...
+ frames = null;
+ try
+ {
+ Thread.sleep(10);
+ } catch (Exception f)
+ {
+ }
+ ;
+ }
+ } while (frames == null);
+ // search for any Jmol windows already open from other
+ // alignment views that exactly match the stored structure state
+ for (int f = 0; comp == null && f < frames.length; f++)
+ {
+ if (frames[f] instanceof AppJmol)
+ {
+ if (sviewid != null
+ && ((AppJmol) frames[f]).getViewId().equals(sviewid))
+ {
+ // post jalview 2.4 schema includes structure view id
+ comp = (AppJmol) frames[f];
+ }
+ else if (frames[f].getX() == x && frames[f].getY() == y
+ && frames[f].getHeight() == height
+ && frames[f].getWidth() == width)
+ {
+ comp = (AppJmol) frames[f];
+ }
+ }
+ }
+
+ if (comp == null)
+ {
+ // create a new Jmol window.
+ // First parse the Jmol state to translate filenames loaded into the
+ // view, and record the order in which files are shown in the Jmol
+ // view, so we can add the sequence mappings in same order.
+ StringBuffer newFileLoc = null;
+ int cp = 0, ncp, ecp;
+ while ((ncp = state.indexOf("load ", cp)) > -1)
+ {
+ if (newFileLoc == null)
+ {
+ newFileLoc = new StringBuffer();
+ }
+ newFileLoc.append(state.substring(cp,
+ ncp = (state.indexOf("\"", ncp + 1) + 1)));
+ String oldfilenam = state.substring(ncp,
+ ecp = state.indexOf("\"", ncp));
+ // recover the new mapping data for this old filename
+ // have to normalize filename - since Jmol and jalview do filename
+ // translation differently.
+ Object[] filedat = oldFiles.get(new File(oldfilenam)
+ .toString());
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append("\"");
+ cp = ecp + 1; // advance beyond last \" and set cursor so we can
+ // look for next file statement.
+ }
+ if (cp > 0)
+ {
+ // just append rest of state
+ newFileLoc.append(state.substring(cp));
+ }
+ else
+ {
+ System.err
+ .print("Ignoring incomplete Jmol state for PDB ids: ");
+ newFileLoc = new StringBuffer(state);
+ newFileLoc.append("; load append ");
+ for (String id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in
+ // the viewer
+ Object[] filedat = oldFiles.get(id);
+ String nfilename;
+ newFileLoc.append(((String) filedat[0]));
+ pdbfilenames.addElement((String) filedat[0]);
+ pdbids.addElement((String) filedat[1]);
+ seqmaps.addElement((SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]));
+ newFileLoc.append(" \"");
+ newFileLoc.append((String) filedat[0]);
+ newFileLoc.append("\"");
+
+ }
+ newFileLoc.append(";");
+ }
+
+ if (newFileLoc != null)
+ {
+ int histbug = newFileLoc.indexOf("history = ");
+ histbug += 10;
+ int diff = histbug == -1 ? -1 : newFileLoc.indexOf(";",
+ histbug);
+ String val = (diff == -1) ? null : newFileLoc.substring(
+ histbug, diff);
+ if (val != null && val.length() >= 4)
+ {
+ if (val.contains("e"))
+ {
+ if (val.trim().equals("true"))
+ {
+ val = "1";
+ }
+ else
+ {
+ val = "0";
+ }
+ newFileLoc.replace(histbug, diff, val);
+ }
+ }
+ // TODO: assemble String[] { pdb files }, String[] { id for each
+ // file }, orig_fileloc, SequenceI[][] {{ seqs_file 1 }, {
+ // seqs_file 2}} from hash
+ final String[] pdbf = (String[]) pdbfilenames
+ .toArray(new String[pdbfilenames.size()]), id = (String[]) pdbids
+ .toArray(new String[pdbids.size()]);
+ final SequenceI[][] sq = (SequenceI[][]) seqmaps
+ .toArray(new SequenceI[seqmaps.size()][]);
+ final String fileloc = newFileLoc.toString(), vid = sviewid;
+ final AlignFrame alf = af;
+ final java.awt.Rectangle rect = new java.awt.Rectangle(x, y,
+ width, height);
+ try
+ {
+ javax.swing.SwingUtilities.invokeAndWait(new Runnable()
+ {
+ public void run()
+ {
+ AppJmol sview=null;
+ try {
+ sview=new AppJmol(pdbf, id, sq, alf.alignPanel, fileloc,
+
+ rect, vid);
+ }
+ catch (OutOfMemoryError ex)
+ {
+ new OOMWarning("restoring structure view for PDB id "+id,(OutOfMemoryError) ex.getCause());
+ if (sview!=null && sview.isVisible())
+ {
+ sview.closeViewer();
+ sview.setVisible(false);
+ sview.dispose();
+ }
+ }
+ }
+ });
+ } catch (InvocationTargetException ex)
+ {
+ warn("Unexpected error when opening Jmol view.",ex);
+
+ } catch (InterruptedException e)
+ {
+ // e.printStackTrace();
+ }
+ }
+
+ }
+ else
+ // if (comp != null)
+ {
+ // NOTE: if the jalview project is part of a shared session then
+ // view synchronization should/could be done here.
+
+ // add mapping for sequences in this view to an already open Jmol
+ // instance
+ for (String id : oldFiles.keySet())
+ {
+ // add this and any other pdb files that should be present in the
+ // viewer
+ Object[] filedat = oldFiles.get(id);
+ String pdbFile = (String) filedat[0];
+ SequenceI[] seq = (SequenceI[]) ((Vector<SequenceI>) filedat[2])
+ .toArray(new SequenceI[0]);
+ StructureSelectionManager.getStructureSelectionManager()
+ .setMapping(seq, null, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+ ((AppJmol) comp).jmb.addSequenceForStructFile(pdbFile, seq);
+ }
+ }
+ }
+ }
+ }
+ // and finally return.
+ return af;
+ }
+
+ AlignFrame loadViewport(String file, JSeq[] JSEQ, Vector hiddenSeqs,
+ Alignment al, boolean hideConsensus, boolean hideQuality,
+ boolean hideConservation, JalviewModelSequence jms,
+ Viewport view, String uniqueSeqSetId, String viewId)
+ {
+ AlignFrame af = null;
+ af = new AlignFrame(al, view.getWidth(), view.getHeight(),
+ uniqueSeqSetId, viewId);
+
+ 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()));
+ }
+
+ 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)
+ {
+ // propagate shared settings to this new view
+ af.viewport.historyList = av.historyList;
+ af.viewport.redoList = av.redoList;
+ }
+ else
+ {
+ viewportsAdded.put(uniqueSeqSetId, af.viewport);
+ }
+ // TODO: check if this method can be called repeatedly without
+ // side-effects if alignpanel already registered.
+ PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+ }
+ // apply Hidden regions to view.
+ 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);
+
+ }
+ // set visibility of annotation in view
+ 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();
+ }
+ // recover view properties and display parameters
+ 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.setShowUnconserved(view.hasShowUnconserved() ? view
+ .isShowUnconserved() : false);
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
+
+ ColourSchemeI cs = null;
+ // apply colourschemes
+ if (view.getBgColour() != null)
+ {
+ if (view.getBgColour().startsWith("ucs"))
+ {
+ cs = GetUserColourScheme(jms, view.getBgColour());
+ }
+ else if (view.getBgColour().startsWith("Annotation"))
+ {
+ // int find annotation
+ if (af.viewport.alignment.getAlignmentAnnotation() != null)
+ {
+ 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 (view.hasCentreColumnLabels())
+ {
+ af.viewport.setCentreColumnLabels(view.getCentreColumnLabels());
+ }
+ if (view.hasIgnoreGapsinConsensus())
+ {
+ af.viewport.ignoreGapsInConsensusCalculation = view
+ .getIgnoreGapsinConsensus();
+ }
+ if (view.hasFollowHighlight())
+ {
+ af.viewport.followHighlight = view.getFollowHighlight();
+ }
+ if (view.hasFollowSelection())
+ {
+ af.viewport.followSelection = view.getFollowSelection();
+ }
+ if (view.hasShowConsensusHistogram())
+ {
+ af.viewport.setShowConsensusHistogram(view
+ .getShowConsensusHistogram());
+ }
+ else
+ {
+ af.viewport.setShowConsensusHistogram(true);
+ }
+ if (view.hasShowSequenceLogo())
+ {
+ af.viewport.showSequenceLogo = view.getShowSequenceLogo();
+ }
+ else
+ {
+ af.viewport.showSequenceLogo = false;
+ }
+ if (view.hasShowDbRefTooltip())
+ {
+ af.viewport.setShowDbRefs(view.getShowDbRefTooltip());
+ }
+ if (view.hasShowNPfeatureTooltip())
+ {
+ af.viewport.setShowNpFeats(view.hasShowNPfeatureTooltip());
+ }
+ if (view.hasShowGroupConsensus())
+ {
+ af.viewport.setShowGroupConsensus(view.getShowGroupConsensus());
+ }
+ else
+ {
+ af.viewport.setShowGroupConsensus(false);
+ }
+ if (view.hasShowGroupConservation())
+ {
+ af.viewport.setShowGroupConservation(view.getShowGroupConservation());
+ }
+ else
+ {
+ af.viewport.setShowGroupConservation(false);
+ }
+
+ // recover featre settings
+ 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);
+ if (setting.hasMincolour())
+ {
+ GraduatedColor gc = setting.hasMin() ? new GraduatedColor(
+ new java.awt.Color(setting.getMincolour()),
+ new java.awt.Color(setting.getColour()),
+ setting.getMin(), setting.getMax()) : new GraduatedColor(
+ new java.awt.Color(setting.getMincolour()),
+ new java.awt.Color(setting.getColour()), 0, 1);
+ if (setting.hasThreshold())
+ {
+ gc.setThresh(setting.getThreshold());
+ gc.setThreshType(setting.getThreshstate());
+ }
+ gc.setAutoScaled(true); // default
+ if (setting.hasAutoScale())
+ {
+ gc.setAutoScaled(setting.getAutoScale());
+ }
+ if (setting.hasColourByLabel())
+ {
+ gc.setColourByLabel(setting.getColourByLabel());
+ }
+ // and put in the feature colour table.
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(
+ setting.getType(), gc);
+ }
+ else
+ {
+ 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 < jms.getFeatureSettings().getGroupCount(); gs++)
+ {
+ Group grp = jms.getFeatureSettings().getGroup(gs);
+ fgtable.put(grp.getName(), new Boolean(grp.getDisplay()));
+ }
+ }
+
+ if (view.getHiddenColumnsCount() > 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);
+ // TODO: we don't need to do this if the viewport is aready visible.
+ Desktop.addInternalFrame(af, view.getTitle(), view.getWidth(),
+ view.getHeight());
+ af.alignPanel.updateAnnotation(false); // recompute any autoannotation
+ return af;
+ }
+
+ Hashtable skipList = null;
+
+ /**
+ * TODO remove this method
+ *
+ * @param view
+ * @return AlignFrame bound to sequenceSetId from view, if one exists. private
+ * AlignFrame getSkippedFrame(Viewport view) { if (skipList==null) {
+ * throw new Error("Implementation Error. No skipList defined for this
+ * Jalview2XML instance."); } return (AlignFrame)
+ * skipList.get(view.getSequenceSetId()); }
+ */
+
+ /**
+ * Check if the Jalview view contained in object should be skipped or not.
+ *
+ * @param object
+ * @return true if view's sequenceSetId is a key in skipList
+ */
+ private boolean skipViewport(JalviewModel object)
+ {
+ if (skipList == null)
+ {
+ return false;
+ }
+ String id;
+ if (skipList.containsKey(id = object.getJalviewModelSequence()
+ .getViewport()[0].getSequenceSetId()))
+ {
+ if (Cache.log != null && Cache.log.isDebugEnabled())
+ {
+ Cache.log.debug("Skipping seuqence set id " + id);
+ }
+ return true;
+ }
+ return false;
+ }
+
+ public void AddToSkipList(AlignFrame af)
+ {
+ if (skipList == null)
+ {
+ skipList = new Hashtable();
+ }
+ skipList.put(af.getViewport().getSequenceSetId(), af);
+ }
+
+ public void clearSkipList()
+ {
+ if (skipList != null)
+ {
+ skipList.clear();
+ skipList = null;
+ }
+ }
+
+ private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al)
+ {
+ jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId());
+ Vector dseqs = null;
+ if (ds == null)
+ {
+ // create a list of new dataset sequences
+ dseqs = new Vector();
+ }
+ for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++)
+ {
+ Sequence vamsasSeq = vamsasSet.getSequence(i);
+ ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs);
+ }
+ // create a new dataset
+ if (ds == null)
+ {
+ SequenceI[] dsseqs = new SequenceI[dseqs.size()];
+ dseqs.copyInto(dsseqs);
+ ds = new jalview.datamodel.Alignment(dsseqs);
+ debug("Created new dataset " + vamsasSet.getDatasetId()
+ + " for alignment " + System.identityHashCode(al));
+ addDatasetRef(vamsasSet.getDatasetId(), ds);
+ }
+ // set the dataset for the newly imported alignment.
+ if (al.getDataset() == null)
+ {
+ al.setDataset(ds);
+ }
+ }
+
+ /**
+ *
+ * @param vamsasSeq
+ * sequence definition to create/merge dataset sequence for
+ * @param ds
+ * dataset alignment
+ * @param dseqs
+ * vector to add new dataset sequence to
+ */
+ private void ensureJalviewDatasetSequence(Sequence vamsasSeq,
+ AlignmentI ds, Vector dseqs)
+ {
+ // JBP TODO: Check this is called for AlCodonFrames to support recovery of
+ // xRef Codon Maps
+ jalview.datamodel.Sequence sq = (jalview.datamodel.Sequence) seqRefIds
+ .get(vamsasSeq.getId());
+ jalview.datamodel.SequenceI dsq = null;
+ if (sq != null && sq.getDatasetSequence() != null)
+ {
+ dsq = (jalview.datamodel.SequenceI) sq.getDatasetSequence();
+ }
+
+ String sqid = vamsasSeq.getDsseqid();
+ if (dsq == null)
+ {
+ // need to create or add a new dataset sequence reference to this sequence
+ if (sqid != null)
+ {
+ dsq = (jalview.datamodel.SequenceI) seqRefIds.get(sqid);
+ }
+ // check again
+ if (dsq == null)
+ {
+ // make a new dataset sequence
+ dsq = sq.createDatasetSequence();
+ if (sqid == null)
+ {
+ // make up a new dataset reference for this sequence
+ sqid = seqHash(dsq);
+ }
+ dsq.setVamsasId(uniqueSetSuffix + sqid);
+ seqRefIds.put(sqid, dsq);
+ if (ds == null)
+ {
+ if (dseqs != null)
+ {
+ dseqs.addElement(dsq);
+ }
+ }
+ else
+ {
+ ds.addSequence(dsq);
+ }
+ }
+ else
+ {
+ if (sq != dsq)
+ { // make this dataset sequence sq's dataset sequence
+ sq.setDatasetSequence(dsq);
+ }
+ }
+ }
+ // TODO: refactor this as a merge dataset sequence function
+ // now check that sq (the dataset sequence) sequence really is the union of
+ // all references to it
+ // boolean pre = sq.getStart() < dsq.getStart();
+ // boolean post = sq.getEnd() > dsq.getEnd();
+ // if (pre || post)
+ if (sq != dsq)
+ {
+ StringBuffer sb = new StringBuffer();
+ String newres = jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, sq.getSequenceAsString());
+ if (!newres.equalsIgnoreCase(dsq.getSequenceAsString())
+ && newres.length() > dsq.getLength())
+ {
+ // Update with the longer sequence.
+ synchronized (dsq)
+ {
+ /*
+ * if (pre) { sb.insert(0, newres .substring(0, dsq.getStart() -
+ * sq.getStart())); dsq.setStart(sq.getStart()); } if (post) {
+ * sb.append(newres.substring(newres.length() - sq.getEnd() -
+ * dsq.getEnd())); dsq.setEnd(sq.getEnd()); }
+ */
+ dsq.setSequence(sb.toString());
+ }
+ // TODO: merges will never happen if we 'know' we have the real dataset
+ // sequence - this should be detected when id==dssid
+ System.err.println("DEBUG Notice: Merged dataset sequence"); // ("
+ // + (pre ? "prepended" : "") + " "
+ // + (post ? "appended" : ""));
+ }
+ }
+ }
+
+ java.util.Hashtable datasetIds = null;
+
+ java.util.IdentityHashMap dataset2Ids = null;
+
+ private Alignment getDatasetFor(String datasetId)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ return null;
+ }
+ if (datasetIds.containsKey(datasetId))
+ {
+ return (Alignment) datasetIds.get(datasetId);
+ }
+ return null;
+ }
+
+ private void addDatasetRef(String datasetId, Alignment dataset)
+ {
+ if (datasetIds == null)
+ {
+ datasetIds = new Hashtable();
+ }
+ datasetIds.put(datasetId, dataset);
+ }
+
+ /**
+ * make a new dataset ID for this jalview dataset alignment
+ *
+ * @param dataset
+ * @return
+ */
+ private String getDatasetIdRef(jalview.datamodel.Alignment dataset)
+ {
+ if (dataset.getDataset() != null)
+ {
+ warn("Serious issue! Dataset Object passed to getDatasetIdRef is not a Jalview DATASET alignment...");
+ }
+ String datasetId = makeHashCode(dataset, null);
+ if (datasetId == null)
+ {
+ // make a new datasetId and record it
+ if (dataset2Ids == null)
+ {
+ dataset2Ids = new IdentityHashMap();
+ }
+ else
+ {
+ datasetId = (String) dataset2Ids.get(dataset);
+ }
+ if (datasetId == null)
+ {
+ datasetId = "ds" + dataset2Ids.size() + 1;
+ dataset2Ids.put(dataset, datasetId);
+ }
+ }
+ return datasetId;
+ }
+
+ private void addDBRefs(SequenceI datasetSequence, Sequence sequence)
+ {
+ for (int d = 0; d < sequence.getDBRefCount(); d++)
+ {
+ DBRef dr = sequence.getDBRef(d);
+ jalview.datamodel.DBRefEntry entry = new jalview.datamodel.DBRefEntry(
+ sequence.getDBRef(d).getSource(), sequence.getDBRef(d)
+ .getVersion(), sequence.getDBRef(d).getAccessionId());
+ if (dr.getMapping() != null)
+ {
+ entry.setMap(addMapping(dr.getMapping()));
+ }
+ datasetSequence.addDBRef(entry);
+ }
+ }
+
+ private jalview.datamodel.Mapping addMapping(Mapping m)
+ {
+ SequenceI dsto = null;
+ // Mapping m = dr.getMapping();
+ int fr[] = new int[m.getMapListFromCount() * 2];
+ Enumeration f = m.enumerateMapListFrom();
+ for (int _i = 0; f.hasMoreElements(); _i += 2)
+ {
+ MapListFrom mf = (MapListFrom) f.nextElement();
+ fr[_i] = mf.getStart();
+ fr[_i + 1] = mf.getEnd();
+ }
+ int fto[] = new int[m.getMapListToCount() * 2];
+ f = m.enumerateMapListTo();
+ for (int _i = 0; f.hasMoreElements(); _i += 2)
+ {
+ MapListTo mf = (MapListTo) f.nextElement();
+ fto[_i] = mf.getStart();
+ fto[_i + 1] = mf.getEnd();
+ }
+ jalview.datamodel.Mapping jmap = new jalview.datamodel.Mapping(dsto,
+ fr, fto, (int) m.getMapFromUnit(), (int) m.getMapToUnit());
+ if (m.getMappingChoice() != null)
+ {
+ MappingChoice mc = m.getMappingChoice();
+ if (mc.getDseqFor() != null)
+ {
+ String dsfor = "" + mc.getDseqFor();
+ if (seqRefIds.containsKey(dsfor))
+ {
+ /**
+ * recover from hash
+ */
+ jmap.setTo((SequenceI) seqRefIds.get(dsfor));
+ }
+ else
+ {
+ frefedSequence.add(new Object[]
+ { dsfor, jmap });
+ }
+ }
+ else
+ {
+ /**
+ * local sequence definition
+ */
+ Sequence ms = mc.getSequence();
+ jalview.datamodel.Sequence djs = null;
+ String sqid = ms.getDsseqid();
+ if (sqid != null && sqid.length() > 0)
+ {
+ /*
+ * recover dataset sequence
+ */
+ djs = (jalview.datamodel.Sequence) seqRefIds.get(sqid);
+ }
+ else
+ {
+ System.err
+ .println("Warning - making up dataset sequence id for DbRef sequence map reference");
+ sqid = ((Object) ms).toString(); // make up a new hascode for
+ // undefined dataset sequence hash
+ // (unlikely to happen)
+ }
+
+ if (djs == null)
+ {
+ /**
+ * make a new dataset sequence and add it to refIds hash
+ */
+ djs = new jalview.datamodel.Sequence(ms.getName(),
+ ms.getSequence());
+ djs.setStart(jmap.getMap().getToLowest());
+ djs.setEnd(jmap.getMap().getToHighest());
+ djs.setVamsasId(uniqueSetSuffix + sqid);
+ jmap.setTo(djs);
+ seqRefIds.put(sqid, djs);
+
+ }
+ jalview.bin.Cache.log.debug("about to recurse on addDBRefs.");
+ addDBRefs(djs, ms);
+
+ }
+ }
+ return (jmap);
+
+ }
+
+ public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
+ boolean keepSeqRefs)
+ {
+ initSeqRefs();
+ jalview.schemabinding.version2.JalviewModel jm = SaveState(ap, null,
+ null);
+
+ if (!keepSeqRefs)
+ {
+ clearSeqRefs();
+ jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+ }
+ else
+ {
+ uniqueSetSuffix = "";
+ jm.getJalviewModelSequence().getViewport(0).setId(null); // we don't
+ // overwrite the
+ // view we just
+ // copied
+ }
+ if (this.frefedSequence == null)
+ {
+ frefedSequence = new Vector();
+ }
+
+ viewportsAdded = new Hashtable();
+
+ AlignFrame af = LoadFromObject(jm, null, false, null);
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ /*
+ * if(ap.av.alignment.getAlignmentAnnotation()!=null) { for(int i=0;
+ * i<ap.av.alignment.getAlignmentAnnotation().length; i++) {
+ * if(!ap.av.alignment.getAlignmentAnnotation()[i].autoCalculated) {
+ * af.alignPanel.av.alignment.getAlignmentAnnotation()[i] =
+ * ap.av.alignment.getAlignmentAnnotation()[i]; } } }
+ */
+
+ return af.alignPanel;
+ }
+
+ /**
+ * flag indicating if hashtables should be cleared on finalization TODO this
+ * flag may not be necessary
+ */
+ private boolean _cleartables = true;
+
+ private Hashtable jvids2vobj;
+
+ /*
+ * (non-Javadoc)
+ *
+ * @see java.lang.Object#finalize()
+ */
+ protected void finalize() throws Throwable
+ {
+ // really make sure we have no buried refs left.
+ if (_cleartables)
+ {
+ clearSeqRefs();
+ }
+ this.seqRefIds = null;
+ this.seqsToIds = null;
+ super.finalize();
+ }
+
+ private void warn(String msg)
+ {
+ warn(msg, null);
+ }
+
+ private void warn(String msg, Exception e)
+ {
+ if (Cache.log != null)
+ {
+ if (e != null)
+ {
+ Cache.log.warn(msg, e);
+ }
+ else
+ {
+ Cache.log.warn(msg);
+ }
+ }
+ else
+ {
+ System.err.println("Warning: " + msg);
+ if (e != null)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ private void debug(String string)
+ {
+ debug(string, null);
+ }
+
+ private void debug(String msg, Exception e)
+ {
+ if (Cache.log != null)
+ {
+ if (e != null)
+ {
+ Cache.log.debug(msg, e);
+ }
+ else
+ {
+ Cache.log.debug(msg);
+ }
+ }
+ else
+ {
+ System.err.println("Warning: " + msg);
+ if (e != null)
+ {
+ e.printStackTrace();
+ }
+ }
+ }
+
+ /**
+ * set the object to ID mapping tables used to write/recover objects and XML
+ * ID strings for the jalview project. If external tables are provided then
+ * finalize and clearSeqRefs will not clear the tables when the Jalview2XML
+ * object goes out of scope. - also populates the datasetIds hashtable with
+ * alignment objects containing dataset sequences
+ *
+ * @param vobj2jv
+ * Map from ID strings to jalview datamodel
+ * @param jv2vobj
+ * Map from jalview datamodel to ID strings
+ *
+ *
+ */
+ public void setObjectMappingTables(Hashtable vobj2jv,
+ IdentityHashMap jv2vobj)
+ {
+ this.jv2vobj = jv2vobj;
+ this.vobj2jv = vobj2jv;
+ Iterator ds = jv2vobj.keySet().iterator();
+ String id;
+ while (ds.hasNext())
+ {
+ Object jvobj = ds.next();
+ id = jv2vobj.get(jvobj).toString();
+ if (jvobj instanceof jalview.datamodel.Alignment)
+ {
+ if (((jalview.datamodel.Alignment) jvobj).getDataset() == null)
+ {
+ addDatasetRef(id, (jalview.datamodel.Alignment) jvobj);
+ }
+ }
+ else if (jvobj instanceof jalview.datamodel.Sequence)
+ {
+ // register sequence object so the XML parser can recover it.
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+ if (seqsToIds == null)
+ {
+ seqsToIds = new IdentityHashMap();
+ }
+ seqRefIds.put(jv2vobj.get(jvobj).toString(), jvobj);
+ seqsToIds.put(jvobj, id);
+ }
+ else if (jvobj instanceof jalview.datamodel.AlignmentAnnotation)
+ {
+ if (annotationIds == null)
+ {
+ annotationIds = new Hashtable();
+ }
+ String anid;
+ annotationIds.put(anid = jv2vobj.get(jvobj).toString(), jvobj);
+ jalview.datamodel.AlignmentAnnotation jvann = (jalview.datamodel.AlignmentAnnotation) jvobj;
+ if (jvann.annotationId == null)
+ {
+ jvann.annotationId = anid;
+ }
+ if (!jvann.annotationId.equals(anid))
+ {
+ // TODO verify that this is the correct behaviour
+ this.warn("Overriding Annotation ID for " + anid
+ + " from different id : " + jvann.annotationId);
+ jvann.annotationId = anid;
+ }
+ }
+ else if (jvobj instanceof String)
+ {
+ if (jvids2vobj == null)
+ {
+ jvids2vobj = new Hashtable();
+ jvids2vobj.put(jvobj, jv2vobj.get(jvobj).toString());
+ }
+ }
+ else
+ Cache.log.debug("Ignoring " + jvobj.getClass() + " (ID = " + id);
+ }
+ }
+
+ /**
+ * set the uniqueSetSuffix used to prefix/suffix object IDs for jalview
+ * objects created from the project archive. If string is null (default for
+ * construction) then suffix will be set automatically.
+ *
+ * @param string
+ */
+ public void setUniqueSetSuffix(String string)
+ {
+ uniqueSetSuffix = string;
+
+ }
+
+ /**
+ * uses skipList2 as the skipList for skipping views on sequence sets
+ * associated with keys in the skipList
+ *
+ * @param skipList2
+ */
+ public void setSkipList(Hashtable skipList2)
+ {
+ skipList = skipList2;
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff