-/*\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
- jalview.datamodel.AlignmentI jalhidden = null;\r
-\r
- if(av.hasHiddenRows)\r
- {\r
- jalhidden = jal;\r
- jal = jal.getHiddenSequences().getFullAlignment();\r
- }\r
-\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
- Vector pdbfiles = null;\r
-\r
- //SAVE SEQUENCES\r
- int id = 0;\r
- for (int i = 0; i < jal.getHeight(); i++)\r
- {\r
- seqids.add(jal.getSequenceAt(i));\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
- if(jal.getSequenceAt(i).getDatasetSequence().getDBRef()!=null)\r
- {\r
- jalview.datamodel.DBRefEntry [] dbrefs =\r
- jal.getSequenceAt(i).getDatasetSequence().getDBRef();\r
-\r
- for(int d=0; d<dbrefs.length; d++)\r
- {\r
- DBRef dbref = new DBRef();\r
- dbref.setSource( dbrefs[d].getSource() );\r
- dbref.setVersion( dbrefs[d].getVersion());\r
- dbref.setAccessionId(dbrefs[d].getAccessionId());\r
- vamsasSeq.addDBRef(dbref);\r
- }\r
- }\r
-\r
- jseq = new JSeq();\r
- jseq.setStart(jal.getSequenceAt(i).getStart());\r
- jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
- jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
-\r
- jseq.setId(id);\r
-\r
- if (av.hasHiddenRows)\r
- {\r
- jseq.setHidden(jalhidden.getHiddenSequences().isHidden(\r
- jal.getSequenceAt(i)));\r
-\r
- if(jal.getSequenceAt(i).getHiddenSequences()!=null)\r
- {\r
- jalview.datamodel.SequenceI [] reps =\r
- jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);\r
-\r
- for(int h=0; h<reps.length; h++)\r
- {\r
- jseq.addHiddenSequences(\r
- jal.findIndex(reps[h])\r
- );\r
- }\r
- }\r
- }\r
-\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.getFile()!=null)\r
- {\r
- if(pdbfiles==null)\r
- pdbfiles = new Vector();\r
-\r
-\r
- if(!pdbfiles.contains(entry.getId()))\r
- {\r
- pdbfiles.addElement(entry.getId());\r
- try\r
- {\r
- File file = new File(entry.getFile());\r
- if(file.exists())\r
- {\r
- byte[] data = new byte[ (int) file.length()];\r
- jout.putNextEntry(new JarEntry(entry.getId()));\r
- DataInputStream dis = new DataInputStream(new\r
- FileInputStream(file));\r
- dis.readFully(data);\r
-\r
- DataOutputStream dout = new DataOutputStream(jout);\r
- dout.write(data, 0, data.length);\r
- jout.closeEntry();\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
- }\r
-\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(false); 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
- if(av.hasHiddenColumns)\r
- {\r
- for(int c=0; c<av.getColumnSelection().getHiddenColumns().size(); c++)\r
- {\r
- int [] region = (int[]) av.getColumnSelection().getHiddenColumns().elementAt(c);\r
- HiddenColumns hc = new HiddenColumns();\r
- hc.setStart(region[0]);\r
- hc.setEnd(region[1]);\r
- view.addHiddenColumns(hc);\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
- jalview.gui.AlignFrame af = null;\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
- if (jarentry != null && jarentry.getName().endsWith(".xml"))\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, file);\r
- entryCount++;\r
- }\r
- else if (jarentry != null)\r
- {\r
- //Some other file here.\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
- String loadPDBFile(String file, String pdbId)\r
- {\r
- System.out.println("load file "+file);\r
- try\r
- {\r
- JarInputStream jin = null;\r
-\r
- if (file.startsWith("http://"))\r
- {\r
- jin = new JarInputStream(new URL(file).openStream());\r
- }\r
- else\r
- {\r
- jin = new JarInputStream(new FileInputStream(file));\r
- }\r
-\r
- JarEntry entry = null;\r
- do\r
- {\r
- entry = jin.getNextJarEntry();\r
- }\r
- while (!entry.getName().equals(pdbId));\r
-\r
- BufferedReader in = new BufferedReader(new InputStreamReader(jin));\r
- File outFile = File.createTempFile("jalview_pdb", ".txt");\r
- outFile.deleteOnExit();\r
- PrintWriter out = new PrintWriter(new FileOutputStream(outFile));\r
- String data;\r
-\r
- while ( (data = in.readLine()) != null)\r
- {\r
- out.println(data);\r
- }\r
- out.close();\r
- return outFile.getAbsolutePath();\r
-\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
-\r
- return null;\r
- }\r
-\r
-\r
- AlignFrame LoadFromObject(JalviewModel object, String file)\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
- Vector hiddenSeqs = null;\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
- if(JSEQ[i].getHidden())\r
- {\r
- if(hiddenSeqs == null)\r
- hiddenSeqs = new Vector();\r
- hiddenSeqs.addElement(jseqs[i]);\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
-\r
- Hashtable pdbloaded = new Hashtable();\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
- if (ids[p].getFile() != null)\r
- {\r
- if (!pdbloaded.containsKey(ids[p].getFile()))\r
- {\r
- String tmppdb = loadPDBFile(file, ids[p].getId());\r
- entry.setFile(tmppdb);\r
- pdbloaded.put(ids[p].getId(), tmppdb);\r
- }\r
- else\r
- entry.setFile(pdbloaded.get(ids[p].getId()).toString());\r
- }\r
-\r
- al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
- }\r
- }\r
- if(vamsasSeq[i].getDBRefCount()>0)\r
- {\r
- for(int d=0; d<vamsasSeq[i].getDBRefCount(); d++)\r
- {\r
- jalview.datamodel.DBRefEntry entry =\r
- new jalview.datamodel.DBRefEntry(\r
- vamsasSeq[i].getDBRef(d).getSource(),\r
- vamsasSeq[i].getDBRef(d).getVersion(),\r
- vamsasSeq[i].getDBRef(d).getAccessionId()\r
- );\r
- al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);\r
- }\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.getSequences(false), 0,\r
- sg.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, 25);\r
- sg.cs.setConservation(c);\r
- }\r
-\r
- al.addGroup(sg);\r
- }\r
- }\r
-\r
-\r
- /////////////////////////////////\r
- // LOAD VIEWPORT\r
- Viewport[] views = jms.getViewport();\r
- Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\r
-\r
-\r
- AlignFrame af = new AlignFrame(al);\r
-\r
- if(hiddenSeqs!=null)\r
- {\r
- for(int s=0; s<JSEQ.length; s++)\r
- {\r
- for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)\r
- {\r
- al.getSequenceAt(s).addHiddenSequence(\r
- al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )\r
- );\r
- }\r
- }\r
-\r
- for(int s=0; s<hiddenSeqs.size(); s++)\r
- {\r
- af.viewport.hideSequence(\r
- (jalview.datamodel.SequenceI)hiddenSeqs.elementAt(s));\r
- }\r
- }\r
-\r
-\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
- af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
-\r
- af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
- af.viewport.setShowAnnotation(view.getShowAnnotation());\r
- af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
-\r
- 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
- if (view.getHiddenColumnsCount() > 0)\r
- {\r
- for (int c = 0; c < view.getHiddenColumnsCount(); c++)\r
- {\r
- af.viewport.hideColumns(\r
- view.getHiddenColumns(c).getStart(),\r
- view.getHiddenColumns(c).getEnd()+1\r
- );\r
- }\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
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
+ * GNU General Public License for more details.
+ *
+ * You should have received a copy of the GNU General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ */
+package jalview.gui;
+
+import java.io.*;
+import java.net.*;
+import java.util.*;
+import java.util.jar.*;
+
+import javax.swing.*;
+
+import org.exolab.castor.xml.*;
+import jalview.schemabinding.version2.*;
+import jalview.schemes.*;
+import jalview.structure.StructureSelectionManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class Jalview2XML
+{
+
+ Hashtable seqRefIds;
+
+ /**
+ * This maintains a list of viewports, the key being the
+ * seqSetId. Important to set historyItem and redoList
+ * for multiple views
+ */
+ Hashtable viewportsAdded;
+
+ Hashtable annotationIds = new Hashtable();
+
+ String uniqueSetSuffix = "";
+ /**
+ * List of pdbfiles added to Jar
+ */
+ Vector pdbfiles = null;
+
+ // SAVES SEVERAL ALIGNMENT WINDOWS TO SAME JARFILE
+ public void SaveState(File statefile)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ if (frames == null)
+ {
+ return;
+ }
+
+ try
+ {
+ FileOutputStream fos = new FileOutputStream(statefile);
+ JarOutputStream jout = new JarOutputStream(fos);
+
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS
+ ////////////////////////////////////////////////////
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+
+ Vector shortNames = new Vector();
+
+ //REVERSE ORDER
+ for (int i = frames.length - 1; i > -1; i--)
+ {
+ if (frames[i] instanceof AlignFrame)
+ {
+ AlignFrame af = (AlignFrame) frames[i];
+
+ String shortName = af.getTitle();
+
+ if (shortName.indexOf(File.separatorChar) > -1)
+ {
+ shortName = shortName.substring(shortName.lastIndexOf(
+ File.separatorChar) + 1);
+ }
+
+ int count = 1;
+
+ while (shortNames.contains(shortName))
+ {
+ if (shortName.endsWith("_" + (count - 1)))
+ {
+ shortName = shortName.substring(0,
+ shortName.lastIndexOf("_"));
+ }
+
+ shortName = shortName.concat("_" + count);
+ count++;
+ }
+
+ shortNames.addElement(shortName);
+
+ if (!shortName.endsWith(".xml"))
+ {
+ shortName = shortName + ".xml";
+ }
+
+ int ap, apSize = af.alignPanels.size();
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.
+ elementAt(ap);
+
+ SaveState(apanel,
+ apSize == 1 ? shortName : ap + shortName,
+ jout, out);
+ }
+ }
+ }
+
+ out.close();
+ jout.close();
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW
+ public boolean SaveAlignment(AlignFrame af, String jarFile,
+ String fileName)
+ {
+ try
+ {
+ int ap, apSize = af.alignPanels.size();
+ FileOutputStream fos = new FileOutputStream(jarFile);
+ JarOutputStream jout = new JarOutputStream(fos);
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,
+ "UTF-8"));
+ for (ap = 0; ap < apSize; ap++)
+ {
+ AlignmentPanel apanel = (AlignmentPanel) af.alignPanels.elementAt(ap);
+
+ SaveState(apanel,
+ apSize == 1 ? fileName : fileName + ap,
+ jout, out);
+ }
+
+ out.close();
+ jout.close();
+ return true;
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ return false;
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param af DOCUMENT ME!
+ * @param timeStamp DOCUMENT ME!
+ * @param fileName DOCUMENT ME!
+ * @param jout DOCUMENT ME!
+ * @param out DOCUMENT ME!
+ */
+ public JalviewModel SaveState(AlignmentPanel ap,
+ String fileName,
+ JarOutputStream jout,
+ PrintWriter out)
+ {
+ if (seqRefIds == null)
+ {
+ seqRefIds = new Hashtable();
+ }
+
+ Vector userColours = new Vector();
+
+ AlignViewport av = ap.av;
+
+ JalviewModel object = new JalviewModel();
+ object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());
+
+ object.setCreationDate(new java.util.Date(System.currentTimeMillis()));
+ object.setVersion(jalview.bin.Cache.getProperty("VERSION"));
+
+ jalview.datamodel.AlignmentI jal = av.alignment;
+
+ if (av.hasHiddenRows)
+ {
+ jal = jal.getHiddenSequences().getFullAlignment();
+ }
+
+ SequenceSet vamsasSet = new SequenceSet();
+ Sequence vamsasSeq;
+ JalviewModelSequence jms = new JalviewModelSequence();
+
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");
+
+ JSeq jseq;
+
+ //SAVE SEQUENCES
+ int id = 0;
+ jalview.datamodel.SequenceI jds;
+ for (int i = 0; i < jal.getHeight(); i++)
+ {
+ jds = jal.getSequenceAt(i);
+ id = jds.hashCode();
+
+ if (seqRefIds.get(id + "") != null)
+ {
+
+ }
+ else
+ {
+ vamsasSeq = new Sequence();
+ vamsasSeq.setId(id + "");
+ vamsasSeq.setName(jds.getName());
+ vamsasSeq.setSequence(jds.getSequenceAsString());
+ vamsasSeq.setDescription(jds.getDescription());
+
+ if (jds.getDatasetSequence().getDBRef() != null)
+ {
+ jalview.datamodel.DBRefEntry[] dbrefs =
+ jds.getDatasetSequence().getDBRef();
+
+ for (int d = 0; d < dbrefs.length; d++)
+ {
+ DBRef dbref = new DBRef();
+ dbref.setSource(dbrefs[d].getSource());
+ dbref.setVersion(dbrefs[d].getVersion());
+ dbref.setAccessionId(dbrefs[d].getAccessionId());
+ vamsasSeq.addDBRef(dbref);
+ }
+ }
+
+ vamsasSet.addSequence(vamsasSeq);
+ seqRefIds.put(id + "", jal.getSequenceAt(i));
+ }
+
+ jseq = new JSeq();
+ jseq.setStart(jds.getStart());
+ jseq.setEnd(jds.getEnd());
+ jseq.setColour(av.getSequenceColour(jds).getRGB());
+
+ jseq.setId(id);
+
+ if (av.hasHiddenRows)
+ {
+ jseq.setHidden(av.alignment.getHiddenSequences().isHidden(jds));
+
+ if (av.hiddenRepSequences != null
+ && av.hiddenRepSequences.containsKey(jal.getSequenceAt(i)))
+ {
+ jalview.datamodel.SequenceI[] reps =
+ ( (jalview.datamodel.SequenceGroup)
+ av.hiddenRepSequences.get(
+ jal.getSequenceAt(i))).getSequencesInOrder(jal);
+
+ for (int h = 0; h < reps.length; h++)
+ {
+ if (reps[h] != jal.getSequenceAt(i))
+ {
+ jseq.addHiddenSequences(
+ jal.findIndex(reps[h])
+ );
+ }
+ }
+ }
+ }
+
+ if (jds.getDatasetSequence().getSequenceFeatures() != null)
+ {
+ jalview.datamodel.SequenceFeature[] sf
+ = jds.getDatasetSequence().getSequenceFeatures();
+ int index = 0;
+ while (index < sf.length)
+ {
+ Features features = new Features();
+
+ features.setBegin(sf[index].getBegin());
+ features.setEnd(sf[index].getEnd());
+ features.setDescription(sf[index].getDescription());
+ features.setType(sf[index].getType());
+ features.setFeatureGroup(sf[index].getFeatureGroup());
+ features.setScore(sf[index].getScore());
+ if (sf[index].links != null)
+ {
+ for (int l = 0; l < sf[index].links.size(); l++)
+ {
+ OtherData keyValue = new OtherData();
+ keyValue.setKey("LINK_" + l);
+ keyValue.setValue(sf[index].links.elementAt(l).toString());
+ features.addOtherData(keyValue);
+ }
+ }
+ if (sf[index].otherDetails != null)
+ {
+ String key;
+ Enumeration keys = sf[index].otherDetails.keys();
+ while (keys.hasMoreElements())
+ {
+ key = keys.nextElement().toString();
+ OtherData keyValue = new OtherData();
+ keyValue.setKey(key);
+ keyValue.setValue(
+ sf[index].otherDetails.get(key).toString());
+ features.addOtherData(keyValue);
+ }
+ }
+
+ jseq.addFeatures(features);
+ index++;
+ }
+ }
+
+ if (jds.getDatasetSequence().getPDBId() != null)
+ {
+ Enumeration en = jds.getDatasetSequence().getPDBId().elements();
+ while (en.hasMoreElements())
+ {
+ Pdbids pdb = new Pdbids();
+ jalview.datamodel.PDBEntry entry
+ = (jalview.datamodel.PDBEntry) en.nextElement();
+
+ pdb.setId(entry.getId());
+ pdb.setType(entry.getType());
+
+ AppJMol jmol;
+ //This must have been loaded, is it still visible?
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+ for (int f = frames.length - 1; f > -1; f--)
+ {
+ if (frames[f] instanceof AppJMol)
+ {
+ jmol = (AppJMol) frames[f];
+ if (!jmol.pdbentry.getId().equals(entry.getId()))
+ continue;
+
+ StructureState state = new StructureState();
+ state.setVisible(true);
+ state.setXpos(jmol.getX());
+ state.setYpos(jmol.getY());
+ state.setWidth(jmol.getWidth());
+ state.setHeight(jmol.getHeight());
+
+ state.setContent(jmol.viewer.getStateInfo().replaceAll("\n", ""));
+
+ for (int s = 0; s < jmol.sequence.length; s++)
+ {
+ if (jal.findIndex(jmol.sequence[s]) > -1)
+ {
+ pdb.addStructureState(state);
+ }
+ }
+ }
+ }
+
+
+ if (entry.getFile() != null)
+ {
+ pdb.setFile(entry.getFile());
+ if (pdbfiles == null)
+ {
+ pdbfiles = new Vector();
+ }
+
+ if (!pdbfiles.contains(entry.getId()))
+ {
+ pdbfiles.addElement(entry.getId());
+ try
+ {
+ File file = new File(entry.getFile());
+ if (file.exists() && jout != null)
+ {
+ byte[] data = new byte[ (int) file.length()];
+ jout.putNextEntry(new JarEntry(entry.getId()));
+ DataInputStream dis = new DataInputStream(new
+ FileInputStream(file));
+ dis.readFully(data);
+
+ DataOutputStream dout = new DataOutputStream(jout);
+ dout.write(data, 0, data.length);
+ jout.closeEntry();
+ }
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ }
+ }
+
+ if (entry.getProperty() != null)
+ {
+ PdbentryItem item = new PdbentryItem();
+ Hashtable properties = entry.getProperty();
+ Enumeration en2 = properties.keys();
+ while (en2.hasMoreElements())
+ {
+ Property prop = new Property();
+ String key = en2.nextElement().toString();
+ prop.setName(key);
+ prop.setValue(properties.get(key).toString());
+ item.addProperty(prop);
+ }
+ pdb.addPdbentryItem(item);
+ }
+
+ jseq.addPdbids(pdb);
+ }
+ }
+
+ jms.addJSeq(jseq);
+ }
+
+ if (av.hasHiddenRows)
+ {
+ jal = av.alignment;
+ }
+
+ //SAVE TREES
+ ///////////////////////////////////
+ if (av.currentTree != null)
+ {
+ // FIND ANY ASSOCIATED TREES
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT
+ if (Desktop.desktop != null)
+ {
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();
+
+ for (int t = 0; t < frames.length; t++)
+ {
+ if (frames[t] instanceof TreePanel)
+ {
+ TreePanel tp = (TreePanel) frames[t];
+
+ if (tp.treeCanvas.av.alignment == jal)
+ {
+ Tree tree = new Tree();
+ tree.setTitle(tp.getTitle());
+ tree.setCurrentTree( (av.currentTree == tp.getTree()));
+ tree.setNewick(tp.getTree().toString());
+ tree.setThreshold(tp.treeCanvas.threshold);
+
+ tree.setFitToWindow(tp.fitToWindow.getState());
+ tree.setFontName(tp.getTreeFont().getName());
+ tree.setFontSize(tp.getTreeFont().getSize());
+ tree.setFontStyle(tp.getTreeFont().getStyle());
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());
+
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());
+ tree.setShowDistances(tp.distanceMenu.getState());
+
+ tree.setHeight(tp.getHeight());
+ tree.setWidth(tp.getWidth());
+ tree.setXpos(tp.getX());
+ tree.setYpos(tp.getY());
+
+ jms.addTree(tree);
+ }
+ }
+ }
+ }
+ }
+
+ //SAVE ANNOTATIONS
+ if (jal.getAlignmentAnnotation() != null)
+ {
+ jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();
+
+ for (int i = 0; i < aa.length; i++)
+ {
+ Annotation an = new Annotation();
+
+ if (aa[i].annotationId != null)
+ {
+ annotationIds.put(aa[i].annotationId, aa[i]);
+ }
+
+ an.setId(aa[i].annotationId);
+
+ if (aa[i] == av.quality ||
+ aa[i] == av.conservation ||
+ aa[i] == av.consensus)
+ {
+ an.setLabel(aa[i].label);
+ an.setGraph(true);
+ vamsasSet.addAnnotation(an);
+ continue;
+ }
+
+ an.setDescription(aa[i].description);
+
+ if (aa[i].sequenceRef != null)
+ {
+ an.setSequenceRef(aa[i].sequenceRef.getName());
+ }
+
+ if (aa[i].graph > 0)
+ {
+ an.setGraph(true);
+ an.setGraphType(aa[i].graph);
+ an.setGraphGroup(aa[i].graphGroup);
+ if (aa[i].getThreshold() != null)
+ {
+ ThresholdLine line = new ThresholdLine();
+ line.setLabel(aa[i].getThreshold().label);
+ line.setValue(aa[i].getThreshold().value);
+ line.setColour(aa[i].getThreshold().colour.getRGB());
+ an.setThresholdLine(line);
+ }
+ }
+ else
+ {
+ an.setGraph(false);
+ }
+
+ an.setLabel(aa[i].label);
+ if (aa[i].hasScore())
+ {
+ an.setScore(aa[i].getScore());
+ }
+ AnnotationElement ae;
+ if (aa[i].annotations!=null)
+ {
+ an.setScoreOnly(false);
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ ae.setDescription(aa[i].annotations[a].description);
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+ ae.setValue(aa[i].annotations[a].value);
+ ae.setPosition(a);
+ ae
+ .setSecondaryStructure(aa[i].annotations[a].secondaryStructure
+ + "");
+
+ if (aa[i].annotations[a].colour != java.awt.Color.black)
+ {
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+ }
+
+ an.addAnnotationElement(ae);
+ }
+ } else {
+ an.setScoreOnly(true);
+ }
+ vamsasSet.addAnnotation(an);
+ }
+ }
+
+ //SAVE GROUPS
+ if (jal.getGroups() != null)
+ {
+ JGroup[] groups = new JGroup[jal.getGroups().size()];
+
+ for (int i = 0; i < groups.length; i++)
+ {
+ groups[i] = new JGroup();
+
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)
+ jal.getGroups()
+ .elementAt(i);
+ groups[i].setStart(sg.getStartRes());
+ groups[i].setEnd(sg.getEndRes());
+ groups[i].setName(sg.getName());
+ if (sg.cs != null)
+ {
+ if (sg.cs.conservationApplied())
+ {
+ groups[i].setConsThreshold(sg.cs.getConservationInc());
+
+ if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ {
+ groups[i].setColour(SetUserColourScheme(sg.cs,
+ userColours,
+ jms));
+ }
+ else
+ {
+ groups[i].setColour(ColourSchemeProperty.getColourName(sg.
+ cs));
+ }
+ }
+ else if (sg.cs instanceof jalview.schemes.AnnotationColourGradient)
+ {
+ groups[i].setColour(
+ ColourSchemeProperty.getColourName(
+ ( (jalview.schemes.AnnotationColourGradient) sg.cs).
+ getBaseColour()));
+ }
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)
+ {
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,
+ jms));
+ }
+ else
+ {
+ groups[i].setColour(ColourSchemeProperty.getColourName(
+ sg.cs));
+ }
+
+ groups[i].setPidThreshold(sg.cs.getThreshold());
+ }
+
+ groups[i].setOutlineColour(sg.getOutlineColour().getRGB());
+ groups[i].setDisplayBoxes(sg.getDisplayBoxes());
+ groups[i].setDisplayText(sg.getDisplayText());
+ groups[i].setColourText(sg.getColourText());
+ groups[i].setTextCol1(sg.textColour.getRGB());
+ groups[i].setTextCol2(sg.textColour2.getRGB());
+ groups[i].setTextColThreshold(sg.thresholdTextColour);
+
+ for (int s = 0; s < sg.getSize(); s++)
+ {
+ jalview.datamodel.Sequence seq =
+ (jalview.datamodel.Sequence) sg.getSequenceAt(s);
+ groups[i].addSeq(seq.hashCode());
+ }
+ }
+
+ jms.setJGroup(groups);
+ }
+
+ ///////////SAVE VIEWPORT
+ Viewport view = new Viewport();
+ view.setTitle(ap.alignFrame.getTitle());
+ view.setSequenceSetId(av.getSequenceSetId());
+ view.setViewName(av.viewName);
+ view.setGatheredViews(av.gatherViewsHere);
+
+
+
+ if (ap.av.explodedPosition != null)
+ {
+ view.setXpos(av.explodedPosition.x);
+ view.setYpos(av.explodedPosition.y);
+ view.setWidth(av.explodedPosition.width);
+ view.setHeight(av.explodedPosition.height);
+ }
+ else
+ {
+ view.setXpos(ap.alignFrame.getBounds().x);
+ view.setYpos(ap.alignFrame.getBounds().y);
+ view.setWidth(ap.alignFrame.getBounds().width);
+ view.setHeight(ap.alignFrame.getBounds().height);
+ }
+
+ view.setStartRes(av.startRes);
+ view.setStartSeq(av.startSeq);
+
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),
+ userColours, jms));
+ }
+ else if (av.getGlobalColourScheme() instanceof jalview.schemes.
+ AnnotationColourGradient)
+ {
+ jalview.schemes.AnnotationColourGradient acg
+ = (jalview.schemes.AnnotationColourGradient) av.getGlobalColourScheme();
+
+ AnnotationColours ac = new AnnotationColours();
+ ac.setAboveThreshold(acg.getAboveThreshold());
+ ac.setThreshold(acg.getAnnotationThreshold());
+ ac.setAnnotation(acg.getAnnotation());
+ if (acg.getBaseColour() instanceof jalview.schemes.UserColourScheme)
+ {
+ ac.setColourScheme(SetUserColourScheme(acg.getBaseColour(),
+ userColours, jms));
+ }
+ else
+ {
+ ac.setColourScheme(ColourSchemeProperty.getColourName(acg.getBaseColour()));
+ }
+
+ ac.setMaxColour(acg.getMaxColour().getRGB());
+ ac.setMinColour(acg.getMinColour().getRGB());
+ view.setAnnotationColours(ac);
+ view.setBgColour("AnnotationColourGradient");
+ }
+ else
+ {
+ view.setBgColour(ColourSchemeProperty.getColourName(
+ av.getGlobalColourScheme()));
+ }
+
+ ColourSchemeI cs = av.getGlobalColourScheme();
+
+ if (cs != null)
+ {
+ if (cs.conservationApplied())
+ {
+ view.setConsThreshold(cs.getConservationInc());
+ if (cs instanceof jalview.schemes.UserColourScheme)
+ {
+ view.setBgColour(SetUserColourScheme(cs, userColours, jms));
+ }
+ }
+
+ if (cs instanceof ResidueColourScheme)
+ {
+ view.setPidThreshold(cs.getThreshold());
+ }
+ }
+
+ view.setConservationSelected(av.getConservationSelected());
+ view.setPidSelected(av.getAbovePIDThreshold());
+ view.setFontName(av.font.getName());
+ view.setFontSize(av.font.getSize());
+ view.setFontStyle(av.font.getStyle());
+ view.setRenderGaps(av.renderGaps);
+ view.setShowAnnotation(av.getShowAnnotation());
+ view.setShowBoxes(av.getShowBoxes());
+ view.setShowColourText(av.getColourText());
+ view.setShowFullId(av.getShowJVSuffix());
+ view.setRightAlignIds(av.rightAlignIds);
+ view.setShowSequenceFeatures(av.showSequenceFeatures);
+ view.setShowText(av.getShowText());
+ view.setWrapAlignment(av.getWrapAlignment());
+ view.setTextCol1(av.textColour.getRGB());
+ view.setTextCol2(av.textColour2.getRGB());
+ view.setTextColThreshold(av.thresholdTextColour);
+
+ if (av.featuresDisplayed != null)
+ {
+ jalview.schemabinding.version2.FeatureSettings fs
+ = new jalview.schemabinding.version2.FeatureSettings();
+
+ String[] renderOrder =
+ ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;
+
+ Vector settingsAdded = new Vector();
+ for (int ro = 0; ro < renderOrder.length; ro++)
+ {
+ Setting setting = new Setting();
+ setting.setType(renderOrder[ro]);
+ setting.setColour(
+ ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).
+ getRGB()
+ );
+
+ setting.setDisplay(
+ av.featuresDisplayed.containsKey(renderOrder[ro])
+ );
+ float rorder=ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(renderOrder[ro]);
+ if (rorder>-1) {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(renderOrder[ro]);
+ }
+
+ //Make sure we save none displayed feature settings
+ Enumeration en =
+ ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys();
+ while (en.hasMoreElements())
+ {
+ String key = en.nextElement().toString();
+ if (settingsAdded.contains(key))
+ {
+ continue;
+ }
+
+ Setting setting = new Setting();
+ setting.setType(key);
+ setting.setColour(
+ ap.seqPanel.seqCanvas.getFeatureRenderer().getColour(key).getRGB()
+ );
+
+ setting.setDisplay(false);
+ float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer().getOrder(key);
+ if (rorder>-1)
+ {
+ setting.setOrder(rorder);
+ }
+ fs.addSetting(setting);
+ settingsAdded.addElement(key);
+ }
+ en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.keys();
+ Vector groupsAdded=new Vector();
+ while (en.hasMoreElements())
+ {
+ String grp = en.nextElement().toString();
+ if (groupsAdded.contains(grp))
+ {
+ continue;
+ }
+ Group g = new Group();
+ g.setName(grp);
+ g.setDisplay(((Boolean)ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups.get(grp)).booleanValue());
+ fs.addGroup(g);
+ groupsAdded.addElement(grp);
+ }
+ jms.setFeatureSettings(fs);
+
+ }
+
+ if (av.hasHiddenColumns)
+ {
+ for (int c = 0; c < av.getColumnSelection().getHiddenColumns().size(); c++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns().
+ elementAt(c);
+ HiddenColumns hc = new HiddenColumns();
+ hc.setStart(region[0]);
+ hc.setEnd(region[1]);
+ view.addHiddenColumns(hc);
+ }
+ }
+
+ jms.addViewport(view);
+
+ object.setJalviewModelSequence(jms);
+ object.getVamsasModel().addSequenceSet(vamsasSet);
+
+ if (out != null)
+ {
+ //We may not want to right the object to disk,
+ //eg we can copy the alignViewport to a new view object
+ //using save and then load
+ try
+ {
+ if (!fileName.endsWith(".xml"))
+ {
+ fileName = fileName + ".xml";
+ }
+
+ JarEntry entry = new JarEntry(fileName);
+ jout.putNextEntry(entry);
+
+ object.marshal(out);
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+ return object;
+ }
+
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,
+ Vector userColours, JalviewModelSequence jms)
+ {
+ String id = null;
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)
+ cs;
+
+ if (!userColours.contains(ucs))
+ {
+ userColours.add(ucs);
+
+ java.awt.Color[] colours = ucs.getColours();
+ jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.
+ version2.UserColours();
+ jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.
+ schemabinding.version2.UserColourScheme();
+
+ for (int i = 0; i < colours.length; i++)
+ {
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
+ version2.Colour();
+ col.setName(ResidueProperties.aa[i]);
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ jbucs.addColour(col);
+ }
+ if (ucs.getLowerCaseColours() != null)
+ {
+ colours = ucs.getLowerCaseColours();
+ for (int i = 0; i < colours.length; i++)
+ {
+ jalview.schemabinding.version2.Colour col = new jalview.schemabinding.
+ version2.Colour();
+ col.setName(ResidueProperties.aa[i].toLowerCase());
+ col.setRGB(jalview.util.Format.getHexString(colours[i]));
+ jbucs.addColour(col);
+ }
+ }
+
+ id = "ucs" + userColours.indexOf(ucs);
+ uc.setId(id);
+ uc.setUserColourScheme(jbucs);
+ jms.addUserColours(uc);
+ }
+
+ return id;
+ }
+
+ jalview.schemes.UserColourScheme GetUserColourScheme(
+ JalviewModelSequence jms, String id)
+ {
+ UserColours[] uc = jms.getUserColours();
+ UserColours colours = null;
+
+ for (int i = 0; i < uc.length; i++)
+ {
+ if (uc[i].getId().equals(id))
+ {
+ colours = uc[i];
+
+ break;
+ }
+ }
+
+ java.awt.Color[] newColours = new java.awt.Color[24];
+
+ for (int i = 0; i < 24; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i).getRGB(), 16));
+ }
+
+ jalview.schemes.UserColourScheme ucs =
+ new jalview.schemes.UserColourScheme(newColours);
+
+ if (colours.getUserColourScheme().getColourCount() > 24)
+ {
+ newColours = new java.awt.Color[23];
+ for (int i = 0; i < 23; i++)
+ {
+ newColours[i] = new java.awt.Color(Integer.parseInt(
+ colours.getUserColourScheme().getColour(i + 24).getRGB(), 16));
+ }
+ ucs.setLowerCaseColours(newColours);
+ }
+
+ return ucs;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param file DOCUMENT ME!
+ */
+ public AlignFrame LoadJalviewAlign(final String file)
+ {
+ uniqueSetSuffix = System.currentTimeMillis() % 100000 + "";
+
+ jalview.gui.AlignFrame af = null;
+
+ seqRefIds = new Hashtable();
+ viewportsAdded = new Hashtable();
+
+ Hashtable gatherToThisFrame = new Hashtable();
+
+ try
+ {
+ //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING
+ URL url = null;
+
+ if (file.startsWith("http://"))
+ {
+ url = new URL(file);
+ }
+
+ JarInputStream jin = null;
+ JarEntry jarentry = null;
+ int entryCount = 1;
+
+ do
+ {
+ if (url != null)
+ {
+ jin = new JarInputStream(url.openStream());
+ }
+ else
+ {
+ jin = new JarInputStream(new FileInputStream(file));
+ }
+
+ for (int i = 0; i < entryCount; i++)
+ {
+ jarentry = jin.getNextJarEntry();
+ }
+
+ if (jarentry != null && jarentry.getName().endsWith(".xml"))
+ {
+ InputStreamReader in = new InputStreamReader(jin, "UTF-8");
+ JalviewModel object = new JalviewModel();
+
+ Unmarshaller unmar = new Unmarshaller(object);
+ unmar.setValidation(false);
+ object = (JalviewModel) unmar.unmarshal(in);
+
+ af = LoadFromObject(object, file, true);
+ if (af.viewport.gatherViewsHere)
+ {
+ gatherToThisFrame.put(af.viewport.getSequenceSetId(), af);
+ }
+ entryCount++;
+ }
+ else if (jarentry != null)
+ {
+ //Some other file here.
+ entryCount++;
+ }
+ }
+ while (jarentry != null);
+ }
+ catch (java.net.UnknownHostException ex)
+ {
+ ex.printStackTrace();
+ System.err.println("Couldn't locate Jalview XML file : " +
+ ex + "\n");
+
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Couldn't locate " + file,
+ "URL not found",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+ catch (Exception ex)
+ {
+ //Is Version 1 Jar file?
+ af = new Jalview2XML_V1().LoadJalviewAlign(file);
+
+ if (af != null)
+ {
+ System.out.println("Successfully loaded archive file");
+ return af;
+ }
+ ex.printStackTrace();
+
+ System.err.println("Exception whilst loading jalview XML file : " +
+ ex + "\n");
+ javax.swing.SwingUtilities.invokeLater(new Runnable()
+ {
+ public void run()
+ {
+
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,
+ "Error loading " + file,
+ "Error loading Jalview file",
+ JOptionPane.WARNING_MESSAGE);
+ }
+ });
+ }
+
+ if (Desktop.instance != null)
+ {
+ Desktop.instance.stopLoading();
+ }
+
+ Enumeration en = gatherToThisFrame.elements();
+ while(en.hasMoreElements())
+ {
+ Desktop.instance.gatherViews(
+ (AlignFrame) en.nextElement());
+ }
+
+ return af;
+ }
+
+ Hashtable alreadyLoadedPDB;
+ String loadPDBFile(String file, String pdbId)
+ {
+ if (alreadyLoadedPDB == null)
+ alreadyLoadedPDB = new Hashtable();
+
+ if (alreadyLoadedPDB.containsKey(pdbId))
+ return alreadyLoadedPDB.get(pdbId).toString();
+
+ try
+ {
+ JarInputStream jin = null;
+
+ if (file.startsWith("http://"))
+ {
+ jin = new JarInputStream(new URL(file).openStream());
+ }
+ else
+ {
+ jin = new JarInputStream(new FileInputStream(file));
+ }
+
+ JarEntry entry = null;
+ do
+ {
+ entry = jin.getNextJarEntry();
+ }
+ while (!entry.getName().equals(pdbId));
+
+ BufferedReader in = new BufferedReader(new InputStreamReader(jin));
+ File outFile = File.createTempFile("jalview_pdb", ".txt");
+ outFile.deleteOnExit();
+ PrintWriter out = new PrintWriter(new FileOutputStream(outFile));
+ String data;
+
+ while ( (data = in.readLine()) != null)
+ {
+ out.println(data);
+ }
+ out.close();
+
+ alreadyLoadedPDB.put(pdbId, outFile.getAbsolutePath());
+ return outFile.getAbsolutePath();
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return null;
+ }
+
+ AlignFrame LoadFromObject(JalviewModel object,
+ String file,
+ boolean loadTreesAndStructures)
+ {
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);
+ Sequence[] vamsasSeq = vamsasSet.getSequence();
+
+ JalviewModelSequence jms = object.getJalviewModelSequence();
+
+ Viewport view = jms.getViewport(0);
+
+ //////////////////////////////////
+ //LOAD SEQUENCES
+
+ Vector hiddenSeqs = null;
+ jalview.datamodel.Sequence jseq;
+
+ ArrayList tmpseqs = new ArrayList();
+
+ boolean multipleView = false;
+
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ String seqId = JSEQ[i].getId() + "";
+
+ if (seqRefIds.get(seqId) != null)
+ {
+ tmpseqs.add( (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ multipleView = true;
+ }
+ else
+ {
+ jseq = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),
+ vamsasSeq[i].getSequence());
+ jseq.setDescription(vamsasSeq[i].getDescription());
+ jseq.setStart(JSEQ[i].getStart());
+ jseq.setEnd(JSEQ[i].getEnd());
+ seqRefIds.put(vamsasSeq[i].getId(), jseq);
+ tmpseqs.add(jseq);
+ }
+
+ if (JSEQ[i].getHidden())
+ {
+ if (hiddenSeqs == null)
+ {
+ hiddenSeqs = new Vector();
+ }
+
+ hiddenSeqs.addElement(
+ (jalview.datamodel.Sequence) seqRefIds.get(seqId));
+ }
+
+ }
+
+ ///SequenceFeatures are added to the DatasetSequence,
+ // so we must create the dataset before loading features
+ /////////////////////////////////
+
+
+ jalview.datamodel.Sequence[] orderedSeqs = new jalview.datamodel.Sequence[
+ tmpseqs.size()];
+
+ tmpseqs.toArray(orderedSeqs);
+
+ jalview.datamodel.Alignment al =
+ new jalview.datamodel.Alignment(orderedSeqs);
+
+ al.setDataset(null);
+ /////////////////////////////////
+
+
+ Hashtable pdbloaded = new Hashtable();
+
+ if (!multipleView)
+ {
+ for (int i = 0; i < vamsasSeq.length; i++)
+ {
+ if (JSEQ[i].getFeaturesCount() > 0)
+ {
+ Features[] features = JSEQ[i].getFeatures();
+ for (int f = 0; f < features.length; f++)
+ {
+ jalview.datamodel.SequenceFeature sf
+ = new jalview.datamodel.SequenceFeature(features[f].getType(),
+ features[f].getDescription(), features[f].getStatus(),
+ features[f].getBegin(), features[f].getEnd(),
+ features[f].getFeatureGroup());
+
+ sf.setScore(features[f].getScore());
+ for (int od = 0; od < features[f].getOtherDataCount(); od++)
+ {
+ OtherData keyValue = features[f].getOtherData(od);
+ if (keyValue.getKey().startsWith("LINK"))
+ {
+ sf.addLink(keyValue.getValue());
+ }
+ else
+ {
+ sf.setValue(keyValue.getKey(), keyValue.getValue());
+ }
+
+ }
+
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);
+ }
+ }
+
+ if (JSEQ[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.
+ PDBEntry();
+ entry.setId(ids[p].getId());
+ entry.setType(ids[p].getType());
+ if (ids[p].getFile() != null)
+ {
+ if (!pdbloaded.containsKey(ids[p].getFile()))
+ {
+ entry.setFile(loadPDBFile(file, ids[p].getId()));
+ }
+ else
+ {
+ entry.setFile(pdbloaded.get(ids[p].getId()).toString());
+ }
+ }
+
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);
+ }
+ }
+ if (vamsasSeq[i].getDBRefCount() > 0)
+ {
+ for (int d = 0; d < vamsasSeq[i].getDBRefCount(); d++)
+ {
+ jalview.datamodel.DBRefEntry entry =
+ new jalview.datamodel.DBRefEntry(
+ vamsasSeq[i].getDBRef(d).getSource(),
+ vamsasSeq[i].getDBRef(d).getVersion(),
+ vamsasSeq[i].getDBRef(d).getAccessionId()
+ );
+ al.getSequenceAt(i).getDatasetSequence().addDBRef(entry);
+ }
+
+ }
+ }
+ }
+
+ /////////////////////////////////
+ //////////////////////////////////
+ //LOAD ANNOTATIONS
+ boolean hideQuality = true,
+ hideConservation = true,
+ hideConsensus = true;
+
+ if (vamsasSet.getAnnotationCount() > 0)
+ {
+ Annotation[] an = vamsasSet.getAnnotation();
+
+ for (int i = 0; i < an.length; i++)
+ {
+ if (an[i].getLabel().equals("Quality"))
+ {
+ hideQuality = false;
+ continue;
+ }
+ else if (an[i].getLabel().equals("Conservation"))
+ {
+ hideConservation = false;
+ continue;
+ }
+ else if (an[i].getLabel().equals("Consensus"))
+ {
+ hideConsensus = false;
+ continue;
+ }
+
+ if (an[i].getId() != null
+ && annotationIds.containsKey(an[i].getId()))
+ {
+ al.addAnnotation(
+ (jalview.datamodel.AlignmentAnnotation) annotationIds.get(an[i].
+ getId())
+ );
+
+ continue;
+ }
+
+ AnnotationElement[] ae = an[i].getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = null;
+ if (!an[i].getScoreOnly())
+ {
+ anot = new jalview.datamodel.Annotation[
+ al.getWidth()];
+
+ for (int aa = 0; aa < ae.length && aa < anot.length; aa++)
+ {
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].
+ getDisplayCharacter(),
+ ae[aa].getDescription(),
+ ae[aa].getSecondaryStructure().length() == 0 ? ' ' :
+ ae[aa].getSecondaryStructure().charAt(0),
+ ae[aa].getValue());
+ anot[ae[aa].getPosition()].colour = new java.awt.Color(ae[aa].
+ getColour());
+ }
+ }
+ jalview.datamodel.AlignmentAnnotation jaa = null;
+
+ if (an[i].getGraph())
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot, 0, 0,
+ an[i].getGraphType());
+
+ jaa.graphGroup = an[i].getGraphGroup();
+
+ if (an[i].getThresholdLine() != null)
+ {
+ jaa.setThreshold(new jalview.datamodel.GraphLine(
+ an[i].getThresholdLine().getValue(),
+ an[i].getThresholdLine().getLabel(),
+ new java.awt.Color(an[i].getThresholdLine().getColour()))
+ );
+
+ }
+
+ }
+ else
+ {
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),
+ an[i].getDescription(), anot);
+ }
+
+ if (an[i].getId() != null)
+ {
+ annotationIds.put(an[i].getId(), jaa);
+ jaa.annotationId = an[i].getId();
+ }
+
+ if (an[i].getSequenceRef() != null)
+ {
+ jaa.createSequenceMapping(
+ al.findName(an[i].getSequenceRef()), 1, true
+ );
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ }
+ if (an[i].hasScore())
+ {
+ jaa.setScore(an[i].getScore());
+ }
+ al.addAnnotation(jaa);
+ }
+ }
+
+ /////////////////////////
+ //LOAD GROUPS
+ if (jms.getJGroupCount() > 0)
+ {
+ JGroup[] groups = jms.getJGroup();
+
+ for (int i = 0; i < groups.length; i++)
+ {
+ ColourSchemeI cs = null;
+
+ if (groups[i].getColour() != null)
+ {
+ if (groups[i].getColour().startsWith("ucs"))
+ {
+ cs = GetUserColourScheme(jms, groups[i].getColour());
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al,
+ groups[i].getColour());
+ }
+
+ if (cs != null)
+ {
+ cs.setThreshold(groups[i].getPidThreshold(), true);
+ }
+ }
+
+ Vector seqs = new Vector();
+
+ for (int s = 0; s < groups[i].getSeqCount(); s++)
+ {
+ String seqId = groups[i].getSeq(s) + "";
+ jalview.datamodel.SequenceI ts = (jalview.datamodel.SequenceI)
+ seqRefIds.get(seqId);
+
+ if (ts != null)
+ {
+ seqs.addElement(ts);
+ }
+ }
+
+ if (seqs.size() < 1)
+ {
+ continue;
+ }
+
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.
+ SequenceGroup(seqs,
+ groups[i].getName(), cs, groups[i].getDisplayBoxes(),
+ groups[i].getDisplayText(), groups[i].getColourText(),
+ groups[i].getStart(), groups[i].getEnd());
+
+ sg.setOutlineColour(new java.awt.Color(
+ groups[i].getOutlineColour()));
+
+ sg.textColour = new java.awt.Color(groups[i].getTextCol1());
+ sg.textColour2 = new java.awt.Color(groups[i].getTextCol2());
+ sg.thresholdTextColour = groups[i].getTextColThreshold();
+
+ if (groups[i].getConsThreshold() != 0)
+ {
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation(
+ "All",
+ ResidueProperties.propHash, 3, sg.getSequences(null), 0,
+ sg.getWidth() - 1);
+ c.calculate();
+ c.verdict(false, 25);
+ sg.cs.setConservation(c);
+ }
+
+ al.addGroup(sg);
+ }
+ }
+
+ /////////////////////////////////
+ // LOAD VIEWPORT
+
+ AlignFrame af = new AlignFrame(al,
+ view.getWidth(),
+ view.getHeight());
+
+ af.setFileName(file, "Jalview");
+
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ af.viewport.setSequenceColour(
+ af.viewport.alignment.getSequenceAt(i),
+ new java.awt.Color(
+ JSEQ[i].getColour()));
+ }
+
+ //If we just load in the same jar file again, the sequenceSetId
+ //will be the same, and we end up with multiple references
+ //to the same sequenceSet. We must modify this id on load
+ //so that each load of the file gives a unique id
+ String uniqueSeqSetId = view.getSequenceSetId() + uniqueSetSuffix;
+
+ af.viewport.gatherViewsHere = view.getGatheredViews();
+
+ if (view.getSequenceSetId() != null)
+ {
+ jalview.gui.AlignViewport av =
+ (jalview.gui.AlignViewport)
+ viewportsAdded.get(uniqueSeqSetId);
+
+ af.viewport.sequenceSetID = uniqueSeqSetId;
+ if (av != null)
+ {
+
+ af.viewport.historyList = av.historyList;
+ af.viewport.redoList = av.redoList;
+ }
+ else
+ {
+ viewportsAdded.put(uniqueSeqSetId, af.viewport);
+ }
+
+ PaintRefresher.Register(af.alignPanel, uniqueSeqSetId);
+ }
+ if (hiddenSeqs != null)
+ {
+ for (int s = 0; s < JSEQ.length; s++)
+ {
+ jalview.datamodel.SequenceGroup hidden =
+ new jalview.datamodel.SequenceGroup();
+
+ for (int r = 0; r < JSEQ[s].getHiddenSequencesCount(); r++)
+ {
+ hidden.addSequence(
+ al.getSequenceAt(JSEQ[s].getHiddenSequences(r))
+ , false
+ );
+ }
+ af.viewport.hideRepSequences(al.getSequenceAt(s), hidden);
+ }
+
+ jalview.datamodel.SequenceI[] hseqs = new
+ jalview.datamodel.SequenceI[hiddenSeqs.size()];
+
+ for (int s = 0; s < hiddenSeqs.size(); s++)
+ {
+ hseqs[s] = (jalview.datamodel.SequenceI) hiddenSeqs.elementAt(s);
+ }
+
+ af.viewport.hideSequence(hseqs);
+
+ }
+
+ if ( (hideConsensus || hideQuality || hideConservation)
+ && al.getAlignmentAnnotation() != null)
+ {
+ int hSize = al.getAlignmentAnnotation().length;
+ for (int h = 0; h < hSize; h++)
+ {
+ if (
+ (hideConsensus &&
+ al.getAlignmentAnnotation()[h].label.equals("Consensus"))
+ ||
+ (hideQuality &&
+ al.getAlignmentAnnotation()[h].label.equals("Quality"))
+ ||
+ (hideConservation &&
+ al.getAlignmentAnnotation()[h].label.equals("Conservation")))
+ {
+ al.deleteAnnotation(al.getAlignmentAnnotation()[h]);
+ hSize--;
+ h--;
+ }
+ }
+ af.alignPanel.adjustAnnotationHeight();
+ }
+
+ if (view.getViewName() != null)
+ {
+ af.viewport.viewName = view.getViewName();
+ af.setInitialTabVisible();
+ }
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),
+ view.getHeight());
+
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());
+
+ af.viewport.setColourText(view.getShowColourText());
+
+ af.viewport.setConservationSelected(view.getConservationSelected());
+ af.viewport.setShowJVSuffix(view.getShowFullId());
+ af.viewport.rightAlignIds = view.getRightAlignIds();
+ af.viewport.setFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(), view.getFontSize()));
+ af.alignPanel.fontChanged();
+ af.viewport.setRenderGaps(view.getRenderGaps());
+ af.viewport.setWrapAlignment(view.getWrapAlignment());
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());
+ af.viewport.setShowAnnotation(view.getShowAnnotation());
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());
+
+ af.viewport.setShowBoxes(view.getShowBoxes());
+
+ af.viewport.setShowText(view.getShowText());
+
+ af.viewport.textColour = new java.awt.Color(view.getTextCol1());
+ af.viewport.textColour2 = new java.awt.Color(view.getTextCol2());
+ af.viewport.thresholdTextColour = view.getTextColThreshold();
+
+ af.viewport.setStartRes(view.getStartRes());
+ af.viewport.setStartSeq(view.getStartSeq());
+
+ ColourSchemeI cs = null;
+
+ if (view.getBgColour() != null)
+ {
+ if (view.getBgColour().startsWith("ucs"))
+ {
+ cs = GetUserColourScheme(jms, view.getBgColour());
+ }
+ else if (view.getBgColour().startsWith("Annotation"))
+ {
+ //int find annotation
+ for (int i = 0;
+ i < af.viewport.alignment.getAlignmentAnnotation().length; i++)
+ {
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label.
+ equals(view.getAnnotationColours().getAnnotation()))
+ {
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].
+ getThreshold() == null)
+ {
+ af.viewport.alignment.getAlignmentAnnotation()[i].
+ setThreshold(
+ new jalview.datamodel.GraphLine(
+ view.getAnnotationColours().getThreshold(),
+ "Threshold", java.awt.Color.black)
+
+ );
+ }
+
+ if (view.getAnnotationColours().getColourScheme().equals(
+ "None"))
+ {
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(view.getAnnotationColours().
+ getMinColour()),
+ new java.awt.Color(view.getAnnotationColours().
+ getMaxColour()),
+ view.getAnnotationColours().getAboveThreshold());
+ }
+ else if (view.getAnnotationColours().getColourScheme().
+ startsWith("ucs"))
+ {
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ GetUserColourScheme(jms, view.getAnnotationColours().
+ getColourScheme()),
+ view.getAnnotationColours().getAboveThreshold()
+ );
+ }
+ else
+ {
+ cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ ColourSchemeProperty.getColour(al,
+ view.getAnnotationColours().
+ getColourScheme()),
+ view.getAnnotationColours().getAboveThreshold()
+ );
+ }
+
+ // Also use these settings for all the groups
+ if (al.getGroups() != null)
+ {
+ for (int g = 0; g < al.getGroups().size(); g++)
+ {
+ jalview.datamodel.SequenceGroup sg
+ = (jalview.datamodel.SequenceGroup) al.getGroups().
+ elementAt(g);
+
+ if (sg.cs == null)
+ {
+ continue;
+ }
+
+ /* if (view.getAnnotationColours().getColourScheme().equals("None"))
+ {
+ sg.cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ new java.awt.Color(view.getAnnotationColours().
+ getMinColour()),
+ new java.awt.Color(view.getAnnotationColours().
+ getMaxColour()),
+ view.getAnnotationColours().getAboveThreshold());
+ }
+ else*/
+ {
+ sg.cs = new AnnotationColourGradient(
+ af.viewport.alignment.getAlignmentAnnotation()[i],
+ sg.cs,
+ view.getAnnotationColours().getAboveThreshold()
+ );
+ }
+
+ }
+ }
+
+ break;
+ }
+
+ }
+ }
+ else
+ {
+ cs = ColourSchemeProperty.getColour(al, view.getBgColour());
+ }
+
+ if (cs != null)
+ {
+ cs.setThreshold(view.getPidThreshold(), true);
+ cs.setConsensus(af.viewport.hconsensus);
+ }
+ }
+
+ af.viewport.setGlobalColourScheme(cs);
+ af.viewport.setColourAppliesToAllGroups(false);
+
+ if (view.getConservationSelected() && cs != null)
+ {
+ cs.setConservationInc(view.getConsThreshold());
+ }
+
+ af.changeColour(cs);
+
+ af.viewport.setColourAppliesToAllGroups(true);
+
+ if (view.getShowSequenceFeatures())
+ {
+ af.viewport.showSequenceFeatures = true;
+ }
+
+ if (jms.getFeatureSettings() != null)
+ {
+ af.viewport.featuresDisplayed = new Hashtable();
+ String[] renderOrder = new String[jms.getFeatureSettings().
+ getSettingCount()];
+ for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++)
+ {
+ Setting setting = jms.getFeatureSettings().getSetting(fs);
+
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.
+ getType(),
+ new java.awt.Color(setting.getColour()));
+ renderOrder[fs] = setting.getType();
+ if (setting.hasOrder())
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), setting.getOrder());
+ else
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder(setting.getType(), fs/jms.getFeatureSettings().getSettingCount());
+ if (setting.getDisplay())
+ {
+ af.viewport.featuresDisplayed.put(
+ setting.getType(), new Integer(setting.getColour()));
+ }
+ }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder =
+ renderOrder;
+ Hashtable fgtable;
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable=new Hashtable();
+ for (int gs=0;gs<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);
+
+ Desktop.addInternalFrame(af, view.getTitle(),
+ view.getWidth(), view.getHeight());
+
+ //LOAD TREES
+ ///////////////////////////////////////
+ if (loadTreesAndStructures && jms.getTreeCount() > 0)
+ {
+ try
+ {
+ for (int t = 0; t < jms.getTreeCount(); t++)
+ {
+
+ Tree tree = jms.getTree(t);
+
+ TreePanel tp = af.ShowNewickTree(new jalview.io.NewickFile(
+ tree.getNewick()), tree.getTitle(),
+ tree.getWidth(), tree.getHeight(),
+ tree.getXpos(), tree.getYpos());
+
+ tp.fitToWindow.setState(tree.getFitToWindow());
+ tp.fitToWindow_actionPerformed(null);
+
+ if (tree.getFontName() != null)
+ {
+ tp.setTreeFont(new java.awt.Font(tree.getFontName(),
+ tree.getFontStyle(),
+ tree.getFontSize()));
+ }
+ else
+ {
+ tp.setTreeFont(new java.awt.Font(view.getFontName(),
+ view.getFontStyle(),
+ tree.getFontSize()));
+ }
+
+ tp.showPlaceholders(tree.getMarkUnlinked());
+ tp.showBootstrap(tree.getShowBootstrap());
+ tp.showDistances(tree.getShowDistances());
+
+ tp.treeCanvas.threshold = tree.getThreshold();
+
+ if (tree.getCurrentTree())
+ {
+ af.viewport.setCurrentTree(tp.getTree());
+ }
+ }
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+ }
+
+ ////LOAD STRUCTURES
+ if(loadTreesAndStructures)
+ {
+ for (int i = 0; i < JSEQ.length; i++)
+ {
+ if (JSEQ[i].getPdbidsCount() > 0)
+ {
+ Pdbids[] ids = JSEQ[i].getPdbids();
+ for (int p = 0; p < ids.length; p++)
+ {
+ for (int s = 0; s < ids[p].getStructureStateCount(); s++)
+ {
+ jalview.datamodel.PDBEntry jpdb = new jalview.datamodel.PDBEntry();
+
+ jpdb.setFile(loadPDBFile(ids[p].getFile(), ids[p].getId()));
+ jpdb.setId(ids[p].getId());
+
+ int x = ids[p].getStructureState(s).getXpos();
+ int y = ids[p].getStructureState(s).getYpos();
+ int width = ids[p].getStructureState(s).getWidth();
+ int height = ids[p].getStructureState(s).getHeight();
+
+ java.awt.Component comp = Desktop.desktop.getComponentAt(x, y);
+
+ String pdbFile = loadPDBFile(file, ids[p].getId());
+
+ jalview.datamodel.SequenceI[] seq = new jalview.datamodel.SequenceI[]
+ {
+ al.getSequenceAt(i)};
+
+ if (comp == null ||
+ (comp.getWidth() != width && comp.getHeight() != height))
+ {
+ String state = ids[p].getStructureState(s).getContent();
+
+ StringBuffer newFileLoc = new StringBuffer(state.substring(0,
+ state.indexOf("\"", state.indexOf("load")) + 1));
+
+ newFileLoc.append(jpdb.getFile());
+ newFileLoc.append(state.substring(
+ state.indexOf("\"", state.indexOf("load \"") + 6)));
+
+ new AppJMol(pdbFile,
+ ids[p].getId(),
+ seq,
+ af.alignPanel,
+ newFileLoc.toString(),
+ new java.awt.Rectangle(x, y, width, height));
+
+ }
+ else if(comp!=null)
+ {
+ StructureSelectionManager.getStructureSelectionManager()
+ .setMapping(seq, pdbFile,
+ jalview.io.AppletFormatAdapter.FILE);
+
+ ( (AppJMol) comp).addSequence(seq);
+ }
+ }
+ }
+ }
+ }
+ }
+
+ return af;
+ }
+
+ public jalview.gui.AlignmentPanel copyAlignPanel(AlignmentPanel ap,
+ boolean keepSeqRefs)
+ {
+ jalview.schemabinding.version2.JalviewModel jm
+ = SaveState(ap, null, null, null);
+
+ if (!keepSeqRefs)
+ {
+ seqRefIds.clear();
+ jm.getJalviewModelSequence().getViewport(0).setSequenceSetId(null);
+ }
+ else
+ {
+ uniqueSetSuffix = "";
+ }
+
+ viewportsAdded = new Hashtable();
+
+ AlignFrame af = LoadFromObject(jm, null, false);
+ af.alignPanels.clear();
+ af.closeMenuItem_actionPerformed(true);
+
+ /* if(ap.av.alignment.getAlignmentAnnotation()!=null)
+ {
+ for(int i=0; i<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;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff