--- /dev/null
+package jalview.gui;\r
+\r
+import java.io.*;\r
+import java.util.*;\r
+import java.util.jar.*;\r
+\r
+import jalview.binding.*;\r
+import jalview.schemes.*;\r
+import javax.swing.JInternalFrame;\r
+\r
+\r
+public class Jalview2XML\r
+{\r
+\r
+ public static void SaveState(File statefile)\r
+ {\r
+ long creation = System.currentTimeMillis();\r
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+ try{\r
+ JalviewState state = new JalviewState();\r
+\r
+ Vector shortNames = new Vector();\r
+ for (int i = 0; i < frames.length; i++)\r
+ {\r
+ if (frames[i] instanceof AlignFrame)\r
+ {\r
+ AlignFrame af = (AlignFrame) frames[i];\r
+\r
+ String shortName = af.getTitle();\r
+\r
+ shortName = shortName.replace('/', '_');\r
+ shortName = shortName.replace('\\', '_');\r
+ String jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";\r
+\r
+ int count=1;\r
+ while( shortNames.contains(shortName) )\r
+ {\r
+ if(shortName.endsWith("_"+(count-1)))\r
+ shortName = shortName.substring(0, shortName.lastIndexOf("_"));\r
+\r
+ shortName = shortName.concat("_"+count);\r
+ count++;\r
+ }\r
+ shortNames.addElement(shortName);\r
+\r
+ if(!shortName.endsWith(".xml"))\r
+ shortName = shortName+".xml";\r
+\r
+ jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";\r
+\r
+ SaveState( af, creation, shortName, jarFile);\r
+ state.addFile(jarFile);\r
+ }\r
+ }\r
+\r
+ PrintWriter out = new PrintWriter(new FileWriter(statefile));\r
+ state.marshal(out);\r
+ out.close();\r
+ }\r
+ catch(Exception ex){ex.printStackTrace();}\r
+ }\r
+\r
+\r
+ public static void SaveState( AlignFrame af, long timeStamp, String fileName, String jarFile)\r
+ {\r
+\r
+ Vector seqids = new Vector();\r
+\r
+ AlignViewport av = af.viewport;\r
+\r
+ JalviewModel object = new JalviewModel();\r
+ object.setVamsasModel( new VamsasModel() );\r
+\r
+ object.setCreationDate( new java.util.Date(timeStamp) );\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
+\r
+ //SAVE SEQUENCES\r
+ int id = 0;\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
+\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
+ jms.addJSeq(jseq);\r
+ vamsasSet.addSequence(vamsasSeq);\r
+ id++;\r
+ }\r
+\r
+ //SAVE TREES\r
+ if(af.viewport.currentTree!=null)\r
+ {\r
+ object.getVamsasModel().addTree(af.viewport.currentTree.toString());\r
+ }\r
+\r
+ //SAVE ANNOTATIONS\r
+ if(jal.getAlignmentAnnotation()!=null)\r
+ {\r
+\r
+ jalview.datamodel.AlignmentAnnotation [] aa = jal.getAlignmentAnnotation();\r
+ for(int i=0; i<aa.length; i++)\r
+ {\r
+ if(aa[i].label.equals("Quality")\r
+ || aa[i].label.equals("Conservation")\r
+ || aa[i].label.equals("Consensus"))\r
+ { continue;}\r
+\r
+ Annotation an = new Annotation();\r
+ an.setDescription(aa[i].description);\r
+ an.setGraph(aa[i].isGraph);\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
+ continue;\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
+ an.addAnnotationElement(ae);\r
+ }\r
+\r
+ vamsasSet.addAnnotation(an);\r
+ }\r
+\r
+ }\r
+\r
+ //SAVE GROUPS\r
+ if(jal.getGroups()!=null)\r
+ {\r
+ JGroup [] groups = new JGroup[jal.getGroups().size()];\r
+ for(int i=0; i<groups.length; i++)\r
+ {\r
+ groups[i] = new JGroup();\r
+ jalview.datamodel.SequenceGroup sg\r
+ = (jalview.datamodel.SequenceGroup)jal.getGroups().elementAt(i);\r
+ groups[i].setStart( sg.getStartRes() );\r
+ groups[i].setEnd( sg.getEndRes() );\r
+ groups[i].setName( sg.getName());\r
+\r
+ if(sg.cs instanceof ConservationColourScheme)\r
+ groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);\r
+\r
+ if (sg.cs instanceof ResidueColourScheme)\r
+ groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).getThreshold());\r
+ else if (sg.cs instanceof ScoreColourScheme)\r
+ groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());\r
+\r
+\r
+ groups[i].setColour( ColourSchemeProperty.getColourName(sg.cs) );\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
+\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
+ view.setBgColour( ColourSchemeProperty.getColourName\r
+ ( av.getGlobalColourScheme()));\r
+\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme)\r
+ view.setConsThreshold( ((ConservationColourScheme)cs).inc);\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
+ else if (cs instanceof ScoreColourScheme)\r
+ view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\r
+\r
+\r
+ view.setConservationSelected(av.getConservationSelected());\r
+ view.setPidSelected(av.getAbovePIDThreshold());\r
+ view.setFontName(av.font.getFontName());\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.getShowFullId());\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
+ jms.addViewport( view );\r
+\r
+ object.setJalviewModelSequence(jms);\r
+ object.getVamsasModel().addSequenceSet(vamsasSet);\r
+\r
+\r
+ try\r
+ {\r
+ // NAME OF FILE\r
+ FileOutputStream fos = new FileOutputStream(jarFile);\r
+\r
+ //PUT IT IN THIS 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, "UTF-8"));\r
+\r
+ if(!fileName.endsWith(".xml"))\r
+ fileName = fileName+".xml";\r
+\r
+ JarEntry entry = new JarEntry(fileName);\r
+ jout.putNextEntry(entry);\r
+\r
+ object.marshal(out);\r
+ out.close();\r
+ fos.close();\r
+ jout.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ public static void LoadState(String file)\r
+ {\r
+ try{\r
+ JalviewState state = new JalviewState();\r
+ BufferedReader in = new BufferedReader(new FileReader(file));\r
+ state = (JalviewState)state.unmarshal(in);\r
+ Enumeration en = state.enumerateFile();\r
+ while( en.hasMoreElements() )\r
+ {\r
+ LoadJalviewAlign( en.nextElement().toString());\r
+ }\r
+ }\r
+ catch(Exception ex)\r
+ { ex.printStackTrace(); return; }\r
+ }\r
+\r
+ public static void LoadJalviewAlign(String file)\r
+ {\r
+ JalviewModel object = new JalviewModel();\r
+ Vector seqids = new Vector();\r
+ try{\r
+ FileInputStream fis = new FileInputStream(file);\r
+ JarInputStream jin = new JarInputStream(fis);\r
+ jin.getNextJarEntry();\r
+ InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
+ object = (JalviewModel) object.unmarshal(in);\r
+ }\r
+ catch(Exception ex)\r
+ { System.out.println(ex); return; }\r
+\r
+\r
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
+ Sequence [] vamsasSeq = vamsasSet.getSequence();\r
+\r
+ JalviewModelSequence jms = object.getJalviewModelSequence();\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
+\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
+ /////////////////////////////////\r
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+ /////////////////////////////////\r
+\r
+ //////////////////////////////////\r
+ //LOAD ANNOTATIONS\r
+ if(vamsasSet.getAnnotation()!=null)\r
+ {\r
+ Annotation[] an = vamsasSet.getAnnotation();\r
+ for (int i = 0; i < an.length; i++)\r
+ {\r
+ AnnotationElement[] ae = an[i].getAnnotationElement();\r
+ jalview.datamodel.Annotation anot[]\r
+ = new jalview.datamodel.Annotation[al.getWidth()];\r
+ for (int aa = 0; aa < ae.length; aa++)\r
+ {\r
+ anot[ae[aa].getPosition()]\r
+ = new jalview.datamodel.Annotation(\r
+ ae[aa].getDisplayCharacter(),\r
+ ae[aa].getDescription(),\r
+ ae[aa].getSecondaryStructure().charAt(0),\r
+ ae[aa].getValue()\r
+ );\r
+ }\r
+\r
+\r
+ jalview.datamodel.AlignmentAnnotation jaa = null;\r
+ if(an[i].getGraph())\r
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
+ an[i].getDescription(), anot,\r
+ 0,0,1);\r
+ else\r
+ jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
+ an[i].getDescription(), anot);\r
+ al.addAnnotation(jaa);\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
+ // af.changeColour() );\r
+\r
+ /////////////////////////\r
+ //LOAD GROUPS\r
+ if (jms.getJGroupCount()>0)\r
+ {\r
+ JGroup[] groups = jms.getJGroup();\r
+ for (int i = 0; i < groups.length; i++)\r
+ {\r
+ ColourSchemeI cs = ColourSchemeProperty.getColour(al, groups[i].getColour() );\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
+\r
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup\r
+ (groups[i].getName(),\r
+ cs,\r
+ groups[i].getDisplayBoxes(),\r
+ groups[i].getDisplayText(),\r
+ groups[i].getColourText(),\r
+ groups[i].getStart(),\r
+ groups[i].getEnd()) ;\r
+ sg.setOutlineColour( new java.awt.Color(groups[i].getOutlineColour()));\r
+ int [] ids = groups[i].getSeq();\r
+ for(int s=0; s<ids.length; s++)\r
+ sg.addSequence( (jalview.datamodel.SequenceI)seqids.elementAt( ids[s] ));\r
+\r
+ if(groups[i].getConsThreshold()!=0)\r
+ {\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
+ ResidueProperties.propHash, 3,\r
+ sg.sequences, 0,\r
+ sg.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+ cs = new ConservationColourScheme(c, cs);\r
+ sg.cs = cs;\r
+ }\r
+\r
+\r
+ al.addGroup(sg);\r
+ }\r
+ }\r
+\r
+\r
+ Desktop.addInternalFrame(af, view.getTitle(), AlignFrame.NEW_WINDOW_WIDTH, AlignFrame.NEW_WINDOW_HEIGHT);\r
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight());\r
+ af.viewport.setStartRes( view.getStartRes() );\r
+ af.viewport.setStartSeq( view.getStartSeq() );\r
+ af.viewport.setAbovePIDThreshold( view.getPidSelected() );\r
+ af.viewport.setColourText( view.getShowColourText() );\r
+ af.viewport.setConservationSelected( view.getConservationSelected());\r
+ af.viewport.setShowFullId( view.getShowFullId());\r
+ af.viewport.setFont( new java.awt.Font( view.getFontName(),\r
+ view.getFontStyle(),\r
+ view.getFontSize()));\r
+ af.alignPanel.fontChanged();\r
+ af.viewport.setRenderGaps( view.getRenderGaps() );\r
+\r
+ af.viewport.setWrapAlignment( view.getWrapAlignment() );\r
+ if(view.getWrapAlignment())\r
+ {\r
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
+ }\r
+ else\r
+ {\r
+ af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
+ }\r
+\r
+ af.viewport.setShowBoxes( view.getShowBoxes() );\r
+ af.viewport.setShowText( view.getShowText() );\r
+\r
+ af.viewport.setGlobalColourScheme( ColourSchemeProperty.getColour(al, view.getBgColour()));\r
+ af.viewport.setColourAppliesToAllGroups(false);\r
+ af.changeColour( af.viewport.getGlobalColourScheme() );\r
+ af.viewport.setColourAppliesToAllGroups(true);\r
+\r
+ ColourSchemeI cs = af.viewport.getGlobalColourScheme();\r
+ if(cs instanceof ConservationColourScheme)\r
+ ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
+\r
+ if (cs instanceof ResidueColourScheme)\r
+ ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
+ else if (cs instanceof ScoreColourScheme)\r
+ ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
+\r
+ //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
+ if(object.getVamsasModel().getTreeCount()>0)\r
+ {\r
+ try{\r
+ af.ShowNewickTree(new jalview.io.NewickFile(\r
+ (String)object.getVamsasModel().getTree(0)), "Tree");\r
+ }catch(Exception ex){ex.printStackTrace();}\r
+\r
+ }\r
+\r
+ }\r
+}\r
+\r
+\r
+\r
git://source.jalview.org / jalview.git / commitdiff