-/*\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
-\r
-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
-import java.net.URL;\r
-import jalview.io.SequenceFeatureFetcher;\r
-\r
-\r
-public class Jalview2XML\r
-{\r
-\r
- // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
- public static void SaveState(File statefile)\r
- {\r
- long creation = System.currentTimeMillis();\r
- JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
- if(frames==null)\r
- return;\r
-\r
- try{\r
- FileOutputStream fos = new FileOutputStream(statefile);\r
- JarOutputStream jout = new JarOutputStream(fos);\r
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
- ////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
-\r
- Vector shortNames = new Vector();\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
- shortName = shortName.substring(\r
- shortName.lastIndexOf(File.separatorChar)+1);\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
- SaveState( af, creation, shortName, jout, out);\r
- }\r
- }\r
- out.close();\r
- jout.close();\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
- public static void SaveState( AlignFrame af, String jarFile, String fileName)\r
- {\r
- try{\r
- FileOutputStream fos = new FileOutputStream(jarFile);\r
- JarOutputStream jout = new JarOutputStream(fos);\r
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
- ////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
-\r
- SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
- out.close();\r
- jout.close();\r
- }catch(Exception ex){}\r
- }\r
-\r
- public static void SaveState( AlignFrame af, long timeStamp,\r
- String fileName, JarOutputStream jout, PrintWriter out)\r
- {\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 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
- if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours, jms));\r
- else\r
- groups[i].setColour(ColourSchemeProperty.getColourName(sg.cs));\r
-\r
- groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
- groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
- groups[i].setDisplayText(sg.getDisplayText());\r
- groups[i].setColourText(sg.getColourText());\r
-\r
- for(int s=0; s<sg.getSize(); s++)\r
- {\r
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);\r
- int index = seqids.indexOf(seq);\r
- groups[i].addSeq(index);\r
- }\r
-\r
- }\r
- jms.setJGroup(groups);\r
-\r
- }\r
-\r
- ///////////SAVE VIEWPORT\r
- Viewport view = new Viewport();\r
- view.setTitle(af.getTitle());\r
- view.setXpos(af.getX());\r
- view.setYpos(af.getY());\r
- view.setWidth(af.getWidth());\r
- view.setHeight(af.getHeight());\r
- view.setStartRes(av.startRes);\r
- view.setStartSeq(av.startSeq);\r
-\r
-\r
- if( av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
- view.setBgColour( SetUserColourScheme(av.getGlobalColourScheme(),\r
- userColours, jms) );\r
- else\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
- 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
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
-\r
- static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
- Vector userColours,\r
- JalviewModelSequence jms)\r
- {\r
- String id=null;\r
- jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme)cs;\r
- if (!userColours.contains(ucs))\r
- {\r
- userColours.add(ucs);\r
- java.awt.Color [] colours = ucs.getColours();\r
- jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
- jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme();\r
- for(int i=0; i<colours.length; i++)\r
- {\r
- jalview.binding.Colour col = new jalview.binding.Colour();\r
- col.setRGB( jalview.util.Format.getHexString(colours[i]) );\r
- jbucs.addColour(col);\r
- }\r
- id = "ucs"+userColours.indexOf(ucs);\r
- uc.setId(id);\r
- uc.setUserColourScheme(jbucs);\r
- jms.addUserColours(uc);\r
- }\r
- return id;\r
- }\r
-\r
- static jalview.schemes.UserColourScheme GetUserColourScheme(JalviewModelSequence jms, String id)\r
- {\r
- UserColours [] uc = jms.getUserColours();\r
- UserColours colours=null;\r
- for(int i=0; i<uc.length; i++)\r
- {\r
- if(uc[i].getId().equals(id))\r
- { colours = uc[i]; break; }\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
- newColours[i] = new java.awt.Color(\r
- Integer.parseInt( colours.getUserColourScheme().getColour(i).getRGB(), 16) );\r
-\r
- return new jalview.schemes.UserColourScheme(newColours);\r
-\r
- }\r
-\r
-\r
- public static void LoadJalviewAlign(String file)\r
- {\r
- JalviewModel object = new JalviewModel();\r
- try{\r
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
-\r
- URL url = null;\r
- if( file.startsWith("http://"))\r
- url = new URL(file);\r
-\r
- JarInputStream jin = null;\r
- JarEntry jarentry=null;\r
- int entryCount = 1;\r
- do{\r
- if (url != null)\r
- jin = new JarInputStream(url.openStream());\r
- else\r
- jin = new JarInputStream(new FileInputStream(file));\r
-\r
- for(int i=0; i<entryCount; i++)\r
- jarentry = jin.getNextJarEntry();\r
-\r
- if(jarentry!=null)\r
- {\r
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
- object = (JalviewModel) object.unmarshal(in);\r
- LoadFromObject(object);\r
- entryCount++;\r
- }\r
- }while(jarentry!=null);\r
-\r
- }\r
- catch(Exception ex)\r
- { System.err.println("Exception whilst loading jalview XML file : "+ex+"\n");\r
- ex.printStackTrace(); return; }\r
-\r
- }\r
-\r
- static void LoadFromObject(JalviewModel object)\r
- {\r
- Vector seqids = new Vector();\r
- SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
- Sequence [] vamsasSeq = vamsasSet.getSequence();\r
-\r
- JalviewModelSequence jms = object.getJalviewModelSequence();\r
- //////////////////////////////////\r
- //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=null;\r
- if(groups[i].getColour()!=null)\r
- {\r
- if (groups[i].getColour().startsWith("ucs"))\r
- cs = GetUserColourScheme(jms, groups[i].getColour());\r
- else\r
- cs = ColourSchemeProperty.getColour(al, groups[i].getColour());\r
-\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
-\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.showConservation = view.getShowConservation();\r
- af.viewport.showQuality = view.getShowQuality();\r
- af.viewport.showIdentity= view.getShowIdentity();\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
-\r
- af.sequenceFeatures_actionPerformed(null);\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
- ColourSchemeI cs=null;\r
- if(view.getBgColour()!=null)\r
- {\r
-\r
- if (view.getBgColour().startsWith("ucs"))\r
- cs = GetUserColourScheme(jms, view.getBgColour());\r
- else\r
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
-\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
- }\r
- af.viewport.setGlobalColourScheme( cs );\r
-\r
-\r
- af.viewport.setColourAppliesToAllGroups(false);\r
- af.changeColour(af.viewport.getGlobalColourScheme());\r
- af.viewport.setColourAppliesToAllGroups(true);\r
-\r
- System.out.println(view.getShowSequenceFeatures());\r
- if( view.getShowSequenceFeatures() );\r
- {\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al, af.alignPanel);\r
- }\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
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 jalview.schemes.*;
+
+import java.io.*;
+
+import java.net.*;
+
+import java.util.*;
+
+import java.util.jar.*;
+
+import javax.swing.*;
+
+import org.exolab.castor.xml.*;
+
+import jalview.schemabinding.version2.*;
+
+
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @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;
+
+ String uniqueSetSuffix = "";
+
+
+ // 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;
+ Vector pdbfiles = null;
+
+ //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(jal.getSequenceAt(i).getHiddenSequences()!=null)
+ {
+ jalview.datamodel.SequenceI [] reps =
+ jal.getSequenceAt(i).getHiddenSequences().getSequencesInOrder(jal);
+
+ for(int h=0; h<reps.length; h++)
+ {
+ 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());
+
+
+ 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].label.equals("Quality") ||
+ aa[i].label.equals("Conservation") ||
+ aa[i].label.equals("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);
+
+ AnnotationElement ae;
+
+ for (int a = 0; a < aa[i].annotations.length; a++)
+ {
+ if ((aa[i] == null) || (aa[i].annotations[a] == null))
+ {
+ continue;
+ }
+
+ ae = new AnnotationElement();
+ ae.setDescription(aa[i].annotations[a].description);
+ ae.setDisplayCharacter(aa[i].annotations[a].displayCharacter);
+ ae.setValue(aa[i].annotations[a].value);
+ ae.setPosition(a);
+ ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure +
+ "");
+
+ if(aa[i].annotations[a].colour!=java.awt.Color.black)
+ ae.setColour(aa[i].annotations[a].colour.getRGB());
+
+ an.addAnnotationElement(ae);
+ }
+
+ 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(false); 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])
+ );
+
+ 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);
+
+ fs.addSetting(setting);
+ settingsAdded.addElement(key);
+ }
+
+ 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();
+
+ Vector gatherToThisFrame= new Vector();
+
+ 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.add(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;
+ }
+
+ 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();
+
+ for (int i = 0; i < gatherToThisFrame.size(); i++)
+ {
+ Desktop.instance.gatherViews(
+ (AlignFrame) gatherToThisFrame.elementAt(i));
+ }
+
+ return af;
+ }
+
+ String loadPDBFile(String file, String pdbId)
+ {
+ System.out.println(file +" "+pdbId);
+ 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();
+ return outFile.getAbsolutePath();
+
+ }
+ catch (Exception ex)
+ {
+ ex.printStackTrace();
+ }
+
+ return null;
+ }
+
+
+ AlignFrame LoadFromObject(JalviewModel object,
+ String file,
+ boolean loadTrees )
+ {
+ 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()))
+ {
+ String tmppdb = loadPDBFile(file, ids[p].getId());
+ entry.setFile(tmppdb);
+ pdbloaded.put(ids[p].getId(), tmppdb);
+ }
+ 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;
+ }
+
+ AnnotationElement[] ae = an[i].getAnnotationElement();
+ jalview.datamodel.Annotation[] anot = new jalview.datamodel.Annotation[al.getWidth()];
+
+ for (int aa = 0; aa < ae.length; aa++)
+ {
+ anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].getDisplayCharacter(),
+ ae[aa].getDescription(),
+ ae[aa].getSecondaryStructure().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].getSequenceRef()!=null)
+ {
+ jaa.createSequenceMapping(
+ al.findName(an[i].getSequenceRef()), 1, true
+ );
+ al.findName(an[i].getSequenceRef()).addAlignmentAnnotation(jaa);
+ }
+
+ 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)+"";
+ seqs.addElement((jalview.datamodel.SequenceI) seqRefIds.get(seqId));
+ }
+
+ 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(false), 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++)
+ {
+ for(int r=0; r<JSEQ[s].getHiddenSequencesCount(); r++)
+ {
+ al.getSequenceAt(s).addHiddenSequence(
+ al.getSequenceAt( JSEQ[s].getHiddenSequences(r) )
+ );
+ }
+ }
+
+ 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.getDisplay())
+ af.viewport.featuresDisplayed.put(
+ setting.getType(), new Integer(setting.getColour()));
+ }
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;
+ }
+
+ 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 (loadTrees && 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();
+ }
+
+ }
+
+ 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);
+
+ return af.alignPanel;
+ }
+}
+
git://source.jalview.org / jalview.git / blobdiff