+/*\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 jalview.binding.*;\r
-import jalview.schemes.*;\r
-import javax.swing.JInternalFrame;\r
+import javax.swing.*;\r
+\r
+import org.exolab.castor.xml.*;\r
+\r
+import jalview.schemabinding.version2.*;\r
+\r
\r
\r
+\r
+/**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @author $author$\r
+ * @version $Revision$\r
+ */\r
public class Jalview2XML\r
{\r
+ // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE\r
+ public void SaveState(File statefile)\r
+ {\r
+ long creation = System.currentTimeMillis();\r
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+\r
+ if (frames == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ try\r
+ {\r
+ FileOutputStream fos = new FileOutputStream(statefile);\r
+ JarOutputStream jout = new JarOutputStream(fos);\r
+\r
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
+ ////////////////////////////////////////////////////\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
+ "UTF-8"));\r
+\r
+ Vector shortNames = new Vector();\r
+\r
+ //REVERSE ORDER\r
+ for (int i = frames.length - 1; i > -1; i--)\r
+ {\r
+ if (frames[i] instanceof AlignFrame)\r
+ {\r
+ AlignFrame af = (AlignFrame) frames[i];\r
+\r
+ String shortName = af.getTitle();\r
+\r
+ if (shortName.indexOf(File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ File.separatorChar) + 1);\r
+ }\r
+\r
+ int count = 1;\r
+\r
+ while (shortNames.contains(shortName))\r
+ {\r
+ if (shortName.endsWith("_" + (count - 1)))\r
+ {\r
+ shortName = shortName.substring(0,\r
+ shortName.lastIndexOf("_"));\r
+ }\r
+\r
+ shortName = shortName.concat("_" + count);\r
+ count++;\r
+ }\r
+\r
+ shortNames.addElement(shortName);\r
+\r
+ if (!shortName.endsWith(".xml"))\r
+ {\r
+ shortName = shortName + ".xml";\r
+ }\r
+\r
+ SaveState(af, creation, shortName, jout, out);\r
+ }\r
+ }\r
+\r
+ out.close();\r
+ jout.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW\r
+ public void SaveAlignment(AlignFrame af, String jarFile,\r
+ String fileName)\r
+ {\r
+ try\r
+ {\r
+ FileOutputStream fos = new FileOutputStream(jarFile);\r
+ JarOutputStream jout = new JarOutputStream(fos);\r
+\r
+ //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
+ ////////////////////////////////////////////////////\r
+ PrintWriter out = new PrintWriter(new OutputStreamWriter(jout,\r
+ "UTF-8"));\r
+\r
+ SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
+ out.close();\r
+ jout.close();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param af DOCUMENT ME!\r
+ * @param timeStamp DOCUMENT ME!\r
+ * @param fileName DOCUMENT ME!\r
+ * @param jout DOCUMENT ME!\r
+ * @param out DOCUMENT ME!\r
+ */\r
+ public void SaveState(AlignFrame af, long timeStamp,\r
+ String fileName, JarOutputStream jout, PrintWriter out)\r
+ {\r
+ Vector seqids = new Vector();\r
+ Vector userColours = new Vector();\r
+\r
+ AlignViewport av = af.viewport;\r
+\r
+ JalviewModel object = new JalviewModel();\r
+ object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
+\r
+ object.setCreationDate(new java.util.Date(timeStamp));\r
+ object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
+\r
+ jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
+\r
+ SequenceSet vamsasSet = new SequenceSet();\r
+ Sequence vamsasSeq;\r
+ JalviewModelSequence jms = new JalviewModelSequence();\r
+\r
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
+\r
+ JSeq jseq;\r
\r
- 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
+ //SAVE SEQUENCES\r
+ int id = 0;\r
\r
- Vector shortNames = new Vector();\r
- for (int i = 0; i < frames.length; i++)\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
{\r
- if (frames[i] instanceof AlignFrame)\r
+ seqids.add(jal.getSequenceAt(i));\r
+\r
+ vamsasSeq = new Sequence();\r
+ vamsasSeq.setId(id + "");\r
+ vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
+ vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
+ vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription());\r
+\r
+ jseq = new JSeq();\r
+ jseq.setStart(jal.getSequenceAt(i).getStart());\r
+ jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
+\r
+ jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
+\r
+ jseq.setId(id);\r
+\r
+ if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null)\r
+ {\r
+ jalview.datamodel.SequenceFeature[] sf\r
+ = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures();\r
+ int index = 0;\r
+ while(index < sf.length)\r
+ {\r
+ Features features = new Features();\r
+\r
+ features.setBegin(sf[index].getBegin());\r
+ features.setEnd(sf[index].getEnd());\r
+ features.setDescription(sf[index].getDescription());\r
+ features.setStatus(sf[index].getStatus());\r
+ features.setType(sf[index].getType());\r
+ features.setFeatureGroup(sf[index].getFeatureGroup());\r
+ jseq.addFeatures(features);\r
+ index ++;\r
+ }\r
+ }\r
+\r
+ if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null)\r
+ {\r
+ Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements();\r
+ while(en.hasMoreElements())\r
+ {\r
+ Pdbids pdb = new Pdbids();\r
+ jalview.datamodel.PDBEntry entry\r
+ = (jalview.datamodel.PDBEntry)en.nextElement();\r
+\r
+ pdb.setId(entry.getId());\r
+ pdb.setType(entry.getType());\r
+\r
+ if(entry.getProperty()!=null)\r
+ {\r
+ PdbentryItem item = new PdbentryItem();\r
+ Hashtable properties = entry.getProperty();\r
+ Enumeration en2 = properties.keys();\r
+ while(en2.hasMoreElements())\r
+ {\r
+ Property prop = new Property();\r
+ String key = en2.nextElement().toString();\r
+ prop.setName(key);\r
+ prop.setValue( properties.get(key).toString() );\r
+ item.addProperty(prop);\r
+ }\r
+ pdb.addPdbentryItem(item);\r
+ }\r
+\r
+ jseq.addPdbids(pdb);\r
+ }\r
+ }\r
+\r
+ jms.addJSeq(jseq);\r
+ vamsasSet.addSequence(vamsasSeq);\r
+ id++;\r
+ }\r
+\r
+ //SAVE TREES\r
+ ///////////////////////////////////\r
+ if (af.viewport.currentTree != null)\r
+ {\r
+ // FIND ANY ASSOCIATED TREES\r
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
+ if (Desktop.desktop != null)\r
{\r
- AlignFrame af = (AlignFrame) frames[i];\r
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
\r
- String shortName = af.getTitle();\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
- shortName = shortName.replace('/', '_');\r
- shortName = shortName.replace('\\', '_');\r
- String jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";\r
+ //SAVE ANNOTATIONS\r
+ if (jal.getAlignmentAnnotation() != null)\r
+ {\r
+ jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
\r
- int count=1;\r
- while( shortNames.contains(shortName) )\r
+ for (int i = 0; i < aa.length; i++)\r
{\r
- if(shortName.endsWith("_"+(count-1)))\r
- shortName = shortName.substring(0, shortName.lastIndexOf("_"));\r
+ if (aa[i].label.equals("Quality") ||\r
+ aa[i].label.equals("Conservation") ||\r
+ aa[i].label.equals("Consensus"))\r
+ {\r
+ continue;\r
+ }\r
+\r
+ Annotation an = new Annotation();\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
+ 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
+ an.addAnnotationElement(ae);\r
+ }\r
+\r
+ vamsasSet.addAnnotation(an);\r
+ }\r
+ }\r
\r
- shortName = shortName.concat("_"+count);\r
- count++;\r
+ //SAVE GROUPS\r
+ if (jal.getGroups() != null)\r
+ {\r
+ JGroup[] groups = new JGroup[jal.getGroups().size()];\r
+\r
+ for (int i = 0; i < groups.length; i++)\r
+ {\r
+ groups[i] = new JGroup();\r
+\r
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
+ .elementAt(i);\r
+ groups[i].setStart(sg.getStartRes());\r
+ groups[i].setEnd(sg.getEndRes());\r
+ groups[i].setName(sg.getName());\r
+ if(sg.cs!=null)\r
+ {\r
+ if (sg.cs.conservationApplied())\r
+ {\r
+ groups[i].setConsThreshold(sg.cs.getConservationInc());\r
+\r
+ if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ {\r
+ groups[i].setColour(SetUserColourScheme(sg.cs,\r
+ userColours,\r
+ jms));\r
+ }\r
+ else\r
+ {\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
+ cs));\r
+ }\r
+ }\r
+ else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
+ {\r
+ groups[i].setColour(\r
+ ColourSchemeProperty.getColourName(\r
+ ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
+ }\r
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ {\r
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
+ jms));\r
+ }\r
+ else\r
+ {\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(\r
+ sg.cs));\r
+ }\r
+\r
+ groups[i].setPidThreshold(sg.cs.getThreshold());\r
+ }\r
+\r
+ groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
+ groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
+ groups[i].setDisplayText(sg.getDisplayText());\r
+ groups[i].setColourText(sg.getColourText());\r
+\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
+ int index = seqids.indexOf(seq);\r
+ groups[i].addSeq(index);\r
+ }\r
}\r
- shortNames.addElement(shortName);\r
\r
- if(!shortName.endsWith(".xml"))\r
- shortName = shortName+".xml";\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
- jarFile = statefile.getParent()+File.separatorChar+shortName+".jar";\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
- SaveState( af, creation, shortName, jarFile);\r
- state.addFile(jarFile);\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
- PrintWriter out = new PrintWriter(new FileWriter(statefile));\r
- state.marshal(out);\r
- out.close();\r
- }\r
- catch(Exception ex){ex.printStackTrace();}\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
- public static void SaveState( AlignFrame af, long timeStamp, String fileName, String jarFile)\r
- {\r
+ setting.setDisplay(\r
+ av.featuresDisplayed.containsKey(renderOrder[ro])\r
+ );\r
\r
- Vector seqids = new Vector();\r
+ fs.addSetting(setting);\r
\r
- AlignViewport av = af.viewport;\r
+ }\r
+ jms.setFeatureSettings(fs);\r
\r
- JalviewModel object = new JalviewModel();\r
- object.setVamsasModel( new VamsasModel() );\r
+ }\r
\r
- object.setCreationDate( new java.util.Date(timeStamp) );\r
+ jms.addViewport(view);\r
\r
- jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
\r
- SequenceSet vamsasSet = new SequenceSet();\r
- Sequence vamsasSeq;\r
- JalviewModelSequence jms = new JalviewModelSequence();\r
+ object.setJalviewModelSequence(jms);\r
+ object.getVamsasModel().addSequenceSet(vamsasSet);\r
\r
- vamsasSet.setGapChar(jal.getGapCharacter()+"");\r
+ try\r
+ {\r
+ if (!fileName.endsWith(".xml"))\r
+ {\r
+ fileName = fileName + ".xml";\r
+ }\r
\r
- JSeq jseq;\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
- //SAVE SEQUENCES\r
- int id = 0;\r
- for(int i=0; i<jal.getHeight(); i++)\r
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
+ Vector userColours, JalviewModelSequence jms)\r
{\r
- seqids.add(jal.getSequenceAt(i));\r
+ String id = null;\r
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
\r
- vamsasSeq = new Sequence( );\r
- vamsasSeq.setId(id+"");\r
- vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
- vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
+ if (!userColours.contains(ucs))\r
+ {\r
+ userColours.add(ucs);\r
\r
- jseq = new JSeq();\r
- jseq.setStart(jal.getSequenceAt(i).getStart());\r
- jseq.setEnd(jal.getSequenceAt(i).getEnd());\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
- jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\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
- jseq.setId( id );\r
+ id = "ucs" + userColours.indexOf(ucs);\r
+ uc.setId(id);\r
+ uc.setUserColourScheme(jbucs);\r
+ jms.addUserColours(uc);\r
+ }\r
\r
- jms.addJSeq(jseq);\r
- vamsasSet.addSequence(vamsasSeq);\r
- id++;\r
+ return id;\r
}\r
\r
- //SAVE TREES\r
- if(af.viewport.currentTree!=null)\r
+ jalview.schemes.UserColourScheme GetUserColourScheme(\r
+ JalviewModelSequence jms, String id)\r
{\r
- object.getVamsasModel().addTree(af.viewport.currentTree.toString());\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
- //SAVE ANNOTATIONS\r
- if(jal.getAlignmentAnnotation()!=null)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ */\r
+ public AlignFrame LoadJalviewAlign(String file)\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
+ jalview.gui.AlignFrame af = null;\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
+ try\r
+ {\r
+ //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
+ URL url = null;\r
\r
- AnnotationElement ae;\r
+ if (file.startsWith("http://"))\r
+ {\r
+ url = new URL(file);\r
+ }\r
\r
- for(int a=0; a<aa[i].annotations.length; a++)\r
+ JarInputStream jin = null;\r
+ JarEntry jarentry = null;\r
+ int entryCount = 1;\r
+\r
+ do\r
+ {\r
+ if (url != null)\r
+ {\r
+ jin = new JarInputStream(url.openStream());\r
+ }\r
+ else\r
+ {\r
+ jin = new JarInputStream(new FileInputStream(file));\r
+ }\r
+\r
+ for (int i = 0; i < entryCount; i++)\r
+ {\r
+ jarentry = jin.getNextJarEntry();\r
+\r
+ }\r
+\r
+\r
+ class NoDescIDResolver implements IDResolver\r
+ {\r
+ public Object resolve(String idref)\r
+ {\r
+ System.out.println(idref+" used");\r
+ return null;\r
+ }\r
+ }\r
+\r
+\r
+ if (jarentry != null)\r
+ {\r
+ InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
+ JalviewModel object = new JalviewModel();\r
+\r
+ Unmarshaller unmar = new Unmarshaller(object);\r
+ unmar.setValidation(false);\r
+ object = (JalviewModel) unmar.unmarshal( in );\r
+\r
+ af = LoadFromObject(object);\r
+ entryCount++;\r
+ }\r
+ }\r
+ while (jarentry != null);\r
+ }\r
+ catch(java.net.UnknownHostException ex)\r
{\r
- if(aa[i]==null || aa[i].annotations[a]==null)\r
- continue;\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
- 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
+ catch (Exception ex)\r
+ {\r
+ //Is Version 1 Jar file?\r
+ af = new Jalview2XML_V1().LoadJalviewAlign(file);\r
\r
- vamsasSet.addAnnotation(an);\r
- }\r
+ if(af!=null)\r
+ {\r
+ System.out.println("Successfuly 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
- //SAVE GROUPS\r
- if(jal.getGroups()!=null)\r
+ AlignFrame LoadFromObject(JalviewModel object)\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
+ Vector seqids = new Vector();\r
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
+ Sequence[] vamsasSeq = vamsasSet.getSequence();\r
+\r
+ JalviewModelSequence jms = object.getJalviewModelSequence();\r
+\r
+ //////////////////////////////////\r
+ //LOAD SEQUENCES\r
+ jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length];\r
+ JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\r
+ for (int i = 0; i < vamsasSeq.length; i++)\r
+ {\r
+ jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
+ vamsasSeq[i].getSequence());\r
+ jseqs[i].setDescription( vamsasSeq[i].getDescription() );\r
+\r
+ jseqs[i].setStart(JSEQ[i].getStart());\r
+ jseqs[i].setEnd(JSEQ[i].getEnd());\r
+ jseqs[i].setColor(new java.awt.Color(JSEQ[i].getColour()));\r
+ seqids.add(jseqs[i]);\r
+ }\r
\r
- if(sg.cs instanceof ConservationColourScheme)\r
- groups[i].setConsThreshold( ((ConservationColourScheme)sg.cs).inc);\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
- 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
+ for (int i = 0; i < vamsasSeq.length; i++)\r
+ {\r
+ if (JSEQ[i].getFeaturesCount() > 0)\r
+ {\r
+ Features[] features = JSEQ[i].getFeatures();\r
+ for (int f = 0; f < features.length; f++)\r
+ {\r
+ jalview.datamodel.SequenceFeature sf\r
+ = new jalview.datamodel.SequenceFeature(features[f].getType(),\r
+ features[f].getDescription(), features[f].getStatus(),\r
+ features[f].getBegin(), features[f].getEnd(),\r
+ features[f].getFeatureGroup());\r
\r
+ al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf);\r
+ }\r
+ }\r
+ if (JSEQ[i].getPdbidsCount() > 0)\r
+ {\r
+ Pdbids[] ids = JSEQ[i].getPdbids();\r
+ for (int p = 0; p < ids.length; p++)\r
+ {\r
+ jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry();\r
+ entry.setId(ids[p].getId());\r
+ entry.setType(ids[p].getType());\r
+ al.getSequenceAt(i).getDatasetSequence().addPDBId(entry);\r
+ }\r
\r
- 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
+ }\r
\r
- for(int s=0; s<sg.getSize(); s++)\r
+ /////////////////////////////////\r
+ //////////////////////////////////\r
+ //LOAD ANNOTATIONS\r
+ if (vamsasSet.getAnnotation() != null)\r
{\r
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence)sg.getSequenceAt(s);\r
- int index = seqids.indexOf(seq);\r
- groups[i].addSeq(index);\r
+ Annotation[] an = vamsasSet.getAnnotation();\r
+\r
+ for (int i = 0; i < an.length; i++)\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
+ }\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
+ 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
\r
- jms.setJGroup(groups);\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
- ///////////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
+ // af.changeColour() );\r
+ /////////////////////////\r
+ //LOAD GROUPS\r
+ if (jms.getJGroupCount() > 0)\r
+ {\r
+ JGroup[] groups = jms.getJGroup();\r
\r
- //NOTE UTF-8 MUST BE USED FOR WRITING UNICODE CHARS\r
- ////////////////////////////////////////////////////\r
- PrintWriter out = new PrintWriter(new OutputStreamWriter(jout, "UTF-8"));\r
+ for (int i = 0; i < groups.length; i++)\r
+ {\r
+ ColourSchemeI cs = null;\r
+\r
+ if (groups[i].getColour() != null)\r
+ {\r
+ if (groups[i].getColour().startsWith("ucs"))\r
+ {\r
+ cs = GetUserColourScheme(jms, groups[i].getColour());\r
+ }\r
+ else\r
+ {\r
+ cs = ColourSchemeProperty.getColour(al,\r
+ groups[i].getColour());\r
+ }\r
+\r
+ if(cs!=null)\r
+ cs.setThreshold(groups[i].getPidThreshold(), true);\r
+ }\r
+\r
+ Vector seqs = new Vector();\r
+ int[] ids = groups[i].getSeq();\r
+\r
+ for (int s = 0; s < ids.length; s++)\r
+ {\r
+ seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
+ ids[s]));\r
+ }\r
+\r
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
+ groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
+ groups[i].getDisplayText(), groups[i].getColourText(),\r
+ groups[i].getStart(), groups[i].getEnd());\r
+\r
+ sg.setOutlineColour(new java.awt.Color(\r
+ groups[i].getOutlineColour()));\r
+\r
+ if (groups[i].getConsThreshold() != 0)\r
+ {\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
+ ResidueProperties.propHash, 3, sg.sequences, 0,\r
+ sg.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+ sg.cs.setConservation(c);\r
+ }\r
+\r
+ al.addGroup(sg);\r
+ }\r
+ }\r
\r
- 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
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
+ view.getHeight());\r
+ af.viewport.setStartRes(view.getStartRes());\r
+ af.viewport.setStartSeq(view.getStartSeq());\r
+ af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+ af.viewport.showConservation = view.getShowConservation();\r
+ af.viewport.showQuality = view.getShowQuality();\r
+ af.viewport.showIdentity = view.getShowIdentity();\r
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
+ af.abovePIDThreshold.setSelected(view.getPidSelected());\r
+ af.viewport.setColourText(view.getShowColourText());\r
+ af.colourTextMenuItem.setSelected(view.getShowColourText());\r
+ af.viewport.setConservationSelected(view.getConservationSelected());\r
+ af.conservationMenuItem.setSelected(view.getConservationSelected());\r
+\r
+ af.viewport.setShowJVSuffix(view.getShowFullId());\r
+ af.seqLimits.setSelected(view.getShowFullId());\r
+\r
+ af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
+ view.getFontStyle(), view.getFontSize()));\r
+ af.alignPanel.fontChanged();\r
+\r
+ af.viewport.setRenderGaps(view.getRenderGaps());\r
+ af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
+\r
+ af.viewport.setWrapAlignment(view.getWrapAlignment());\r
+ af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
+\r
+ if (view.getWrapAlignment())\r
+ {\r
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
+ }\r
+ else\r
+ {\r
+ af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
+ af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
+ }\r
+\r
+ af.viewport.setShowBoxes(view.getShowBoxes());\r
+ af.viewBoxesMenuItem.setSelected(view.getShowBoxes());\r
+ af.viewport.setShowText(view.getShowText());\r
+ af.viewTextMenuItem.setSelected(view.getShowText());\r
+\r
+ ColourSchemeI cs = null;\r
+\r
+ if (view.getBgColour() != null)\r
+ {\r
+ if (view.getBgColour().startsWith("ucs"))\r
+ {\r
+ cs = GetUserColourScheme(jms, view.getBgColour());\r
+ }\r
+ else if(view.getBgColour().startsWith("Annotation"))\r
+ {\r
+ //int find annotation\r
+ for (int i = 0; i < af.viewport.alignment.getAlignmentAnnotation().length; i++)\r
+ {\r
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].label.\r
+ equals(view.getAnnotationColours().getAnnotation()))\r
+ {\r
+ if (af.viewport.alignment.getAlignmentAnnotation()[i].\r
+ getThreshold() == null)\r
+ {\r
+ af.viewport.alignment.getAlignmentAnnotation()[i].\r
+ setThreshold(\r
+ new jalview.datamodel.GraphLine(\r
+ view.getAnnotationColours().getThreshold(),\r
+ "Threshold", java.awt.Color.black)\r
+\r
+ );\r
+ }\r
+\r
+\r
+ if (view.getAnnotationColours().getColourScheme().equals(\r
+ "None"))\r
+ {\r
+ cs = new AnnotationColourGradient(\r
+ af.viewport.alignment.getAlignmentAnnotation()[i],\r
+ new java.awt.Color(view.getAnnotationColours().\r
+ getMinColour()),\r
+ new java.awt.Color(view.getAnnotationColours().\r
+ getMaxColour()),\r
+ view.getAnnotationColours().getAboveThreshold());\r
+ }\r
+ else if (view.getAnnotationColours().getColourScheme().\r
+ startsWith("ucs"))\r
+ {\r
+ cs = new AnnotationColourGradient(\r
+ af.viewport.alignment.getAlignmentAnnotation()[i],\r
+ GetUserColourScheme(jms, view.getAnnotationColours().\r
+ getColourScheme()),\r
+ view.getAnnotationColours().getAboveThreshold()\r
+ );\r
+ }\r
+ else\r
+ {\r
+ cs = new AnnotationColourGradient(\r
+ af.viewport.alignment.getAlignmentAnnotation()[i],\r
+ ColourSchemeProperty.getColour(al,\r
+ view.getAnnotationColours().getColourScheme()),\r
+ view.getAnnotationColours().getAboveThreshold()\r
+ );\r
+ }\r
+\r
+ // Also use these settings for all the groups\r
+ if (al.getGroups() != null)\r
+ for (int g = 0; g < al.getGroups().size(); g++)\r
+ {\r
+ jalview.datamodel.SequenceGroup sg\r
+ = (jalview.datamodel.SequenceGroup)al.getGroups().elementAt(g);\r
+\r
+ if(sg.cs == null)\r
+ continue;\r
+\r
+\r
+ /* if (view.getAnnotationColours().getColourScheme().equals("None"))\r
+ {\r
+ sg.cs = new AnnotationColourGradient(\r
+ af.viewport.alignment.getAlignmentAnnotation()[i],\r
+ new java.awt.Color(view.getAnnotationColours().\r
+ getMinColour()),\r
+ new java.awt.Color(view.getAnnotationColours().\r
+ getMaxColour()),\r
+ view.getAnnotationColours().getAboveThreshold());\r
+ }\r
+ else*/\r
+ {\r
+ sg.cs = new AnnotationColourGradient(\r
+ af.viewport.alignment.getAlignmentAnnotation()[i],\r
+ sg.cs,\r
+ view.getAnnotationColours().getAboveThreshold()\r
+ );\r
+ }\r
+\r
+ }\r
+\r
+\r
+ break;\r
+ }\r
+\r
+ }\r
+ }\r
+ else\r
+ {\r
+ cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
+ }\r
+\r
+ if(cs!=null)\r
+ {\r
+ cs.setThreshold(view.getPidThreshold(), true);\r
+ cs.setConsensus(af.viewport.vconsensus);\r
+ }\r
+ }\r
+\r
+ af.setColourSelected(view.getBgColour());\r
+ af.viewport.setGlobalColourScheme(cs);\r
+ af.viewport.setColourAppliesToAllGroups(false);\r
+ af.changeColour(cs);\r
+ if (view.getConservationSelected() && cs!=null)\r
+ {\r
+ cs.setConservationInc(view.getConsThreshold());\r
+ }\r
+\r
+ af.viewport.setColourAppliesToAllGroups(true);\r
+\r
+ if (view.getShowSequenceFeatures())\r
+ {\r
+ af.viewport.showSequenceFeatures = true;\r
+ af.showSeqFeatures.setSelected(true);\r
+ }\r
+\r
+ if(jms.getFeatureSettings()!=null)\r
+ {\r
+ af.viewport.featuresDisplayed = new Hashtable();\r
+ String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
+ for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
{\r
- 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
+ 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
- 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
+ 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
- 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
+ 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
- af.viewport.setShowBoxes( view.getShowBoxes() );\r
- af.viewport.setShowText( view.getShowText() );\r
+ Tree tree = jms.getTree(t);\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
+ 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
- ColourSchemeI cs = af.viewport.getGlobalColourScheme();\r
- if(cs instanceof ConservationColourScheme)\r
- ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
+ tp.fitToWindow.setState(tree.getFitToWindow());\r
+ tp.fitToWindow_actionPerformed(null);\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
+ 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
- //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
+ tp.showPlaceholders(tree.getMarkUnlinked());\r
+ tp.showBootstrap(tree.getShowBootstrap());\r
+ tp.showDistances(tree.getShowDistances());\r
\r
- }\r
+ tp.treeCanvas.threshold = tree.getThreshold();\r
\r
- }\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
git://source.jalview.org / jalview.git / blobdiff