*/\r
package jalview.gui;\r
\r
+\r
+import jalview.schemes.*;\r
+\r
+import jalview.gui.*;\r
+\r
import java.io.*;\r
+\r
import java.net.*;\r
+\r
import java.util.*;\r
+\r
import java.util.jar.*;\r
\r
import javax.swing.*;\r
\r
-import jalview.binding.*;\r
-import jalview.io.*;\r
-import jalview.schemes.*;\r
+import org.exolab.castor.xml.*;\r
\r
-public class Jalview2XML\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
+import jalview.schemabinding.version2.*;\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
+ * 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
- //REVERSE ORDER\r
- for (int i = frames.length - 1; i > -1; i--)\r
- {\r
- if (frames[i] instanceof AlignFrame)\r
+ if (frames == null)\r
{\r
- AlignFrame af = (AlignFrame) frames[i];\r
+ return;\r
+ }\r
\r
- String shortName = af.getTitle();\r
+ try\r
+ {\r
+ FileOutputStream fos = new FileOutputStream(statefile);\r
+ JarOutputStream jout = new JarOutputStream(fos);\r
\r
- if (shortName.indexOf(File.separatorChar) > -1)\r
- {\r
- shortName = shortName.substring(shortName.lastIndexOf(\r
- File.separatorChar) + 1);\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
- int count = 1;\r
+ Vector shortNames = new Vector();\r
\r
- while (shortNames.contains(shortName))\r
- {\r
- if (shortName.endsWith("_" + (count - 1)))\r
+ //REVERSE ORDER\r
+ for (int i = frames.length - 1; i > -1; i--)\r
{\r
- shortName = shortName.substring(0,\r
- shortName.lastIndexOf("_"));\r
- }\r
+ if (frames[i] instanceof AlignFrame)\r
+ {\r
+ AlignFrame af = (AlignFrame) frames[i];\r
\r
- shortName = shortName.concat("_" + count);\r
- count++;\r
- }\r
+ String shortName = af.getTitle();\r
\r
- shortNames.addElement(shortName);\r
+ if (shortName.indexOf(File.separatorChar) > -1)\r
+ {\r
+ shortName = shortName.substring(shortName.lastIndexOf(\r
+ File.separatorChar) + 1);\r
+ }\r
\r
- if (!shortName.endsWith(".xml"))\r
- {\r
- shortName = shortName + ".xml";\r
- }\r
+ int count = 1;\r
\r
- SaveState(af, creation, shortName, jout, out);\r
- }\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
- out.close();\r
- jout.close();\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
+ shortName = shortName.concat("_" + count);\r
+ count++;\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
- {\r
- FileOutputStream fos = new FileOutputStream(jarFile);\r
- JarOutputStream jout = new JarOutputStream(fos);\r
+ shortNames.addElement(shortName);\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
+ if (!shortName.endsWith(".xml"))\r
+ {\r
+ shortName = shortName + ".xml";\r
+ }\r
\r
- SaveState(af, System.currentTimeMillis(), fileName, jout, out);\r
- out.close();\r
- jout.close();\r
- }\r
- catch (Exception ex)\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
\r
- public static void SaveState(AlignFrame af, long timeStamp,\r
- String fileName, JarOutputStream jout,\r
- PrintWriter out)\r
- {\r
- Vector seqids = new Vector();\r
- Vector userColours = new Vector();\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
- AlignViewport av = af.viewport;\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
- JalviewModel object = new JalviewModel();\r
- object.setVamsasModel(new VamsasModel());\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
- object.setCreationDate(new java.util.Date(timeStamp));\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
- jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
+ AlignViewport av = af.viewport;\r
\r
- SequenceSet vamsasSet = new SequenceSet();\r
- Sequence vamsasSeq;\r
- JalviewModelSequence jms = new JalviewModelSequence();\r
+ JalviewModel object = new JalviewModel();\r
+ object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel());\r
\r
- vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
+ object.setCreationDate(new java.util.Date(timeStamp));\r
+ object.setVersion(jalview.bin.Cache.getProperty("VERSION"));\r
\r
- JSeq jseq;\r
+ jalview.datamodel.AlignmentI jal = af.viewport.alignment;\r
\r
- //SAVE SEQUENCES\r
- int id = 0;\r
+ SequenceSet vamsasSet = new SequenceSet();\r
+ Sequence vamsasSeq;\r
+ JalviewModelSequence jms = new JalviewModelSequence();\r
\r
- for (int i = 0; i < jal.getHeight(); i++)\r
- {\r
- seqids.add(jal.getSequenceAt(i));\r
+ vamsasSet.setGapChar(jal.getGapCharacter() + "");\r
\r
- vamsasSeq = new Sequence();\r
- vamsasSeq.setId(id + "");\r
- vamsasSeq.setName(jal.getSequenceAt(i).getName());\r
- vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence());\r
+ JSeq jseq;\r
\r
- jseq = new JSeq();\r
- jseq.setStart(jal.getSequenceAt(i).getStart());\r
- jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
+ //SAVE SEQUENCES\r
+ int id = 0;\r
\r
- jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
+ for (int i = 0; i < jal.getHeight(); i++)\r
+ {\r
+ seqids.add(jal.getSequenceAt(i));\r
\r
- jseq.setId(id);\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
- jms.addJSeq(jseq);\r
- vamsasSet.addSequence(vamsasSeq);\r
- id++;\r
- }\r
+ jseq = new JSeq();\r
+ jseq.setStart(jal.getSequenceAt(i).getStart());\r
+ jseq.setEnd(jal.getSequenceAt(i).getEnd());\r
\r
- //SAVE TREES\r
- if (af.viewport.currentTree != null)\r
- {\r
- object.getVamsasModel().addTree(af.viewport.currentTree.toString());\r
- }\r
+ jseq.setColour(jal.getSequenceAt(i).getColor().getRGB());\r
\r
- //SAVE ANNOTATIONS\r
- if (jal.getAlignmentAnnotation() != null)\r
- {\r
- jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
+ jseq.setId(id);\r
\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
- {\r
- continue;\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
- Annotation an = new Annotation();\r
- an.setDescription(aa[i].description);\r
- an.setGraph(aa[i].isGraph);\r
- an.setLabel(aa[i].label);\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
- AnnotationElement ae;\r
+ jms.addJSeq(jseq);\r
+ vamsasSet.addSequence(vamsasSeq);\r
+ id++;\r
+ }\r
\r
- for (int a = 0; a < aa[i].annotations.length; a++)\r
+ //SAVE TREES\r
+ ///////////////////////////////////\r
+ if (af.viewport.currentTree != null)\r
{\r
- if ( (aa[i] == null) || (aa[i].annotations[a] == null))\r
+ // FIND ANY ASSOCIATED TREES\r
+ // NOT IMPLEMENTED FOR HEADLESS STATE AT PRESENT\r
+ if (Desktop.desktop != null)\r
{\r
- continue;\r
+ JInternalFrame[] frames = Desktop.desktop.getAllFrames();\r
+\r
+ for (int t = 0; t < frames.length; t++)\r
+ {\r
+ if (frames[t] instanceof TreePanel)\r
+ {\r
+ TreePanel tp = (TreePanel) frames[t];\r
+\r
+ if (tp.treeCanvas.av.alignment == jal)\r
+ {\r
+ Tree tree = new Tree();\r
+ tree.setTitle(tp.getTitle());\r
+ tree.setCurrentTree( (af.viewport.currentTree == tp.getTree()));\r
+ tree.setNewick(tp.getTree().toString());\r
+ tree.setThreshold(tp.treeCanvas.threshold);\r
+\r
+ tree.setFitToWindow(tp.fitToWindow.getState());\r
+ tree.setFontName(tp.getTreeFont().getName());\r
+ tree.setFontSize(tp.getTreeFont().getSize());\r
+ tree.setFontStyle(tp.getTreeFont().getStyle());\r
+ tree.setMarkUnlinked(tp.placeholdersMenu.getState());\r
+\r
+ tree.setShowBootstrap(tp.bootstrapMenu.getState());\r
+ tree.setShowDistances(tp.distanceMenu.getState());\r
+\r
+ tree.setHeight(tp.getHeight());\r
+ tree.setWidth(tp.getWidth());\r
+ tree.setXpos(tp.getX());\r
+ tree.setYpos(tp.getY());\r
+\r
+ jms.addTree(tree);\r
+ }\r
+ }\r
+ }\r
}\r
+ }\r
\r
- 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
+ //SAVE ANNOTATIONS\r
+ if (jal.getAlignmentAnnotation() != null)\r
+ {\r
+ jalview.datamodel.AlignmentAnnotation[] aa = jal.getAlignmentAnnotation();\r
+\r
+ for (int i = 0; i < aa.length; i++)\r
+ {\r
+ 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
- vamsasSet.addAnnotation(an);\r
- }\r
- }\r
+ //SAVE GROUPS\r
+ if (jal.getGroups() != null)\r
+ {\r
+ JGroup[] groups = new JGroup[jal.getGroups().size()];\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
+\r
+ jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup) jal.getGroups()\r
+ .elementAt(i);\r
+ groups[i].setStart(sg.getStartRes());\r
+ groups[i].setEnd(sg.getEndRes());\r
+ groups[i].setName(sg.getName());\r
+ if(sg.cs!=null)\r
+ {\r
+ if (sg.cs.conservationApplied())\r
+ {\r
+ groups[i].setConsThreshold(sg.cs.getConservationInc());\r
+\r
+ if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ {\r
+ groups[i].setColour(SetUserColourScheme(sg.cs,\r
+ userColours,\r
+ jms));\r
+ }\r
+ else\r
+ {\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(sg.\r
+ cs));\r
+ }\r
+ }\r
+ else if(sg.cs instanceof jalview.schemes.AnnotationColourGradient)\r
+ {\r
+ groups[i].setColour(\r
+ ColourSchemeProperty.getColourName(\r
+ ( (jalview.schemes.AnnotationColourGradient) sg.cs).getBaseColour()));\r
+ }\r
+ else if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ {\r
+ groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
+ jms));\r
+ }\r
+ else\r
+ {\r
+ groups[i].setColour(ColourSchemeProperty.getColourName(\r
+ sg.cs));\r
+ }\r
+\r
+ groups[i].setPidThreshold(sg.cs.getThreshold());\r
+ }\r
+\r
+ groups[i].setOutlineColour(sg.getOutlineColour().getRGB());\r
+ groups[i].setDisplayBoxes(sg.getDisplayBoxes());\r
+ groups[i].setDisplayText(sg.getDisplayText());\r
+ groups[i].setColourText(sg.getColourText());\r
+\r
+ for (int s = 0; s < sg.getSize(); s++)\r
+ {\r
+ jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.getSequenceAt(s);\r
+ int index = seqids.indexOf(seq);\r
+ groups[i].addSeq(index);\r
+ }\r
+ }\r
+\r
+ jms.setJGroup(groups);\r
+ }\r
\r
- for (int i = 0; i < groups.length; i++)\r
- {\r
- groups[i] = new JGroup();\r
\r
- jalview.datamodel.SequenceGroup sg = (jalview.datamodel.SequenceGroup)\r
- jal.getGroups()\r
- .elementAt(i);\r
- groups[i].setStart(sg.getStartRes());\r
- groups[i].setEnd(sg.getEndRes());\r
- groups[i].setName(sg.getName());\r
+ ///////////SAVE VIEWPORT\r
+ Viewport view = new Viewport();\r
+ view.setTitle(af.getTitle());\r
+ view.setXpos(af.getX());\r
+ view.setYpos(af.getY());\r
+ view.setWidth(af.getWidth());\r
+ view.setHeight(af.getHeight());\r
+ view.setStartRes(av.startRes);\r
+ view.setStartSeq(av.startSeq);\r
\r
- if (sg.cs instanceof ConservationColourScheme)\r
+ if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
{\r
- groups[i].setConsThreshold( ( (ConservationColourScheme) sg.cs).inc);\r
+ view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
+ userColours, jms));\r
}\r
-\r
- if (sg.cs instanceof ResidueColourScheme)\r
+ else if(av.getGlobalColourScheme() instanceof jalview.schemes.AnnotationColourGradient)\r
{\r
- groups[i].setPidThreshold( ( (ResidueColourScheme) sg.cs).\r
- getThreshold());\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 if (sg.cs instanceof ScoreColourScheme)\r
+ else\r
{\r
- groups[i].setPidThreshold( ( (ScoreColourScheme) sg.cs).getThreshold());\r
+ view.setBgColour(ColourSchemeProperty.getColourName(\r
+ av.getGlobalColourScheme()));\r
}\r
\r
- if (sg.cs instanceof jalview.schemes.UserColourScheme)\r
+ ColourSchemeI cs = av.getGlobalColourScheme();\r
+\r
+ if(cs!=null)\r
{\r
- groups[i].setColour(SetUserColourScheme(sg.cs, userColours,\r
- jms));\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
- else\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
- groups[i].setColour(ColourSchemeProperty.getColourName(\r
- sg.cs));\r
- }\r
+ jalview.schemabinding.version2.FeatureSettings fs\r
+ = new jalview.schemabinding.version2.FeatureSettings();\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
+ String [] renderOrder =\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder;\r
+ for(int ro=0; ro<renderOrder.length; ro++)\r
+ {\r
+ Setting setting = new Setting();\r
+ setting.setType(renderOrder[ro]);\r
+ setting.setColour(\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(renderOrder[ro]).getRGB()\r
+ );\r
+\r
+ setting.setDisplay(\r
+ av.featuresDisplayed.containsKey(renderOrder[ro])\r
+ );\r
+\r
+ fs.addSetting(setting);\r
+\r
+ }\r
+ jms.setFeatureSettings(fs);\r
\r
- for (int s = 0; s < sg.getSize(); s++)\r
- {\r
- jalview.datamodel.Sequence seq = (jalview.datamodel.Sequence) sg.\r
- getSequenceAt(s);\r
- int index = seqids.indexOf(seq);\r
- groups[i].addSeq(index);\r
}\r
- }\r
\r
- jms.setJGroup(groups);\r
- }\r
+ jms.addViewport(view);\r
\r
- ///////////SAVE VIEWPORT\r
- Viewport view = new Viewport();\r
- view.setTitle(af.getTitle());\r
- view.setXpos(af.getX());\r
- view.setYpos(af.getY());\r
- view.setWidth(af.getWidth());\r
- view.setHeight(af.getHeight());\r
- view.setStartRes(av.startRes);\r
- view.setStartSeq(av.startSeq);\r
-\r
- if (av.getGlobalColourScheme() instanceof jalview.schemes.UserColourScheme)\r
- {\r
- view.setBgColour(SetUserColourScheme(av.getGlobalColourScheme(),\r
- userColours, jms));\r
- }\r
- else\r
- {\r
- view.setBgColour(ColourSchemeProperty.getColourName(\r
- av.getGlobalColourScheme()));\r
- }\r
\r
- ColourSchemeI cs = av.getGlobalColourScheme();\r
+ object.setJalviewModelSequence(jms);\r
+ object.getVamsasModel().addSequenceSet(vamsasSet);\r
\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- view.setConsThreshold( ( (ConservationColourScheme) cs).inc);\r
- }\r
+ try\r
+ {\r
+ if (!fileName.endsWith(".xml"))\r
+ {\r
+ fileName = fileName + ".xml";\r
+ }\r
\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- view.setPidThreshold( ( (ResidueColourScheme) cs).getThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- view.setPidThreshold( ( (ScoreColourScheme) cs).getThreshold());\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
- 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
- try\r
+ String SetUserColourScheme(jalview.schemes.ColourSchemeI cs,\r
+ Vector userColours, JalviewModelSequence jms)\r
{\r
- if (!fileName.endsWith(".xml"))\r
- {\r
- fileName = fileName + ".xml";\r
- }\r
+ String id = null;\r
+ jalview.schemes.UserColourScheme ucs = (jalview.schemes.UserColourScheme) cs;\r
\r
- JarEntry entry = new JarEntry(fileName);\r
- jout.putNextEntry(entry);\r
+ if (!userColours.contains(ucs))\r
+ {\r
+ userColours.add(ucs);\r
\r
- object.marshal(out);\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
+ java.awt.Color[] colours = ucs.getColours();\r
+ jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours();\r
+ jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme();\r
\r
- 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)\r
- cs;\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
- if (!userColours.contains(ucs))\r
- {\r
- userColours.add(ucs);\r
-\r
- java.awt.Color[] colours = ucs.getColours();\r
- jalview.binding.UserColours uc = new jalview.binding.UserColours();\r
- jalview.binding.UserColourScheme jbucs = new jalview.binding.\r
- UserColourScheme();\r
-\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
-\r
- id = "ucs" + userColours.indexOf(ucs);\r
- uc.setId(id);\r
- uc.setUserColourScheme(jbucs);\r
- jms.addUserColours(uc);\r
+ id = "ucs" + userColours.indexOf(ucs);\r
+ uc.setId(id);\r
+ uc.setUserColourScheme(jbucs);\r
+ jms.addUserColours(uc);\r
+ }\r
+\r
+ return id;\r
}\r
\r
- return id;\r
- }\r
+ jalview.schemes.UserColourScheme GetUserColourScheme(\r
+ JalviewModelSequence jms, String id)\r
+ {\r
+ UserColours[] uc = jms.getUserColours();\r
+ UserColours colours = null;\r
\r
- static jalview.schemes.UserColourScheme GetUserColourScheme(\r
- 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
+ {\r
+ colours = uc[i];\r
\r
- for (int i = 0; i < uc.length; i++)\r
- {\r
- if (uc[i].getId().equals(id))\r
- {\r
- colours = uc[i];\r
+ break;\r
+ }\r
+ }\r
\r
- break;\r
- }\r
- }\r
+ int csize = colours.getUserColourScheme().getColourCount();\r
+ java.awt.Color[] newColours = new java.awt.Color[csize];\r
\r
- int csize = colours.getUserColourScheme().getColourCount();\r
- java.awt.Color[] newColours = new java.awt.Color[csize];\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
- 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
+ return new jalview.schemes.UserColourScheme(newColours);\r
}\r
\r
- return new jalview.schemes.UserColourScheme(newColours);\r
- }\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param file DOCUMENT ME!\r
+ */\r
+ public AlignFrame LoadJalviewAlign(String file)\r
+ {\r
\r
- public static void LoadJalviewAlign(String file)\r
- {\r
- JalviewModel object = new JalviewModel();\r
+ jalview.gui.AlignFrame af = null;\r
\r
- try\r
- {\r
- //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
- URL url = null;\r
+ try\r
+ {\r
+ //UNMARSHALLER SEEMS TO CLOSE JARINPUTSTREAM, MOST ANNOYING\r
+ URL url = null;\r
\r
- if (file.startsWith("http://"))\r
- {\r
- url = new URL(file);\r
- }\r
+ if (file.startsWith("http://"))\r
+ {\r
+ url = new URL(file);\r
+ }\r
\r
- JarInputStream jin = null;\r
- JarEntry jarentry = null;\r
- int entryCount = 1;\r
+ 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
+ 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
- else\r
+ catch(java.net.UnknownHostException ex)\r
{\r
- jin = new JarInputStream(new FileInputStream(file));\r
- }\r
+ ex.printStackTrace();\r
+ System.err.println("Couldn't locate Jalview XML file : " +\r
+ ex + "\n");\r
+ JOptionPane.showInternalMessageDialog(Desktop.desktop,\r
+ "Couldn't locate " + file,\r
+ "URL not found",\r
+ JOptionPane.WARNING_MESSAGE);\r
\r
- for (int i = 0; i < entryCount; i++)\r
- {\r
- jarentry = jin.getNextJarEntry();\r
}\r
-\r
- if (jarentry != null)\r
+ catch (Exception ex)\r
{\r
- InputStreamReader in = new InputStreamReader(jin, "UTF-8");\r
- object = (JalviewModel) object.unmarshal(in);\r
- LoadFromObject(object);\r
- entryCount++;\r
+ //Is Version 1 Jar file?\r
+ af = new Jalview2XML_V1().LoadJalviewAlign(file);\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
- while (jarentry != null);\r
+\r
+ return af;\r
}\r
- catch (Exception ex)\r
+\r
+ AlignFrame LoadFromObject(JalviewModel object)\r
{\r
- System.err.println("Exception whilst loading jalview XML file : " +\r
- ex + "\n");\r
- ex.printStackTrace();\r
+ Vector seqids = new Vector();\r
+ SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0);\r
+ Sequence[] vamsasSeq = vamsasSet.getSequence();\r
\r
- return;\r
- }\r
- }\r
+ JalviewModelSequence jms = object.getJalviewModelSequence();\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
+ //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
- JalviewModelSequence jms = object.getJalviewModelSequence();\r
+ ///SequenceFeatures are added to the DatasetSequence,\r
+ // so we must create the dataset before loading features\r
+ /////////////////////////////////\r
+ jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+ al.setDataset(null);\r
+ /////////////////////////////////\r
\r
- //////////////////////////////////\r
- //LOAD SEQUENCES\r
- jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[\r
- vamsasSeq.length];\r
- JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq();\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
- for (int i = 0; i < vamsasSeq.length; i++)\r
- {\r
- jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(),\r
- vamsasSeq[i].getSequence());\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
- 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
\r
- /////////////////////////////////\r
- jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs);\r
+ /////////////////////////////////\r
+ //////////////////////////////////\r
+ //LOAD ANNOTATIONS\r
+ if (vamsasSet.getAnnotation() != null)\r
+ {\r
+ Annotation[] an = vamsasSet.getAnnotation();\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 = 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
+ // LOAD VIEWPORT\r
+ Viewport[] views = jms.getViewport();\r
+ Viewport view = views[0]; // DEAL WITH MULTIPLE VIEWPORTS LATER\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[\r
- al.getWidth()];\r
+ AlignFrame af = new AlignFrame(al);\r
\r
- for (int aa = 0; aa < ae.length; aa++)\r
+\r
+ // af.changeColour() );\r
+ /////////////////////////\r
+ //LOAD GROUPS\r
+ if (jms.getJGroupCount() > 0)\r
{\r
- anot[ae[aa].getPosition()] = new jalview.datamodel.Annotation(ae[aa].\r
- getDisplayCharacter(),\r
- ae[aa].getDescription(),\r
- ae[aa].getSecondaryStructure().charAt(0),\r
- ae[aa].getValue());\r
+ JGroup[] groups = jms.getJGroup();\r
+\r
+ for (int i = 0; i < groups.length; i++)\r
+ {\r
+ ColourSchemeI cs = null;\r
+\r
+ if (groups[i].getColour() != null)\r
+ {\r
+ if (groups[i].getColour().startsWith("ucs"))\r
+ {\r
+ cs = GetUserColourScheme(jms, groups[i].getColour());\r
+ }\r
+ else\r
+ {\r
+ cs = ColourSchemeProperty.getColour(al,\r
+ groups[i].getColour());\r
+ }\r
+\r
+ if(cs!=null)\r
+ cs.setThreshold(groups[i].getPidThreshold(), true);\r
+ }\r
+\r
+ Vector seqs = new Vector();\r
+ int[] ids = groups[i].getSeq();\r
+\r
+ for (int s = 0; s < ids.length; s++)\r
+ {\r
+ seqs.addElement((jalview.datamodel.SequenceI) seqids.elementAt(\r
+ ids[s]));\r
+ }\r
+\r
+ jalview.datamodel.SequenceGroup sg = new jalview.datamodel.SequenceGroup(seqs,\r
+ groups[i].getName(), cs, groups[i].getDisplayBoxes(),\r
+ groups[i].getDisplayText(), groups[i].getColourText(),\r
+ groups[i].getStart(), groups[i].getEnd());\r
+\r
+ sg.setOutlineColour(new java.awt.Color(\r
+ groups[i].getOutlineColour()));\r
+\r
+ if (groups[i].getConsThreshold() != 0)\r
+ {\r
+ jalview.analysis.Conservation c = new jalview.analysis.Conservation("All",\r
+ ResidueProperties.propHash, 3, sg.sequences, 0,\r
+ sg.getWidth() - 1);\r
+ c.calculate();\r
+ c.verdict(false, 25);\r
+ sg.cs.setConservation(c);\r
+ }\r
+\r
+ al.addGroup(sg);\r
+ }\r
}\r
\r
- jalview.datamodel.AlignmentAnnotation jaa = null;\r
\r
- if (an[i].getGraph())\r
+\r
+ af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(),\r
+ view.getHeight());\r
+ af.viewport.setStartRes(view.getStartRes());\r
+ af.viewport.setStartSeq(view.getStartSeq());\r
+ af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+ af.viewport.showConservation = view.getShowConservation();\r
+ af.viewport.showQuality = view.getShowQuality();\r
+ af.viewport.showIdentity = view.getShowIdentity();\r
+ af.viewport.setAbovePIDThreshold(view.getPidSelected());\r
+ af.abovePIDThreshold.setSelected(view.getPidSelected());\r
+ af.viewport.setColourText(view.getShowColourText());\r
+ af.colourTextMenuItem.setSelected(view.getShowColourText());\r
+ af.viewport.setConservationSelected(view.getConservationSelected());\r
+ af.conservationMenuItem.setSelected(view.getConservationSelected());\r
+\r
+ af.viewport.setShowJVSuffix(view.getShowFullId());\r
+ af.seqLimits.setSelected(view.getShowFullId());\r
+\r
+ af.viewport.setFont(new java.awt.Font(view.getFontName(),\r
+ view.getFontStyle(), view.getFontSize()));\r
+ af.alignPanel.fontChanged();\r
+\r
+ af.viewport.setRenderGaps(view.getRenderGaps());\r
+ af.renderGapsMenuItem.setSelected(view.getRenderGaps());\r
+\r
+ af.viewport.setWrapAlignment(view.getWrapAlignment());\r
+ af.wrapMenuItem.setSelected(view.getWrapAlignment());\r
+\r
+ if (view.getWrapAlignment())\r
{\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot, 0, 0, 1);\r
+ af.alignPanel.setWrapAlignment(view.getWrapAlignment());\r
}\r
else\r
{\r
- jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(),\r
- an[i].getDescription(), anot);\r
+ af.annotationPanelMenuItem.setState(view.getShowAnnotation());\r
+ af.viewport.setShowAnnotation(view.getShowAnnotation());\r
+ af.alignPanel.setAnnotationVisible(view.getShowAnnotation());\r
}\r
\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
-\r
- // af.changeColour() );\r
- /////////////////////////\r
- //LOAD GROUPS\r
- if (jms.getJGroupCount() > 0)\r
- {\r
- JGroup[] groups = jms.getJGroup();\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
- for (int i = 0; i < groups.length; i++)\r
- {\r
ColourSchemeI cs = null;\r
\r
- if (groups[i].getColour() != null)\r
+ if (view.getBgColour() != 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
+ 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 instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) cs).setThreshold(groups[i].getPidThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(groups[i].getPidThreshold());\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
- Vector seqs = new Vector();\r
- int[] ids = groups[i].getSeq();\r
+ af.viewport.setColourAppliesToAllGroups(true);\r
\r
- for (int s = 0; s < ids.length; s++)\r
+ if (view.getShowSequenceFeatures())\r
{\r
- seqs.addElement( (jalview.datamodel.SequenceI) seqids.elementAt(\r
- ids[s]));\r
+ af.viewport.showSequenceFeatures = true;\r
+ af.showSeqFeatures.setSelected(true);\r
}\r
\r
- jalview.datamodel.SequenceGroup sg = new jalview.datamodel.\r
- SequenceGroup(seqs, groups[i].getName(),\r
- cs, groups[i].getDisplayBoxes(),\r
- groups[i].getDisplayText(), groups[i].getColourText(),\r
- groups[i].getStart(), groups[i].getEnd());\r
+ if(jms.getFeatureSettings()!=null)\r
+ {\r
+ af.viewport.featuresDisplayed = new Hashtable();\r
+ String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()];\r
+ for(int fs=0; fs<jms.getFeatureSettings().getSettingCount(); fs++)\r
+ {\r
+ Setting setting = jms.getFeatureSettings().getSetting(fs);\r
+\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour(setting.getType(),\r
+ new java.awt.Color(setting.getColour()));\r
+\r
+ renderOrder[fs] = setting.getType();\r
+\r
+ if(setting.getDisplay())\r
+ af.viewport.featuresDisplayed.put(\r
+ setting.getType(), new Integer(setting.getColour()));\r
+ }\r
+ af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder;\r
+ }\r
\r
- sg.setOutlineColour(new java.awt.Color(\r
- groups[i].getOutlineColour()));\r
\r
+ Desktop.addInternalFrame(af, view.getTitle(),\r
+ view.getWidth(), view.getHeight());\r
\r
- if (groups[i].getConsThreshold() != 0)\r
+ //LOAD TREES\r
+ ///////////////////////////////////////\r
+ if (jms.getTreeCount() > 0)\r
{\r
- jalview.analysis.Conservation c = new jalview.analysis.Conservation(\r
- "All",\r
- ResidueProperties.propHash, 3, 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
+ try\r
+ {\r
+ for (int t = 0; t < jms.getTreeCount(); t++)\r
+ {\r
\r
- al.addGroup(sg);\r
- }\r
- }\r
+ Tree tree = jms.getTree(t);\r
\r
- Desktop.addInternalFrame(af, view.getTitle(),\r
- AlignFrame.NEW_WINDOW_WIDTH,\r
- AlignFrame.NEW_WINDOW_HEIGHT);\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.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(), 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
-\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
+ 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
- af.viewport.setShowBoxes(view.getShowBoxes());\r
- af.viewport.setShowText(view.getShowText());\r
+ tp.fitToWindow.setState(tree.getFitToWindow());\r
+ tp.fitToWindow_actionPerformed(null);\r
\r
- ColourSchemeI cs = null;\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
- if (view.getBgColour() != null)\r
- {\r
- if (view.getBgColour().startsWith("ucs"))\r
- {\r
- cs = GetUserColourScheme(jms, view.getBgColour());\r
- }\r
- else\r
- {\r
- cs = ColourSchemeProperty.getColour(al, view.getBgColour());\r
- }\r
-\r
- if (cs instanceof ConservationColourScheme)\r
- {\r
- ( (ConservationColourScheme) cs).inc = view.getConsThreshold();\r
- }\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- ( (ResidueColourScheme) cs).setThreshold(view.getPidThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- ( (ScoreColourScheme) cs).setThreshold(view.getPidThreshold());\r
- }\r
- }\r
+ tp.showPlaceholders(tree.getMarkUnlinked());\r
+ tp.showBootstrap(tree.getShowBootstrap());\r
+ tp.showDistances(tree.getShowDistances());\r
\r
- af.viewport.setGlobalColourScheme(cs);\r
+ tp.treeCanvas.threshold = tree.getThreshold();\r
\r
- af.viewport.setColourAppliesToAllGroups(false);\r
- af.changeColour(af.viewport.getGlobalColourScheme());\r
- af.viewport.setColourAppliesToAllGroups(true);\r
+ if (tree.getCurrentTree())\r
+ af.viewport.setCurrentTree(tp.getTree());\r
+ }\r
\r
- if (view.getShowSequenceFeatures())\r
- {\r
- af.viewport.showSequenceFeatures = true;\r
- SequenceFeatureFetcher sft = new SequenceFeatureFetcher(al,\r
- af.alignPanel);\r
- al.featuresAdded = true;\r
- }\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
\r
- //LOAD TREES - THIS RELEASE ONLY ALLOWS 1 TREE\r
- if (object.getVamsasModel().getTreeCount() > 0)\r
- {\r
- try\r
- {\r
- af.ShowNewickTree(new jalview.io.NewickFile(\r
- (String) object.getVamsasModel().getTree(0)), "Tree");\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
+ }\r
+\r
+ return af;\r
}\r
- }\r
}\r
+\r
git://source.jalview.org / jalview.git / blobdiff