X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=5a4b03a0fea1e94adb5932ac33649b2d988f64e2;hb=14bad6b2390493bb6ad030c6f3ea7cde4cba1b53;hp=81a68871e39025419c14d0b850f5b30c29d0690f;hpb=65f3b4a9eadadb7540c329e710bce082ea1dd8a7;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 81a6887..5a4b03a 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -18,10 +18,11 @@ */ package jalview.gui; -import jalview.io.*; import jalview.schemes.*; +import jalview.gui.*; + import java.io.*; import java.net.*; @@ -32,7 +33,11 @@ import java.util.jar.*; import javax.swing.*; -import jalview.binding.*; +import org.exolab.castor.xml.*; + +import jalview.schemabinding.version2.*; + + /** @@ -44,7 +49,7 @@ import jalview.binding.*; public class Jalview2XML { // SAVES SEVERAL ALIGNEMENT WINDOWS TO SAME JARFILE - public static void SaveState(File statefile) + public void SaveState(File statefile) { long creation = System.currentTimeMillis(); JInternalFrame[] frames = Desktop.desktop.getAllFrames(); @@ -116,7 +121,7 @@ public class Jalview2XML } // USE THIS METHOD TO SAVE A SINGLE ALIGNMENT WINDOW - public static void SaveAlignment(AlignFrame af, String jarFile, + public void SaveAlignment(AlignFrame af, String jarFile, String fileName) { try @@ -148,7 +153,7 @@ public class Jalview2XML * @param jout DOCUMENT ME! * @param out DOCUMENT ME! */ - public static void SaveState(AlignFrame af, long timeStamp, + public void SaveState(AlignFrame af, long timeStamp, String fileName, JarOutputStream jout, PrintWriter out) { Vector seqids = new Vector(); @@ -157,7 +162,7 @@ public class Jalview2XML AlignViewport av = af.viewport; JalviewModel object = new JalviewModel(); - object.setVamsasModel(new jalview.binding.VamsasModel()); + object.setVamsasModel(new jalview.schemabinding.version2.VamsasModel()); object.setCreationDate(new java.util.Date(timeStamp)); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); @@ -183,6 +188,7 @@ public class Jalview2XML vamsasSeq.setId(id + ""); vamsasSeq.setName(jal.getSequenceAt(i).getName()); vamsasSeq.setSequence(jal.getSequenceAt(i).getSequence()); + vamsasSeq.setDescription(jal.getSequenceAt(i).getDescription()); jseq = new JSeq(); jseq.setStart(jal.getSequenceAt(i).getStart()); @@ -194,19 +200,21 @@ public class Jalview2XML if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null) { - Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements(); - while(en.hasMoreElements()) + jalview.datamodel.SequenceFeature[] sf + = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures(); + int index = 0; + while(index < sf.length) { Features features = new Features(); - jalview.datamodel.SequenceFeature sf - = (jalview.datamodel.SequenceFeature)en.nextElement(); - - features.setBegin(sf.getBegin()); - features.setEnd(sf.getEnd()); - features.setDescription(sf.getDescription()); - features.setStatus(sf.getStatus()); - features.setType(sf.getType()); + + features.setBegin(sf[index].getBegin()); + features.setEnd(sf[index].getEnd()); + features.setDescription(sf[index].getDescription()); + features.setStatus(sf[index].getStatus()); + features.setType(sf[index].getType()); + features.setFeatureGroup(sf[index].getFeatureGroup()); jseq.addFeatures(features); + index ++; } } @@ -313,6 +321,9 @@ public class Jalview2XML an.setGraph(true); an.setGraphType(aa[i].graph); } + else + an.setGraph(false); + an.setLabel(aa[i].label); AnnotationElement ae; @@ -456,9 +467,10 @@ public class Jalview2XML view.setShowText(av.getShowText()); view.setWrapAlignment(av.getWrapAlignment()); - if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null) + if(av.featuresDisplayed!=null) { - jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings(); + jalview.schemabinding.version2.FeatureSettings fs + = new jalview.schemabinding.version2.FeatureSettings(); Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys(); while (e.hasMoreElements()) @@ -469,8 +481,9 @@ public class Jalview2XML setting.setColour( af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB() ); + setting.setDisplay( - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type) + av.featuresDisplayed.containsKey(type) ); fs.addSetting(setting); @@ -504,7 +517,7 @@ public class Jalview2XML } } - static String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, + String SetUserColourScheme(jalview.schemes.ColourSchemeI cs, Vector userColours, JalviewModelSequence jms) { String id = null; @@ -515,12 +528,12 @@ public class Jalview2XML userColours.add(ucs); java.awt.Color[] colours = ucs.getColours(); - jalview.binding.UserColours uc = new jalview.binding.UserColours(); - jalview.binding.UserColourScheme jbucs = new jalview.binding.UserColourScheme(); + jalview.schemabinding.version2.UserColours uc = new jalview.schemabinding.version2.UserColours(); + jalview.schemabinding.version2.UserColourScheme jbucs = new jalview.schemabinding.version2.UserColourScheme(); for (int i = 0; i < colours.length; i++) { - jalview.binding.Colour col = new jalview.binding.Colour(); + jalview.schemabinding.version2.Colour col = new jalview.schemabinding.version2.Colour(); col.setRGB(jalview.util.Format.getHexString(colours[i])); jbucs.addColour(col); } @@ -534,7 +547,7 @@ public class Jalview2XML return id; } - static jalview.schemes.UserColourScheme GetUserColourScheme( + jalview.schemes.UserColourScheme GetUserColourScheme( JalviewModelSequence jms, String id) { UserColours[] uc = jms.getUserColours(); @@ -567,9 +580,9 @@ public class Jalview2XML * * @param file DOCUMENT ME! */ - public static AlignFrame LoadJalviewAlign(String file) + public AlignFrame LoadJalviewAlign(String file) { - JalviewModel object = new JalviewModel(); + jalview.gui.AlignFrame af = null; try @@ -600,12 +613,28 @@ public class Jalview2XML for (int i = 0; i < entryCount; i++) { jarentry = jin.getNextJarEntry(); - } + + } + + + class NoDescIDResolver implements IDResolver + { + public Object resolve(String idref) + { + System.out.println(idref+" used"); + return null; + } + } + if (jarentry != null) { InputStreamReader in = new InputStreamReader(jin, "UTF-8"); - object = (JalviewModel) object.unmarshal(in); + JalviewModel object = new JalviewModel(); + + Unmarshaller unmar = new Unmarshaller(object); + object = (JalviewModel) unmar.unmarshal( in ); + af = LoadFromObject(object); entryCount++; } @@ -625,6 +654,14 @@ public class Jalview2XML } catch (Exception ex) { + //Is Version 1 Jar file? + af = new Jalview2XML_V1().LoadJalviewAlign(file); + + if(af!=null) + { + System.out.println("Successfuly loaded archive file"); + return af; + } ex.printStackTrace(); System.err.println("Exception whilst loading jalview XML file : " + ex + "\n"); @@ -638,7 +675,7 @@ public class Jalview2XML return af; } - static AlignFrame LoadFromObject(JalviewModel object) + AlignFrame LoadFromObject(JalviewModel object) { Vector seqids = new Vector(); SequenceSet vamsasSet = object.getVamsasModel().getSequenceSet(0); @@ -654,6 +691,7 @@ public class Jalview2XML { jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), vamsasSeq[i].getSequence()); + jseqs[i].setDescription( vamsasSeq[i].getDescription() ); jseqs[i].setStart(JSEQ[i].getStart()); jseqs[i].setEnd(JSEQ[i].getEnd()); @@ -675,11 +713,12 @@ public class Jalview2XML Features[] features = JSEQ[i].getFeatures(); for (int f = 0; f < features.length; f++) { - //features[f].getBegin() jalview.datamodel.SequenceFeature sf = new jalview.datamodel.SequenceFeature(features[f].getType(), features[f].getDescription(), features[f].getStatus(), - features[f].getBegin(), features[f].getEnd()); + features[f].getBegin(), features[f].getEnd(), + features[f].getFeatureGroup()); + al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); } } @@ -696,7 +735,8 @@ public class Jalview2XML } } - ///////////////////////////////// + + ///////////////////////////////// ////////////////////////////////// //LOAD ANNOTATIONS if (vamsasSet.getAnnotation() != null) @@ -734,6 +774,7 @@ public class Jalview2XML } } + ///////////////////////////////// // LOAD VIEWPORT Viewport[] views = jms.getViewport(); @@ -800,6 +841,7 @@ public class Jalview2XML } + af.setBounds(view.getXpos(), view.getYpos(), view.getWidth(), view.getHeight()); af.viewport.setStartRes(view.getStartRes()); @@ -877,27 +919,31 @@ public class Jalview2XML if (view.getShowSequenceFeatures()) { - af.featureSettings.setEnabled(true); af.viewport.showSequenceFeatures = true; - af.sequenceFeatures.setSelected(true); + af.showSeqFeatures.setSelected(true); } if(jms.getFeatureSettings()!=null) { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed = new Vector(); - // af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null) - // jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings(); + af.viewport.featuresDisplayed = new Hashtable(); + String [] renderOrder = new String[jms.getFeatureSettings().getSettingCount()]; for(int fs=0; fs