X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=81a68871e39025419c14d0b850f5b30c29d0690f;hb=cc6f7ebe59c148e62cd9f1947d9ba30638db2980;hp=d2d55f8c7c182a05893ded920e784ff11ee0aca4;hpb=bb19b02db6a50024556a86d7c4eba1053cf9fb57;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index d2d55f8..81a6887 100755 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -27,6 +27,7 @@ import java.io.*; import java.net.*; import java.util.*; + import java.util.jar.*; import javax.swing.*; @@ -156,7 +157,7 @@ public class Jalview2XML AlignViewport av = af.viewport; JalviewModel object = new JalviewModel(); - object.setVamsasModel(new VamsasModel()); + object.setVamsasModel(new jalview.binding.VamsasModel()); object.setCreationDate(new java.util.Date(timeStamp)); object.setVersion(jalview.bin.Cache.getProperty("VERSION")); @@ -191,6 +192,56 @@ public class Jalview2XML jseq.setId(id); + if(jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures()!=null) + { + Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getSequenceFeatures().elements(); + while(en.hasMoreElements()) + { + 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()); + jseq.addFeatures(features); + } + } + + if(jal.getSequenceAt(i).getDatasetSequence().getPDBId()!=null) + { + Enumeration en = jal.getSequenceAt(i).getDatasetSequence().getPDBId().elements(); + while(en.hasMoreElements()) + { + Pdbids pdb = new Pdbids(); + jalview.datamodel.PDBEntry entry + = (jalview.datamodel.PDBEntry)en.nextElement(); + + pdb.setId(entry.getId()); + pdb.setType(entry.getType()); + + if(entry.getProperty()!=null) + { + PdbentryItem item = new PdbentryItem(); + Hashtable properties = entry.getProperty(); + Enumeration en2 = properties.keys(); + while(en2.hasMoreElements()) + { + Property prop = new Property(); + String key = en2.nextElement().toString(); + prop.setName(key); + prop.setValue( properties.get(key).toString() ); + item.addProperty(prop); + } + pdb.addPdbentryItem(item); + } + + jseq.addPdbids(pdb); + } + } + jms.addJSeq(jseq); vamsasSet.addSequence(vamsasSeq); id++; @@ -225,6 +276,7 @@ public class Jalview2XML tree.setFontSize(tp.getTreeFont().getSize()); tree.setFontStyle(tp.getTreeFont().getStyle()); tree.setMarkUnlinked(tp.placeholdersMenu.getState()); + tree.setShowBootstrap(tp.bootstrapMenu.getState()); tree.setShowDistances(tp.distanceMenu.getState()); @@ -256,7 +308,11 @@ public class Jalview2XML Annotation an = new Annotation(); an.setDescription(aa[i].description); - an.setGraph(aa[i].isGraph); + if(aa[i].graph>0) + { + an.setGraph(true); + an.setGraphType(aa[i].graph); + } an.setLabel(aa[i].label); AnnotationElement ae; @@ -344,6 +400,7 @@ public class Jalview2XML jms.setJGroup(groups); } + ///////////SAVE VIEWPORT Viewport view = new Viewport(); view.setTitle(af.getTitle()); @@ -392,15 +449,40 @@ public class Jalview2XML view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowConservation(av.showConservation); - view.setShowFullId(av.getShowFullId()); + view.setShowFullId(av.getShowJVSuffix()); view.setShowIdentity(av.showIdentity); view.setShowQuality(av.showQuality); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setWrapAlignment(av.getWrapAlignment()); + if(af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed!=null) + { + jalview.binding.FeatureSettings fs = new jalview.binding.FeatureSettings(); + + Enumeration e = af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureColours.keys(); + while (e.hasMoreElements()) + { + String type = e.nextElement().toString(); + Setting setting = new Setting(); + setting.setType(type); + setting.setColour( + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().getColour(type).getRGB() + ); + setting.setDisplay( + af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featuresDisplayed.contains(type) + ); + + fs.addSetting(setting); + + } + jms.setFeatureSettings(fs); + + } + jms.addViewport(view); + object.setJalviewModelSequence(jms); object.getVamsasModel().addSequenceSet(vamsasSet); @@ -568,7 +650,6 @@ public class Jalview2XML //LOAD SEQUENCES jalview.datamodel.Sequence[] jseqs = new jalview.datamodel.Sequence[vamsasSeq.length]; JSeq[] JSEQ = object.getJalviewModelSequence().getJSeq(); - for (int i = 0; i < vamsasSeq.length; i++) { jseqs[i] = new jalview.datamodel.Sequence(vamsasSeq[i].getName(), @@ -580,9 +661,41 @@ public class Jalview2XML seqids.add(jseqs[i]); } + ///SequenceFeatures are added to the DatasetSequence, + // so we must create the dataset before loading features ///////////////////////////////// jalview.datamodel.Alignment al = new jalview.datamodel.Alignment(jseqs); + al.setDataset(null); + ///////////////////////////////// + + for (int i = 0; i < vamsasSeq.length; i++) + { + if (JSEQ[i].getFeaturesCount() > 0) + { + Features[] features = JSEQ[i].getFeatures(); + for (int f = 0; f < features.length; f++) + { + //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()); + al.getSequenceAt(i).getDatasetSequence().addSequenceFeature(sf); + } + } + if (JSEQ[i].getPdbidsCount() > 0) + { + Pdbids[] ids = JSEQ[i].getPdbids(); + for (int p = 0; p < ids.length; p++) + { + jalview.datamodel.PDBEntry entry = new jalview.datamodel.PDBEntry(); + entry.setId(ids[p].getId()); + entry.setType(ids[p].getType()); + al.getSequenceAt(i).getDatasetSequence().addPDBId(entry); + } + } + } ///////////////////////////////// ////////////////////////////////// //LOAD ANNOTATIONS @@ -608,7 +721,8 @@ public class Jalview2XML if (an[i].getGraph()) { jaa = new jalview.datamodel.AlignmentAnnotation(an[i].getLabel(), - an[i].getDescription(), anot, 0, 0, 1); + an[i].getDescription(), anot, 0, 0, + an[i].getGraphType()); } else { @@ -627,6 +741,7 @@ public class Jalview2XML AlignFrame af = new AlignFrame(al); + // af.changeColour() ); ///////////////////////// //LOAD GROUPS @@ -689,6 +804,7 @@ public class Jalview2XML view.getHeight()); af.viewport.setStartRes(view.getStartRes()); af.viewport.setStartSeq(view.getStartSeq()); + af.viewport.setShowAnnotation(view.getShowAnnotation()); af.viewport.showConservation = view.getShowConservation(); af.viewport.showQuality = view.getShowQuality(); af.viewport.showIdentity = view.getShowIdentity(); @@ -699,8 +815,8 @@ public class Jalview2XML af.viewport.setConservationSelected(view.getConservationSelected()); af.conservationMenuItem.setSelected(view.getConservationSelected()); - af.viewport.setShowFullId(view.getShowFullId()); - af.fullSeqId.setSelected(view.getShowFullId()); + af.viewport.setShowJVSuffix(view.getShowFullId()); + af.seqLimits.setSelected(view.getShowFullId()); af.viewport.setFont(new java.awt.Font(view.getFontName(), view.getFontStyle(), view.getFontSize())); @@ -761,10 +877,25 @@ public class Jalview2XML if (view.getShowSequenceFeatures()) { - af.viewport.showSequenceFeatures = true; - af.sequenceFeatures.setSelected(true); - new SequenceFeatureFetcher(al, af.alignPanel); - al.featuresAdded = true; + af.featureSettings.setEnabled(true); + af.viewport.showSequenceFeatures = true; + af.sequenceFeatures.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(); + for(int fs=0; fs