X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=5d11901aa7135516f4eebe95e0d7ee55901b7502;hb=b5d61763044c1d72f06ce0e50da2171422a3774b;hp=dfacd544137b169f01c7ce82aca82aa149325829;hpb=9c37999eb4b461a5c7a94e10ac39583c1c29200a;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index dfacd54..5d11901 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -69,6 +69,8 @@ import jalview.util.MessageManager; import jalview.util.Platform; import jalview.util.jarInputStreamProvider; import jalview.viewmodel.AlignmentViewport; +import jalview.viewmodel.seqfeatures.FeatureRendererSettings; +import jalview.viewmodel.seqfeatures.FeaturesDisplayed; import jalview.ws.jws2.Jws2Discoverer; import jalview.ws.jws2.dm.AAConSettings; import jalview.ws.jws2.jabaws2.Jws2Instance; @@ -498,7 +500,7 @@ public class Jalview2XML for (String dssids : dsses.keySet()) { AlignFrame _af = dsses.get(dssids); - String jfileName = MessageManager.formatMessage("label.dataset_for", new String[]{fileName,_af.getTitle()}); + String jfileName = fileName + " Dataset for " + _af.getTitle(); if (!jfileName.endsWith(".xml")) { jfileName = jfileName + ".xml"; @@ -1127,8 +1129,8 @@ public class Jalview2XML view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowFullId(av.getShowJVSuffix()); - view.setRightAlignIds(av.rightAlignIds); - view.setShowSequenceFeatures(av.showSequenceFeatures); + view.setRightAlignIds(av.isRightAlignIds()); + view.setShowSequenceFeatures(av.isShowSequenceFeatures()); view.setShowText(av.getShowText()); view.setShowUnconserved(av.getShowUnconserved()); view.setWrapAlignment(av.getWrapAlignment()); @@ -1145,11 +1147,12 @@ public class Jalview2XML view.setFollowHighlight(av.followHighlight); view.setFollowSelection(av.followSelection); view.setIgnoreGapsinConsensus(av.getIgnoreGapsConsensus()); - if (av.featuresDisplayed != null) + if (av.getFeaturesDisplayed() != null) { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; + String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + .getRenderOrder().toArray(new String[0]); Vector settingsAdded = new Vector(); Object gstyle = null; @@ -1158,7 +1161,7 @@ public class Jalview2XML { for (int ro = 0; ro < renderOrder.length; ro++) { - gstyle = ap.seqPanel.seqCanvas.getFeatureRenderer() + gstyle = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getFeatureStyle(renderOrder[ro]); Setting setting = new Setting(); setting.setType(renderOrder[ro]); @@ -1176,13 +1179,13 @@ public class Jalview2XML } else { - setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getColour(renderOrder[ro]).getRGB()); } - setting.setDisplay(av.featuresDisplayed - .containsKey(renderOrder[ro])); - float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() + setting.setDisplay(av.getFeaturesDisplayed().isVisible( + renderOrder[ro])); + float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getOrder(renderOrder[ro]); if (rorder > -1) { @@ -1194,8 +1197,8 @@ public class Jalview2XML } // Make sure we save none displayed feature settings - Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours - .keySet().iterator(); + Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() + .getFeatureColours().keySet().iterator(); while (en.hasNext()) { String key = en.next().toString(); @@ -1206,11 +1209,11 @@ public class Jalview2XML Setting setting = new Setting(); setting.setType(key); - setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getColour(key).getRGB()); setting.setDisplay(false); - float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() + float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getOrder(key); if (rorder > -1) { @@ -1219,8 +1222,9 @@ public class Jalview2XML fs.addSetting(setting); settingsAdded.addElement(key); } - en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups - .keySet().iterator(); + // is groups actually supposed to be a map here ? + en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups() + .iterator(); Vector groupsAdded = new Vector(); while (en.hasNext()) { @@ -1231,8 +1235,8 @@ public class Jalview2XML } Group g = new Group(); g.setName(grp); - g.setDisplay(((Boolean) ap.seqPanel.seqCanvas - .getFeatureRenderer().featureGroups.get(grp)) + g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas + .getFeatureRenderer().checkGroupVisibility(grp, false)) .booleanValue()); fs.addGroup(g); groupsAdded.addElement(grp); @@ -1419,6 +1423,16 @@ public class Jalview2XML calcIdSet.add(aa[i].getCalcId()); an.setCalcId(aa[i].getCalcId()); } + if (aa[i].hasProperties()) + { + for (String pr : aa[i].getProperties()) + { + Property prop = new Property(); + prop.setName(pr); + prop.setValue(aa[i].getProperty(pr)); + an.addProperty(prop); + } + } AnnotationElement ae; if (aa[i].annotations != null) @@ -1447,8 +1461,7 @@ public class Jalview2XML } ae.setPosition(a); - if (aa[i].annotations[a].secondaryStructure != ' ' - && aa[i].annotations[a].secondaryStructure != '\0') + if (aa[i].annotations[a].secondaryStructure > ' ') { ae.setSecondaryStructure(aa[i].annotations[a].secondaryStructure + ""); @@ -2305,7 +2318,10 @@ public class Jalview2XML } else { - recoverDatasetFor(vamsasSet, al); + // recover dataset - passing on flag indicating if this a 'viewless' + // sequence set (a.k.a. a stored dataset for the project) + recoverDatasetFor(vamsasSet, al, object.getJalviewModelSequence() + .getViewportCount() == 0); } // /////////////////////////////// @@ -2631,6 +2647,14 @@ public class Jalview2XML jaa.belowAlignment = an[i].isBelowAlignment(); } jaa.setCalcId(an[i].getCalcId()); + if (an[i].getPropertyCount() > 0) + { + for (jalview.schemabinding.version2.Property prop : an[i] + .getProperty()) + { + jaa.setProperty(prop.getName(), prop.getValue()); + } + } if (jaa.autoCalculated) { autoAlan.add(new JvAnnotRow(i, jaa)); @@ -3455,7 +3479,7 @@ public class Jalview2XML af.viewport.setConservationSelected(view.getConservationSelected()); af.viewport.setShowJVSuffix(view.getShowFullId()); - af.viewport.rightAlignIds = view.getRightAlignIds(); + af.viewport.setRightAlignIds(view.getRightAlignIds()); af.viewport.setFont(new java.awt.Font(view.getFontName(), view .getFontStyle(), view.getFontSize())); af.alignPanel.fontChanged(); @@ -3517,10 +3541,8 @@ public class Jalview2XML af.viewport.setColourAppliesToAllGroups(true); - if (view.getShowSequenceFeatures()) - { - af.viewport.showSequenceFeatures = true; - } + af.viewport.setShowSequenceFeatures(view.getShowSequenceFeatures()); + if (view.hasCentreColumnLabels()) { af.viewport.setCentreColumnLabels(view.getCentreColumnLabels()); @@ -3587,9 +3609,14 @@ public class Jalview2XML // recover featre settings if (jms.getFeatureSettings() != null) { - af.viewport.featuresDisplayed = new Hashtable(); + FeaturesDisplayed fdi; + af.viewport.setFeaturesDisplayed(fdi = new FeaturesDisplayed()); String[] renderOrder = new String[jms.getFeatureSettings() .getSettingCount()]; + Hashtable featureGroups = new Hashtable(); + Hashtable featureColours = new Hashtable(); + Hashtable featureOrder = new Hashtable(); + for (int fs = 0; fs < jms.getFeatureSettings().getSettingCount(); fs++) { Setting setting = jms.getFeatureSettings().getSetting(fs); @@ -3616,41 +3643,42 @@ public class Jalview2XML gc.setColourByLabel(setting.getColourByLabel()); } // and put in the feature colour table. - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( - setting.getType(), gc); + featureColours.put(setting.getType(), gc); } else { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( - setting.getType(), + featureColours.put(setting.getType(), new java.awt.Color(setting.getColour())); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( - setting.getType(), setting.getOrder()); + featureOrder.put(setting.getType(), setting.getOrder()); } else { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( - setting.getType(), - fs / jms.getFeatureSettings().getSettingCount()); + featureOrder.put(setting.getType(), new Float(fs + / jms.getFeatureSettings().getSettingCount())); } if (setting.getDisplay()) { - af.viewport.featuresDisplayed.put(setting.getType(), new Integer( - setting.getColour())); + fdi.setVisible(setting.getType()); } } - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; - Hashtable fgtable; - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); + Hashtable fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); fgtable.put(grp.getName(), new Boolean(grp.getDisplay())); } + // FeatureRendererSettings frs = new FeatureRendererSettings(renderOrder, + // fgtable, featureColours, jms.getFeatureSettings().hasTransparency() ? + // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder); + FeatureRendererSettings frs = new FeatureRendererSettings( + renderOrder, fgtable, featureColours, 1.0f, featureOrder); + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() + .transferSettings(frs); + } if (view.getHiddenColumnsCount() > 0) @@ -3969,7 +3997,8 @@ public class Jalview2XML } } - private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al) + private void recoverDatasetFor(SequenceSet vamsasSet, Alignment al, + boolean ignoreUnrefed) { jalview.datamodel.Alignment ds = getDatasetFor(vamsasSet.getDatasetId()); Vector dseqs = null; @@ -3981,7 +4010,7 @@ public class Jalview2XML for (int i = 0, iSize = vamsasSet.getSequenceCount(); i < iSize; i++) { Sequence vamsasSeq = vamsasSet.getSequence(i); - ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs); + ensureJalviewDatasetSequence(vamsasSeq, ds, dseqs, ignoreUnrefed); } // create a new dataset if (ds == null) @@ -3994,7 +4023,7 @@ public class Jalview2XML addDatasetRef(vamsasSet.getDatasetId(), ds); } // set the dataset for the newly imported alignment. - if (al.getDataset() == null) + if (al.getDataset() == null && !ignoreUnrefed) { al.setDataset(ds); } @@ -4010,7 +4039,7 @@ public class Jalview2XML * vector to add new dataset sequence to */ private void ensureJalviewDatasetSequence(Sequence vamsasSeq, - AlignmentI ds, Vector dseqs) + AlignmentI ds, Vector dseqs, boolean ignoreUnrefed) { // JBP TODO: Check this is called for AlCodonFrames to support recovery of // xRef Codon Maps @@ -4021,7 +4050,10 @@ public class Jalview2XML { dsq = sq.getDatasetSequence(); } - + if (sq == null && ignoreUnrefed) + { + return; + } String sqid = vamsasSeq.getDsseqid(); if (dsq == null) { @@ -4508,5 +4540,4 @@ public class Jalview2XML { skipList = skipList2; } - }