X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=9bb27ed5f062c26b759aff032444cd0c8290ce29;hb=c1a4229bd662c4299301ee8827b36096d015c075;hp=2ceb245c3e9ebf6301fe47a52d1374ee35c2e98a;hpb=497958b4e5217efaa3ddeece38f38c3a6e98cb96;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 2ceb245..9bb27ed 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -500,7 +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"; @@ -1125,11 +1125,11 @@ public class Jalview2XML view.setFontSize(av.font.getSize()); view.setFontStyle(av.font.getStyle()); view.setRenderGaps(av.renderGaps); - view.setShowAnnotation(av.getShowAnnotation()); + view.setShowAnnotation(av.isShowAnnotation()); view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowFullId(av.getShowJVSuffix()); - view.setRightAlignIds(av.rightAlignIds); + view.setRightAlignIds(av.isRightAlignIds()); view.setShowSequenceFeatures(av.isShowSequenceFeatures()); view.setShowText(av.getShowText()); view.setShowUnconserved(av.getShowUnconserved()); @@ -1151,7 +1151,7 @@ public class Jalview2XML { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer() + String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getRenderOrder().toArray(new String[0]); Vector settingsAdded = new Vector(); @@ -1161,7 +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]); @@ -1179,13 +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.getFeaturesDisplayed().isVisible( renderOrder[ro])); - float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() + float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getOrder(renderOrder[ro]); if (rorder > -1) { @@ -1197,7 +1197,7 @@ public class Jalview2XML } // Make sure we save none displayed feature settings - Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer() + Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getFeatureColours().keySet().iterator(); while (en.hasNext()) { @@ -1209,11 +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) { @@ -1223,7 +1223,7 @@ public class Jalview2XML settingsAdded.addElement(key); } // is groups actually supposed to be a map here ? - en = ap.seqPanel.seqCanvas.getFeatureRenderer().getFeatureGroups() + en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().getFeatureGroups() .iterator(); Vector groupsAdded = new Vector(); while (en.hasNext()) @@ -1235,7 +1235,7 @@ public class Jalview2XML } Group g = new Group(); g.setName(grp); - g.setDisplay(((Boolean) ap.seqPanel.seqCanvas + g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas .getFeatureRenderer().checkGroupVisibility(grp, false)) .booleanValue()); fs.addGroup(g); @@ -1257,8 +1257,8 @@ public class Jalview2XML for (int c = 0; c < av.getColumnSelection().getHiddenColumns() .size(); c++) { - int[] region = (int[]) av.getColumnSelection() - .getHiddenColumns().elementAt(c); + int[] region = av.getColumnSelection() + .getHiddenColumns().get(c); HiddenColumns hc = new HiddenColumns(); hc.setStart(region[0]); hc.setEnd(region[1]); @@ -1461,8 +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 + ""); @@ -2319,7 +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); } // /////////////////////////////// @@ -3477,7 +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(); @@ -3674,7 +3676,7 @@ public class Jalview2XML // jms.getFeatureSettings().getTransparency() : 0.0, featureOrder); FeatureRendererSettings frs = new FeatureRendererSettings( renderOrder, fgtable, featureColours, 1.0f, featureOrder); - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer() + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer() .transferSettings(frs); } @@ -3995,7 +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; @@ -4007,7 +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) @@ -4020,7 +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); } @@ -4036,7 +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 @@ -4047,7 +4050,10 @@ public class Jalview2XML { dsq = sq.getDatasetSequence(); } - + if (sq == null && ignoreUnrefed) + { + return; + } String sqid = vamsasSeq.getDsseqid(); if (dsq == null) {