X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FJalview2XML.java;h=4e72236db292af3e40dffb847b88ccd8946b1966;hb=ead72caff9aef9b7103dbb15907aeae777200832;hp=158ae509dc1667065990448a8bfefc0b23295d28;hpb=227ee1c1c69c228b67d408a0a83ae51bf5811272;p=jalview.git diff --git a/src/jalview/gui/Jalview2XML.java b/src/jalview/gui/Jalview2XML.java index 158ae50..4e72236 100644 --- a/src/jalview/gui/Jalview2XML.java +++ b/src/jalview/gui/Jalview2XML.java @@ -498,7 +498,7 @@ 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"; @@ -1127,7 +1127,7 @@ public class Jalview2XML view.setShowBoxes(av.getShowBoxes()); view.setShowColourText(av.getColourText()); view.setShowFullId(av.getShowJVSuffix()); - view.setRightAlignIds(av.rightAlignIds); + view.setRightAlignIds(av.isRightAlignIds()); view.setShowSequenceFeatures(av.showSequenceFeatures); view.setShowText(av.getShowText()); view.setShowUnconserved(av.getShowUnconserved()); @@ -1149,7 +1149,7 @@ public class Jalview2XML { jalview.schemabinding.version2.FeatureSettings fs = new jalview.schemabinding.version2.FeatureSettings(); - String[] renderOrder = ap.seqPanel.seqCanvas.getFeatureRenderer().renderOrder; + String[] renderOrder = ap.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder; Vector settingsAdded = new Vector(); Object gstyle = null; @@ -1158,7 +1158,7 @@ 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 +1176,13 @@ public class Jalview2XML } else { - setting.setColour(ap.seqPanel.seqCanvas.getFeatureRenderer() + setting.setColour(ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getColour(renderOrder[ro]).getRGB()); } setting.setDisplay(av.getFeaturesDisplayed() .containsKey(renderOrder[ro])); - float rorder = ap.seqPanel.seqCanvas.getFeatureRenderer() + float rorder = ap.getSeqPanel().seqCanvas.getFeatureRenderer() .getOrder(renderOrder[ro]); if (rorder > -1) { @@ -1194,7 +1194,7 @@ public class Jalview2XML } // Make sure we save none displayed feature settings - Iterator en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureColours + Iterator en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureColours .keySet().iterator(); while (en.hasNext()) { @@ -1206,11 +1206,11 @@ 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) { @@ -1219,7 +1219,7 @@ public class Jalview2XML fs.addSetting(setting); settingsAdded.addElement(key); } - en = ap.seqPanel.seqCanvas.getFeatureRenderer().featureGroups + en = ap.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups .keySet().iterator(); Vector groupsAdded = new Vector(); while (en.hasNext()) @@ -1231,7 +1231,7 @@ public class Jalview2XML } Group g = new Group(); g.setName(grp); - g.setDisplay(((Boolean) ap.seqPanel.seqCanvas + g.setDisplay(((Boolean) ap.getSeqPanel().seqCanvas .getFeatureRenderer().featureGroups.get(grp)) .booleanValue()); fs.addGroup(g); @@ -1456,8 +1456,7 @@ 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 + ""); @@ -2314,7 +2313,10 @@ 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); } // /////////////////////////////// @@ -3472,7 +3474,7 @@ 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(); @@ -3633,24 +3635,24 @@ public class Jalview2XML gc.setColourByLabel(setting.getColourByLabel()); } // and put in the feature colour table. - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour( setting.getType(), gc); } else { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setColour( + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setColour( setting.getType(), new java.awt.Color(setting.getColour())); } renderOrder[fs] = setting.getType(); if (setting.hasOrder()) { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder( setting.getType(), setting.getOrder()); } else { - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().setOrder( + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().setOrder( setting.getType(), fs / jms.getFeatureSettings().getSettingCount()); } @@ -3660,9 +3662,9 @@ public class Jalview2XML setting.getColour())); } } - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().renderOrder = renderOrder; + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().renderOrder = renderOrder; Hashtable fgtable; - af.alignPanel.seqPanel.seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); + af.alignPanel.getSeqPanel().seqCanvas.getFeatureRenderer().featureGroups = fgtable = new Hashtable(); for (int gs = 0; gs < jms.getFeatureSettings().getGroupCount(); gs++) { Group grp = jms.getFeatureSettings().getGroup(gs); @@ -3986,7 +3988,8 @@ 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; @@ -3998,7 +4001,7 @@ 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) @@ -4011,7 +4014,7 @@ 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); } @@ -4027,7 +4030,7 @@ 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 @@ -4038,7 +4041,10 @@ public class Jalview2XML { dsq = sq.getDatasetSequence(); } - + if (sq == null && ignoreUnrefed) + { + return; + } String sqid = vamsasSeq.getDsseqid(); if (dsq == null) {