X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fproject%2FJalview2XML.java;h=2c93ee52d0f156c7de70fca6871c48163084067b;hb=14bfc6fb57f123b815f08dbf5b35544abd33b3af;hp=b0315e809bc2051d680babbb8dd4add07f037f1f;hpb=6b74ef88014ba574bd60a14eae8167390e012421;p=jalview.git diff --git a/src/jalview/project/Jalview2XML.java b/src/jalview/project/Jalview2XML.java index b0315e8..2c93ee5 100644 --- a/src/jalview/project/Jalview2XML.java +++ b/src/jalview/project/Jalview2XML.java @@ -35,6 +35,7 @@ import jalview.api.analysis.ScoreModelI; import jalview.api.analysis.SimilarityParamsI; import jalview.api.structures.JalviewStructureDisplayI; import jalview.bin.Cache; +import jalview.bin.Jalview; import jalview.datamodel.AlignedCodonFrame; import jalview.datamodel.Alignment; import jalview.datamodel.AlignmentAnnotation; @@ -189,7 +190,6 @@ import java.util.jar.JarInputStream; import java.util.jar.JarOutputStream; import javax.swing.JInternalFrame; -import javax.swing.SwingUtilities; import javax.xml.bind.JAXBContext; import javax.xml.bind.JAXBElement; import javax.xml.bind.Marshaller; @@ -2784,8 +2784,9 @@ public class Jalview2XML { try { + // BH 2019 -- can't wait - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -3354,16 +3355,16 @@ public class Jalview2XML * data source provider * @return alignment frame created from view stored in DOM */ - AlignFrame loadFromObject(JalviewModel jalviewModel, String file, + private AlignFrame loadFromObject(JalviewModel jalviewModel, String file, boolean loadTreesAndStructures, jarInputStreamProvider jprovider) { -// Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject0", Platform.TIME_MARK); - SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet().get(0); + SequenceSet vamsasSet = jalviewModel.getVamsasModel().getSequenceSet() + .get(0); List vamsasSeqs = vamsasSet.getSequence(); - // JalviewModelSequence jms = object.getJalviewModelSequence(); // Viewport view = (jms.getViewportCount() > 0) ? jms.getViewport(0) @@ -3394,7 +3395,7 @@ public class Jalview2XML : view.getId() + uniqueSetSuffix); } -// Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject1", Platform.TIME_MARK); // //////////////////////////////// // LOAD SEQUENCES @@ -3480,8 +3481,8 @@ public class Jalview2XML } } -// Platform.timeCheck("Jalview2XML.loadFromObject-seq", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-seq", + // Platform.TIME_MARK); // / // Create the alignment object from the sequence set // /////////////////////////////// @@ -3522,8 +3523,8 @@ public class Jalview2XML recoverDatasetFor(vamsasSet, al, isdsal, uniqueSeqSetId); } -// Platform.timeCheck("Jalview2XML.loadFromObject-align", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-align", + // Platform.TIME_MARK); if (referenceseqForView != null) { al.setSeqrep(referenceseqForView); @@ -3536,8 +3537,8 @@ public class Jalview2XML al.setProperty(ssp.getKey(), ssp.getValue()); } -// Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-setseqprop", + // Platform.TIME_MARK); // /////////////////////////////// Hashtable pdbloaded = new Hashtable(); // TODO nothing writes to this?? @@ -3551,7 +3552,7 @@ public class Jalview2XML // now, for 2.10 projects, this is also done if the xml doc includes // dataset sequences not actually present in any particular view. // -// Platform.timeCheck("J2XML features0", Platform.TIME_RESET); + // Platform.timeCheck("J2XML features0", Platform.TIME_RESET); for (int i = 0; i < vamsasSeqs.size(); i++) { JSeq jseq = jseqs.get(i); @@ -3606,9 +3607,9 @@ public class Jalview2XML } // adds feature to datasequence's feature set (since Jalview 2.10) -// Platform.timeCheck(null, Platform.TIME_SET); + // Platform.timeCheck(null, Platform.TIME_SET); al.getSequenceAt(i).addSequenceFeature(sf); -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); } } if (vamsasSeqs.get(i).getDBRef().size() > 0) @@ -3668,8 +3669,7 @@ public class Jalview2XML { entry.setProperty(prop.getName(), prop.getValue()); } - Desktop.getStructureSelectionManager() - .registerPDBEntry(entry); + Desktop.getStructureSelectionManager().registerPDBEntry(entry); // adds PDBEntry to datasequence's set (since Jalview 2.10) if (al.getSequenceAt(i).getDatasetSequence() != null) { @@ -3684,9 +3684,9 @@ public class Jalview2XML } -// Platform.timeCheck("features done", Platform.TIME_GET); -// Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", -// Platform.TIME_MARK); + // Platform.timeCheck("features done", Platform.TIME_GET); + // Platform.timeCheck("Jalview2XML.loadFromObject-endmultiview", + // Platform.TIME_MARK); } // end !multipleview // /////////////////////////////// @@ -3720,16 +3720,16 @@ public class Jalview2XML else { // defer to later - frefedSequence.add( - newAlcodMapRef(map.getDnasq(), cf, mapping)); + frefedSequence + .add(newAlcodMapRef(map.getDnasq(), cf, mapping)); } } } al.addCodonFrame(cf); } } -// Platform.timeCheck("Jalview2XML.loadFromObject-seqmap", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-seqmap", + // Platform.TIME_MARK); } // //////////////////////////////// @@ -3790,8 +3790,8 @@ public class Jalview2XML } // Construct new annotation from model. List ae = annotation.getAnnotationElement(); -// System.err.println( -// "Jalview2XML processing " + ae.size() + " annotations"); + // System.err.println( + // "Jalview2XML processing " + ae.size() + " annotations"); jalview.datamodel.Annotation[] anot = null; java.awt.Color firstColour = null; @@ -3936,8 +3936,7 @@ public class Jalview2XML jaa.setCalcId(annotation.getCalcId()); if (annotation.getProperty().size() > 0) { - for (Annotation.Property prop : annotation - .getProperty()) + for (Annotation.Property prop : annotation.getProperty()) { jaa.setProperty(prop.getName(), prop.getValue()); } @@ -3954,8 +3953,8 @@ public class Jalview2XML al.addAnnotation(jaa); } } -// Platform.timeCheck("Jalview2XML.loadFromObject-annot", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-annot", + // Platform.TIME_MARK); } // /////////////////////// // LOAD GROUPS @@ -4020,9 +4019,9 @@ public class Jalview2XML sg.setShowNonconserved(safeBoolean(jGroup.isShowUnconserved())); sg.thresholdTextColour = safeInt(jGroup.getTextColThreshold()); // attributes with a default in the schema are never null - sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); - sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); - sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); + sg.setShowConsensusHistogram(jGroup.isShowConsensusHistogram()); + sg.setshowSequenceLogo(jGroup.isShowSequenceLogo()); + sg.setNormaliseSequenceLogo(jGroup.isNormaliseSequenceLogo()); sg.setIgnoreGapsConsensus(jGroup.isIgnoreGapsinConsensus()); if (jGroup.getConsThreshold() != null && jGroup.getConsThreshold().intValue() != 0) @@ -4066,12 +4065,13 @@ public class Jalview2XML if (addAnnotSchemeGroup) { // reconstruct the annotation colourscheme - sg.setColourScheme(constructAnnotationColour( - jGroup.getAnnotationColours(), null, al, jalviewModel, false)); + sg.setColourScheme( + constructAnnotationColour(jGroup.getAnnotationColours(), + null, al, jalviewModel, false)); } } -// Platform.timeCheck("Jalview2XML.loadFromObject-groups", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-groups", + // Platform.TIME_MARK); } if (view == null) { @@ -4111,8 +4111,8 @@ public class Jalview2XML } } -// Platform.timeCheck("Jalview2XML.loadFromObject-viewport", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-viewport", + // Platform.TIME_MARK); } /** * indicate that annotation colours are applied across all groups (pre @@ -4165,47 +4165,47 @@ public class Jalview2XML final AlignFrame af0 = af; final AlignViewport av0 = av; final AlignmentPanel ap0 = ap; -// Platform.timeCheck("Jalview2XML.loadFromObject-beforetree", -// Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadFromObject-beforetree", + // Platform.TIME_MARK); if (loadTreesAndStructures) { if (!jalviewModel.getTree().isEmpty()) { - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() { -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); loadTrees(jalviewModel, view, af0, av0, ap0); -// Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadTrees", Platform.TIME_MARK); } }); } if (!jalviewModel.getPcaViewer().isEmpty()) { - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() { -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); loadPCAViewers(jalviewModel, ap0); -// Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadPCA", Platform.TIME_MARK); } }); } - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() { -// Platform.timeCheck(null, Platform.TIME_MARK); + // Platform.timeCheck(null, Platform.TIME_MARK); loadPDBStructures(jprovider, jseqs, af0, ap0); -// Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); + // Platform.timeCheck("Jalview2XML.loadPDB", Platform.TIME_MARK); } }); - SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -4213,6 +4213,7 @@ public class Jalview2XML loadRnaViewers(jprovider, jseqs, ap0); } }); + } // and finally return. // but do not set holdRepaint true just yet, because this could be the @@ -4773,7 +4774,7 @@ public class Jalview2XML svattrib.getWidth(), svattrib.getHeight()); // try // { - javax.swing.SwingUtilities.invokeLater(new Runnable() + Jalview.execRunnable(new Runnable() { @Override public void run() @@ -4799,7 +4800,8 @@ public class Jalview2XML } } } - }); + }); + // javax.swing.SwingUtilities.invokeLater(r); // } catch (InvocationTargetException ex) // { // warn("Unexpected error when opening Jmol view.", ex);