X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=3ea689fdba5fd1dc131601f116aaa32e0f2b8b18;hb=57b121a5f97c475b3078281ea2e3f3035e2c8703;hp=175adeaef9f78a89741cc0e205de229df98c556a;hpb=d305e02d8b425bb501141ad32142aeb8572adc57;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index 175adea..3ea689f 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -22,12 +22,12 @@ package jalview.gui; import jalview.analysis.AAFrequency; import jalview.analysis.AlignmentAnnotationUtils; -import jalview.analysis.AnnotationSorter; -import jalview.analysis.AnnotationSorter.SortOrder; import jalview.analysis.Conservation; import jalview.commands.ChangeCaseCommand; import jalview.commands.EditCommand; +import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentAnnotation; +import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; import jalview.datamodel.DBRefEntry; import jalview.datamodel.PDBEntry; @@ -374,12 +374,12 @@ public class PopupMenu extends JPopupMenu { AlignmentAnnotation[] aa = ap.av.getAlignment() .getAlignmentAnnotation(); - for (int i = 0; i < aa.length; i++) + for (int i = 0; aa != null && i < aa.length; i++) { - if (aa[i].getRNAStruc() != null) + if (aa[i].isValidStruc() && aa[i].sequenceRef == null) { final String rnastruc = aa[i].getRNAStruc(); - final String structureLine = aa[i].label; + final String structureLine = aa[i].label + " (alignment)"; menuItem = new JMenuItem(); menuItem.setText(MessageManager.formatMessage( "label.2d_rna_structure_line", new String[] @@ -389,15 +389,15 @@ public class PopupMenu extends JPopupMenu @Override public void actionPerformed(ActionEvent e) { - // System.out.println("1:"+structureLine); - System.out.println("1:sname" + seq.getName()); - System.out.println("2:seq" + seq); - - // System.out.println("3:"+seq.getSequenceAsString()); - System.out.println("3:strucseq" + rnastruc); - // System.out.println("4:struc"+seq.getRNA()); - System.out.println("5:name" + seq.getName()); - System.out.println("6:ap" + ap); + // // System.out.println("1:"+structureLine); + // System.out.println("1:sname" + seq.getName()); + // System.out.println("2:seq" + seq); + // + // // System.out.println("3:"+seq.getSequenceAsString()); + // System.out.println("3:strucseq" + rnastruc); + // // System.out.println("4:struc"+seq.getRNA()); + // System.out.println("5:name" + seq.getName()); + // System.out.println("6:ap" + ap); new AppVarna(structureLine, seq, seq.getSequenceAsString(), rnastruc, seq.getName(), ap); // new AppVarna(seq.getName(),seq,rnastruc,seq.getRNA(), @@ -416,7 +416,7 @@ public class PopupMenu extends JPopupMenu AlignmentAnnotation seqAnno[] = seq.getAnnotation(); for (int i = 0; i < seqAnno.length; i++) { - if (seqAnno[i].getRNAStruc() != null) + if (seqAnno[i].isValidStruc()) { final String rnastruc = seqAnno[i].getRNAStruc(); @@ -1766,12 +1766,13 @@ public class PopupMenu extends JPopupMenu /** * Check for any annotations on the underlying dataset sequences (for the - * current selection group) which are not on the alignment annotations for the - * sequence. If any are found, enable the option to add them to the alignment. - * The criteria for 'on the alignment' is finding an alignment annotation on - * the sequence, that matches on calcId and label. A tooltip is also - * constructed that displays the source (calcId) and type (label) of the - * annotations that can be added. + * current selection group) which are not 'on the alignment'.If any are found, + * enable the option to add them to the alignment. The criteria for 'on the + * alignment' is finding an alignment annotation on the alignment, matched on + * calcId, label and sequenceRef. + * + * A tooltip is also constructed that displays the source (calcId) and type + * (label) of the annotations that can be added. * * @param menuItem * @param forSequences @@ -1798,10 +1799,11 @@ public class PopupMenu extends JPopupMenu /* * For each sequence selected in the alignment, make a list of any * annotations on the underlying dataset sequence which are not already on - * the sequence in the alignment. + * the alignment. * * Build a map of { alignmentSequence, } */ + AlignmentI al = this.ap.av.getAlignment(); final Map> candidates = new LinkedHashMap>(); for (SequenceI seq : forSequences) { @@ -1819,11 +1821,12 @@ public class PopupMenu extends JPopupMenu for (AlignmentAnnotation dsann : datasetAnnotations) { /* - * If the sequence has no annotation that matches this one, then add - * this one to the results list. + * Find matching annotations on the alignment. */ - if (seq.getAlignmentAnnotations(dsann.getCalcId(), dsann.label) - .isEmpty()) + final Iterable matchedAlignmentAnnotations = al + .findAnnotations(seq, dsann.getCalcId(), + dsann.label); + if (!matchedAlignmentAnnotations.iterator().hasNext()) { result.add(dsann); tipEntries.put(dsann.getCalcId(), dsann.label); @@ -1892,8 +1895,14 @@ public class PopupMenu extends JPopupMenu } copyAnn.restrict(startRes, endRes); - // add to the sequence (sets copyAnn.datasetSequence) - seq.addAlignmentAnnotation(copyAnn); + /* + * Add to the sequence (sets copyAnn.datasetSequence), unless the + * original annotation is already on the sequence. + */ + if (!seq.hasAnnotation(ann)) + { + seq.addAlignmentAnnotation(copyAnn); + } // adjust for gaps copyAnn.adjustForAlignment(); // add to the alignment and set visible @@ -1901,11 +1910,6 @@ public class PopupMenu extends JPopupMenu copyAnn.visible = true; } } - // TODO: save annotation sort order on AlignViewport - // do sorting from AlignmentPanel.updateAnnotation() - new AnnotationSorter(this.ap.getAlignment()).sort(this.ap - .getAlignment().getAlignmentAnnotation(), - SortOrder.SEQUENCE_AND_TYPE); refresh(); } @@ -1939,7 +1943,9 @@ public class PopupMenu extends JPopupMenu true, true, false, - (ap.seqPanel.seqCanvas.fr != null) ? ap.seqPanel.seqCanvas.fr.minmax + (ap.getSeqPanel().seqCanvas.fr != null) ? ap + .getSeqPanel().seqCanvas.fr + .getMinMax() : null); contents.append("

"); } @@ -2573,7 +2579,8 @@ public class PopupMenu extends JPopupMenu String choice = chooser.getSelectedFile().getPath(); jalview.bin.Cache.setProperty("LAST_DIRECTORY", choice); new AssociatePdbFileWithSeq().associatePdbWithSeq(choice, - jalview.io.AppletFormatAdapter.FILE, sequence, true); + jalview.io.AppletFormatAdapter.FILE, sequence, true, + Desktop.instance); } } @@ -2655,7 +2662,7 @@ public class PopupMenu extends JPopupMenu System.arraycopy(features, 0, tfeatures, 0, rsize); features = tfeatures; seqs = rseqs; - if (ap.seqPanel.seqCanvas.getFeatureRenderer().amendFeatures(seqs, + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { ap.alignFrame.setShowSeqFeatures(true); @@ -2713,7 +2720,7 @@ public class PopupMenu extends JPopupMenu { EditCommand editCommand = new EditCommand( MessageManager.getString("label.edit_sequences"), - EditCommand.REPLACE, dialog.getName().replace(' ', + Action.REPLACE, dialog.getName().replace(' ', ap.av.getGapCharacter()), sg.getSequencesAsArray(ap.av.getHiddenRepSequences()), sg.getStartRes(), sg.getEndRes() + 1, ap.av.getAlignment());