X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FPopupMenu.java;h=9a6c760fc8757a446e22681ad4ec13e7b35d8caf;hb=331cd27699e0303dd42fd01e293f5fae9445e125;hp=e186145b0e24d34e3a5f7cb92e741c22d4917116;hpb=fd7eebe6dcf2346692d718ef91bb468cc12ebf44;p=jalview.git diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java index e186145..9a6c760 100644 --- a/src/jalview/gui/PopupMenu.java +++ b/src/jalview/gui/PopupMenu.java @@ -31,8 +31,8 @@ import jalview.commands.EditCommand.Action; import jalview.datamodel.AlignmentAnnotation; import jalview.datamodel.AlignmentI; import jalview.datamodel.Annotation; -import jalview.datamodel.ColumnSelection; import jalview.datamodel.DBRefEntry; +import jalview.datamodel.HiddenColumns; import jalview.datamodel.PDBEntry; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; @@ -43,12 +43,10 @@ import jalview.io.FileFormatI; import jalview.io.FileFormats; import jalview.io.FormatAdapter; import jalview.io.SequenceAnnotationReport; -import jalview.schemes.AnnotationColourGradient; import jalview.schemes.Blosum62ColourScheme; import jalview.schemes.ColourSchemeI; import jalview.schemes.ColourSchemes; import jalview.schemes.PIDColourScheme; -import jalview.schemes.ResidueColourScheme; import jalview.util.GroupUrlLink; import jalview.util.GroupUrlLink.UrlStringTooLongException; import jalview.util.MessageManager; @@ -57,7 +55,9 @@ import jalview.util.UrlLink; import java.awt.Color; import java.awt.event.ActionEvent; import java.awt.event.ActionListener; +import java.util.ArrayList; import java.util.Arrays; +import java.util.BitSet; import java.util.Collection; import java.util.Collections; import java.util.Hashtable; @@ -414,7 +414,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener add(menuItem); } - } SequenceGroup sg = ap.av.getSelectionGroup(); @@ -428,6 +427,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener ColourMenuHelper.setColourSelected(colourMenu, sg.getColourScheme()); + conservationMenuItem.setEnabled(!sg.isNucleotide()); + if (sg.cs != null) { if (sg.cs.conservationApplied()) @@ -1178,12 +1179,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener hideInsertions_actionPerformed(e); } }); - /* - * annotationMenuItem.setText("By Annotation"); - * annotationMenuItem.addActionListener(new ActionListener() { public void - * actionPerformed(ActionEvent actionEvent) { - * annotationMenuItem_actionPerformed(actionEvent); } }); - */ + groupMenu.add(sequenceSelDetails); add(groupMenu); add(sequenceMenu); @@ -1261,7 +1257,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @Override public void actionPerformed(ActionEvent e) { - abovePIDColour_actionPerformed(); + abovePIDColour_actionPerformed(abovePIDColour.isSelected()); } }); @@ -1283,7 +1279,8 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener @Override public void actionPerformed(ActionEvent e) { - conservationMenuItem_actionPerformed(); + conservationMenuItem_actionPerformed(conservationMenuItem + .isSelected()); } }); @@ -1448,16 +1445,59 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener protected void hideInsertions_actionPerformed(ActionEvent actionEvent) { - if (sequence != null) + + HiddenColumns hidden = new HiddenColumns(); + BitSet inserts = new BitSet(), mask = new BitSet(); + + // set mask to preserve existing hidden columns outside selected group + if (ap.av.hasHiddenColumns()) { - ColumnSelection cs = ap.av.getColumnSelection(); - if (cs == null) + ap.av.getAlignment().getHiddenColumns().markHiddenRegions(mask); + } + + boolean markedPopup = false; + // mark inserts in current selection + if (ap.av.getSelectionGroup() != null) + { + // mark just the columns in the selection group to be hidden + inserts.set(ap.av.getSelectionGroup().getStartRes(), ap.av + .getSelectionGroup().getEndRes() + 1); + + // and clear that part of the mask + mask.andNot(inserts); + + // now clear columns without gaps + for (SequenceI sq : ap.av.getSelectionGroup().getSequences()) { - cs = new ColumnSelection(); + if (sq == sequence) + { + markedPopup = true; + } + inserts.and(sq.getInsertionsAsBits()); } - cs.hideInsertionsFor(sequence); - ap.av.setColumnSelection(cs); } + else + { + // initially, mark all columns to be hidden + inserts.set(0, ap.av.getAlignment().getWidth()); + + // and clear out old hidden regions completely + mask.clear(); + } + + // now mark for sequence under popup if we haven't already done it + if (!markedPopup && sequence != null) + { + inserts.and(sequence.getInsertionsAsBits()); + } + + // finally, preserve hidden regions outside selection + inserts.or(mask); + + // and set hidden columns accordingly + hidden.hideMarkedBits(inserts); + + ap.av.getAlignment().setHiddenColumns(hidden); refresh(); } @@ -1528,10 +1568,12 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /** * DOCUMENT ME! * + * @param selected + * * @param e * DOCUMENT ME! */ - protected void abovePIDColour_actionPerformed() + public void abovePIDColour_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -1539,7 +1581,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener return; } - boolean selected = abovePIDColour.isSelected(); if (selected) { sg.cs.setConsensus(AAFrequency.calculate( @@ -1583,7 +1624,7 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener * @param e * DOCUMENT ME! */ - protected void conservationMenuItem_actionPerformed() + public void conservationMenuItem_actionPerformed(boolean selected) { SequenceGroup sg = getGroup(); if (sg.cs == null) @@ -1591,7 +1632,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener return; } - boolean selected = conservationMenuItem.isSelected(); if (selected) { // JBPNote: Conservation name shouldn't be i18n translated @@ -1618,24 +1658,6 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener refresh(); } - public void annotationMenuItem_actionPerformed(ActionEvent actionEvent) - { - SequenceGroup sg = getGroup(); - if (sg == null) - { - return; - } - - AnnotationColourGradient acg = new AnnotationColourGradient( - sequence.getAnnotation()[0], null, - AnnotationColourGradient.NO_THRESHOLD); - - acg.setPredefinedColours(true); - sg.setColourScheme(acg); - - refresh(); - } - /** * DOCUMENT ME! * @@ -1903,28 +1925,25 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener return; } - int rsize = 0, gSize = sg.getSize(); - SequenceI[] rseqs, seqs = new SequenceI[gSize]; - SequenceFeature[] tfeatures, features = new SequenceFeature[gSize]; + List seqs = new ArrayList(); + List features = new ArrayList(); + /* + * assemble dataset sequences, and template new sequence features, + * for the amend features dialog + */ + int gSize = sg.getSize(); for (int i = 0; i < gSize; i++) { int start = sg.getSequenceAt(i).findPosition(sg.getStartRes()); int end = sg.findEndRes(sg.getSequenceAt(i)); if (start <= end) { - seqs[rsize] = sg.getSequenceAt(i).getDatasetSequence(); - features[rsize] = new SequenceFeature(null, null, null, start, end, - "Jalview"); - rsize++; + seqs.add(sg.getSequenceAt(i).getDatasetSequence()); + features.add(new SequenceFeature(null, null, null, start, end, null)); } } - rseqs = new SequenceI[rsize]; - tfeatures = new SequenceFeature[rsize]; - System.arraycopy(seqs, 0, rseqs, 0, rsize); - System.arraycopy(features, 0, tfeatures, 0, rsize); - features = tfeatures; - seqs = rseqs; + if (ap.getSeqPanel().seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, true, ap)) { @@ -1999,33 +2018,26 @@ public class PopupMenu extends JPopupMenu implements ColourChangeListener /** * Action on user selecting an item from the colour menu (that does not have * its bespoke action handler) + * + * @return */ @Override public void changeColour_actionPerformed(String colourSchemeName) { SequenceGroup sg = getGroup(); - if (ResidueColourScheme.USER_DEFINED.equals(colourSchemeName)) - { - /* - * open a panel to load or configure a user-defined colour scheme - */ - new UserDefinedColours(ap, sg); - } - else + /* + * switch to the chosen colour scheme (or null for None) + */ + ColourSchemeI colourScheme = ColourSchemes.getInstance() + .getColourScheme(colourSchemeName, sg, + ap.av.getHiddenRepSequences()); + sg.setColourScheme(colourScheme); + if (colourScheme instanceof Blosum62ColourScheme + || colourScheme instanceof PIDColourScheme) { - /* - * switch to the chosen colour scheme (or null for None) - */ - ColourSchemeI colourScheme = ColourSchemes.getInstance().getColourScheme( - colourSchemeName, sg, ap.av.getHiddenRepSequences()); - sg.setColourScheme(colourScheme); - if (colourScheme instanceof Blosum62ColourScheme - || colourScheme instanceof PIDColourScheme) - { - sg.cs.setConsensus(AAFrequency.calculate( - sg.getSequences(ap.av.getHiddenRepSequences()), - sg.getStartRes(), sg.getEndRes() + 1)); - } + sg.cs.setConsensus(AAFrequency.calculate( + sg.getSequences(ap.av.getHiddenRepSequences()), + sg.getStartRes(), sg.getEndRes() + 1)); } refresh();