X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=cce2ee0880e97b4c68e6467b6da71e1da75748ed;hb=f41f5deaf0c8c1bbfb3fe4ca8be208d27b8e11d7;hp=41c3ce18f1fa8361dc5fcc9988d270186aeb3f54;hpb=16f0c7f1954c5e59f98fbf2aace6eae3229ad152;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 41c3ce1..cce2ee0 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -192,8 +192,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); y -= hgap; @@ -250,8 +249,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -668,11 +666,12 @@ public class SeqPanel extends JPanel implements MouseListener, @Override public void highlightSequence(SearchResults results) { - if (results == null || results.equals(lastSearchResults)) { + if (results == null || results.equals(lastSearchResults)) + { return; } lastSearchResults = results; - + if (av.isFollowHighlight()) { /* @@ -681,7 +680,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @see AlignmentPanel#adjustmentValueChanged */ - ap.setFollowingComplementScroll(true); + ap.setDontScrollComplement(true); if (ap.scrollToPosition(results, false)) { seqCanvas.revalidate(); @@ -696,6 +695,7 @@ public class SeqPanel extends JPanel implements MouseListener, { return this.ap == null ? null : this.ap.av; } + @Override public void updateColours(SequenceI seq, int index) { @@ -767,9 +767,9 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.isShowSequenceFeatures()) { int rpos; - List features = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), - rpos = sequence.findPosition(res)); + List features = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + rpos = sequence.findPosition(res)); seqARep.appendFeatures(tooltipText, rpos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } @@ -801,6 +801,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @see javax.swing.JComponent#getToolTipLocation(java.awt.event.MouseEvent) */ + @Override public Point getToolTipLocation(MouseEvent event) { int x = event.getX(), w = getWidth(); @@ -856,8 +857,9 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - residue = "X".equalsIgnoreCase(displayChar) ? "X" - : ResidueProperties.aa2Triplet.get(displayChar); + residue = "X".equalsIgnoreCase(displayChar) ? "X" : ("*" + .equals(displayChar) ? "STOP" : ResidueProperties.aa2Triplet + .get(displayChar)); if (residue != null) { text.append(" Residue: ").append(residue); @@ -892,6 +894,10 @@ public class SeqPanel extends JPanel implements MouseListener, for (Match m : results.getResults()) { SequenceI seq = m.getSequence(); + if (seq.getDatasetSequence() != null) + { + seq = seq.getDatasetSequence(); + } if (seq == ds) { @@ -899,7 +905,7 @@ public class SeqPanel extends JPanel implements MouseListener, * Convert position in sequence (base 1) to sequence character array * index (base 0) */ - int start = m.getStart() - 1; + int start = m.getStart() - m.getSequence().getStart(); setStatusMessage(seq, start, sequenceIndex); return; } @@ -1029,7 +1035,8 @@ public class SeqPanel extends JPanel implements MouseListener, message.append("Edit group:"); if (editCommand == null) { - editCommand = new EditCommand(MessageManager.getString("action.edit_group")); + editCommand = new EditCommand( + MessageManager.getString("action.edit_group")); } } else @@ -1042,7 +1049,8 @@ public class SeqPanel extends JPanel implements MouseListener, } if (editCommand == null) { - editCommand = new EditCommand(MessageManager.formatMessage("label.edit_params", new String[]{label})); + editCommand = new EditCommand(MessageManager.formatMessage( + "label.edit_params", new String[] { label })); } } @@ -1280,14 +1288,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - appendEdit(Action.INSERT_GAP, new SequenceI[] - { seq }, lastres, startres - lastres); + appendEdit(Action.INSERT_GAP, new SequenceI[] { seq }, lastres, + startres - lastres); } } else @@ -1304,8 +1311,7 @@ public class SeqPanel extends JPanel implements MouseListener, endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1323,8 +1329,8 @@ public class SeqPanel extends JPanel implements MouseListener, if (max > 0) { - appendEdit(Action.DELETE_GAP, new SequenceI[] - { seq }, startres, max); + appendEdit(Action.DELETE_GAP, new SequenceI[] { seq }, + startres, max); } } } @@ -1334,14 +1340,13 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = lastres; j < startres; j++) { - insertChar(j, new SequenceI[] - { seq }, fixedRight); + insertChar(j, new SequenceI[] { seq }, fixedRight); } } else { - appendEdit(Action.INSERT_NUC, new SequenceI[] - { seq }, lastres, startres - lastres); + appendEdit(Action.INSERT_NUC, new SequenceI[] { seq }, lastres, + startres - lastres); } } } @@ -1397,8 +1402,7 @@ public class SeqPanel extends JPanel implements MouseListener, final Edit edit = new EditCommand().new Edit(action, seq, pos, count, av.getAlignment().getGapCharacter()); - editCommand.appendEdit(edit, av.getAlignment(), - true, null); + editCommand.appendEdit(edit, av.getAlignment(), true, null); } void deleteChar(int j, SequenceI[] seq, int fixedColumn) @@ -1464,21 +1468,23 @@ public class SeqPanel extends JPanel implements MouseListener, av.setSelectionGroup(null); } - List features = seqCanvas.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), - sequence.findPosition(findRes(evt))); + List features = seqCanvas.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(findRes(evt))); - if (features != null && features.size()> 0) + if (features != null && features.size() > 0) { SearchResults highlight = new SearchResults(); - highlight.addResult(sequence, features.get(0).getBegin(), - features.get(0).getEnd()); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); } - if (features != null && features.size()> 0) + if (features != null && features.size() > 0) { - seqCanvas.getFeatureRenderer().amendFeatures(new SequenceI[] - { sequence }, features.toArray(new SequenceFeature[features.size()]), false, ap); + seqCanvas.getFeatureRenderer().amendFeatures( + new SequenceI[] { sequence }, + features.toArray(new SequenceFeature[features.size()]), + false, ap); seqCanvas.highlightSearchResults(null); } @@ -1593,10 +1599,11 @@ public class SeqPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(evt)) { - List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), sequence.findPosition(res)); + List allFeatures = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); Vector links = new Vector(); - for (SequenceFeature sf:allFeatures) + for (SequenceFeature sf : allFeatures) { if (sf.links != null) { @@ -1912,8 +1919,7 @@ public class SeqPanel extends JPanel implements MouseListener, // handles selection messages... // TODO: extend config options to allow user to control if selections may be // shared between viewports. - boolean iSentTheSelection = (av == source - || (source instanceof AlignViewport && ((AlignmentViewport) source) + boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))); if (iSentTheSelection || !av.followSelection) { @@ -1957,7 +1963,7 @@ public class SeqPanel extends JPanel implements MouseListener, sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); if ((sgroup == null || sgroup.getSize() == 0) - || (colsel == null || colsel.size() == 0)) + || (colsel == null || colsel.isEmpty())) { // don't copy columns if the region didn't intersect. copycolsel = false; @@ -1978,7 +1984,7 @@ public class SeqPanel extends JPanel implements MouseListener, { // the current selection is unset or from a previous message // so import the new colsel. - if (colsel == null || colsel.size() == 0) + if (colsel == null || colsel.isEmpty()) { if (av.getColumnSelection() != null) { @@ -2029,11 +2035,13 @@ public class SeqPanel extends JPanel implements MouseListener, protected boolean selectionFromTranslation(SequenceGroup seqsel, ColumnSelection colsel, SelectionSource source) { - if (!(source instanceof AlignViewportI)) { + if (!(source instanceof AlignViewportI)) + { return false; } final AlignViewportI sourceAv = (AlignViewportI) source; - if (sourceAv.getCodingComplement() != av && av.getCodingComplement() != sourceAv) + if (sourceAv.getCodingComplement() != av + && av.getCodingComplement() != sourceAv) { return false; }