X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=f476d419dc11cb34f3b6a467c44ac3973e0d0e19;hb=f2d38aaebf121e49be29cb19ae01f1c6a36fe7e0;hp=01653b6221d0efd44a1ba7aa5910d8a301861519;hpb=4099019578bbeb81b76154922851ada38fb0017d;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 01653b6..f476d41 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -21,6 +21,7 @@ package jalview.gui; import jalview.api.AlignViewportI; +import jalview.bin.Cache; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; @@ -54,11 +55,12 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; +import java.util.ArrayList; import java.util.List; -import java.util.Vector; import javax.swing.JOptionPane; import javax.swing.JPanel; +import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; /** @@ -192,8 +194,7 @@ 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 +251,7 @@ public class SeqPanel extends JPanel implements MouseListener, } int cHeight = av.getAlignment().getHeight() * av.getCharHeight() - + hgap - + seqCanvas.getAnnotationHeight(); + + hgap + seqCanvas.getAnnotationHeight(); y -= hgap; @@ -511,6 +511,7 @@ public class SeqPanel extends JPanel implements MouseListener, void insertNucAtCursor(boolean group, String nuc) { + // TODO not called - delete? groupEditing = group; startseq = seqCanvas.cursorY; lastres = seqCanvas.cursorX; @@ -601,7 +602,7 @@ public class SeqPanel extends JPanel implements MouseListener, { lastMousePress = evt.getPoint(); - if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + if (SwingUtilities.isMiddleMouseButton(evt)) { mouseWheelPressed = true; return; @@ -668,11 +669,12 @@ 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 +683,7 @@ 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 +698,7 @@ 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 +770,9 @@ 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 +804,7 @@ 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(); @@ -821,6 +825,20 @@ public class SeqPanel extends JPanel implements MouseListener, String lastTooltip; /** + * set when the current UI interaction has resulted in a change that requires + * overview shading to be recalculated. this could be changed to something + * more expressive that indicates what actually has changed, so selective + * redraws can be applied + */ + private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + + /** + * set if av.getSelectionGroup() refers to a group that is defined on the + * alignment view, rather than a transient selection + */ + private boolean editingDefinedGroup = false; // TODO: refactor to avcontroller or viewModel + + /** * Set status message in alignment panel * * @param sequence @@ -839,7 +857,8 @@ public class SeqPanel extends JPanel implements MouseListener, * Sequence number (if known), and sequence name. */ String seqno = seq == -1 ? "" : " " + (seq + 1); - text.append("Sequence" + seqno + " ID: " + sequence.getName()); + text.append("Sequence").append(seqno).append(" ID: ") + .append(sequence.getName()); String residue = null; /* @@ -904,7 +923,7 @@ 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; } @@ -1034,7 +1053,8 @@ 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 @@ -1047,7 +1067,8 @@ 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 })); } } @@ -1168,8 +1189,7 @@ public class SeqPanel extends JPanel implements MouseListener, { for (int j = 0; j < startres - lastres; j++) { - if (!jalview.util.Comparison.isGap(groupSeqs[g] - .getCharAt(fixedRight - j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -1231,7 +1251,7 @@ public class SeqPanel extends JPanel implements MouseListener, continue; } - if (!jalview.util.Comparison.isGap(groupSeqs[g].getCharAt(j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(j))) { // Not a gap, block edit not valid endEditing(); @@ -1285,14 +1305,13 @@ 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 @@ -1309,8 +1328,7 @@ public class SeqPanel extends JPanel implements MouseListener, endEditing(); break; } - deleteChar(startres, new SequenceI[] - { seq }, fixedRight); + deleteChar(startres, new SequenceI[] { seq }, fixedRight); } } else @@ -1328,8 +1346,8 @@ 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); } } } @@ -1339,14 +1357,13 @@ 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); } } } @@ -1366,7 +1383,7 @@ public class SeqPanel extends JPanel implements MouseListener, for (blankColumn = fixedColumn; blankColumn > j; blankColumn--) { - if (jalview.util.Comparison.isGap(seq[s].getCharAt(blankColumn))) + if (Comparison.isGap(seq[s].getCharAt(blankColumn))) { // Theres a space, so break and insert the gap break; @@ -1402,8 +1419,7 @@ 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) @@ -1469,21 +1485,23 @@ 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); } @@ -1565,10 +1583,12 @@ public class SeqPanel extends JPanel implements MouseListener, && (res < stretchGroup.getEndRes())) { av.setSelectionGroup(stretchGroup); + editingDefinedGroup = true; } else { stretchGroup = null; + editingDefinedGroup = false; } } else if (!stretchGroup.getSequences(null).contains(sequence) @@ -1587,6 +1607,7 @@ public class SeqPanel extends JPanel implements MouseListener, && (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; + editingDefinedGroup = true; break; } } @@ -1596,23 +1617,24 @@ public class SeqPanel extends JPanel implements MouseListener, } - if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) { - List allFeatures = ap.getFeatureRenderer().findFeaturesAtRes( - sequence.getDatasetSequence(), sequence.findPosition(res)); - Vector links = new Vector(); - for (SequenceFeature sf:allFeatures) + List allFeatures = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + List links = new ArrayList(); + for (SequenceFeature sf : allFeatures) { if (sf.links != null) { - for (int j = 0; j < sf.links.size(); j++) + for (String link : sf.links) { - links.addElement(sf.links.elementAt(j)); + links.add(link); } } } - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(ap, null, links); + PopupMenu pop = new PopupMenu(ap, null, links); pop.show(this, evt.getX(), evt.getY()); return; } @@ -1635,7 +1657,7 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); - + editingDefinedGroup = false; stretchGroup = sg; if (av.getConservationSelected()) @@ -1678,9 +1700,10 @@ public class SeqPanel extends JPanel implements MouseListener, { return; } - - stretchGroup.recalcConservation(); // always do this - annotation has own - // state + // always do this - annotation has own state + // but defer colourscheme update until hidden sequences are passed in + boolean vischange = stretchGroup.recalcConservation(true); + needOverviewUpdate |= vischange && editingDefinedGroup; if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1698,8 +1721,9 @@ public class SeqPanel extends JPanel implements MouseListener, } } PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(true); - + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate =false; + editingDefinedGroup = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1753,6 +1777,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= editingDefinedGroup; } } else if (changeStartRes) @@ -1760,6 +1785,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= editingDefinedGroup; } } @@ -1793,6 +1819,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= editingDefinedGroup; } else { @@ -1802,6 +1829,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= editingDefinedGroup; } } @@ -1917,8 +1945,7 @@ 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) { @@ -1944,28 +1971,28 @@ public class SeqPanel extends JPanel implements MouseListener, // do we want to thread this ? (contention with seqsel and colsel locks, I // suspect) - // rules are: colsel is copied if there is a real intersection between - // sequence selection + /* + * only copy colsel if there is a real intersection between + * sequence selection and this panel's alignment + */ boolean repaint = false; - boolean copycolsel = true; + boolean copycolsel = false; SequenceGroup sgroup = null; if (seqsel != null && seqsel.getSize() > 0) { if (av.getAlignment() == null) { - jalview.bin.Cache.log.warn("alignviewport av SeqSetId=" + Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + " ViewId=" + av.getViewId() + " 's alignment is NULL! returning immediately."); return; } sgroup = seqsel.intersect(av.getAlignment(), (av.hasHiddenRows()) ? av.getHiddenRepSequences() : null); - if ((sgroup == null || sgroup.getSize() == 0) - || (colsel == null || colsel.size() == 0)) + if ((sgroup != null && sgroup.getSize() > 0)) { - // don't copy columns if the region didn't intersect. - copycolsel = false; + copycolsel = true; } } if (sgroup != null && sgroup.getSize() > 0) @@ -1983,7 +2010,7 @@ 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) { @@ -2034,11 +2061,13 @@ 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; } @@ -2056,7 +2085,6 @@ public class SeqPanel extends JPanel implements MouseListener, ColumnSelection cs = MappingUtils.mapColumnSelection(colsel, sourceAv, av); av.setColumnSelection(cs); - av.isColSelChanged(true); PaintRefresher.Refresh(this, av.getSequenceSetId());