X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3266fabf5631a665138d9e9f7feb574d451a8434;hb=6631ee3334607cc5e0b670191f9df048c157325a;hp=3fbb8092efcbec2611bf6ffb10ea0a23b1a10615;hpb=69bab27e77ceaca6d12e0de49f8fc62e01678f53;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 3fbb809..3266fab 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -43,6 +43,7 @@ import jalview.structure.VamsasSource; import jalview.util.Comparison; import jalview.util.MappingUtils; import jalview.util.MessageManager; +import jalview.util.Platform; import jalview.viewmodel.AlignmentViewport; import java.awt.BorderLayout; @@ -582,6 +583,13 @@ public class SeqPanel extends JPanel implements MouseListener, mouseDragging = false; mouseWheelPressed = false; + if (evt.isPopupTrigger()) // Windows: mouseReleased + { + showPopupMenu(evt); + evt.consume(); + return; + } + if (!editingSeqs) { doMouseReleasedDefineMode(evt); @@ -608,13 +616,14 @@ public class SeqPanel extends JPanel implements MouseListener, return; } - if (evt.isShiftDown() || evt.isAltDown() || evt.isControlDown()) + boolean isControlDown = Platform.isControlDown(evt); + if (evt.isShiftDown() || isControlDown) { - if (evt.isAltDown() || evt.isControlDown()) + editingSeqs = true; + if (isControlDown) { groupEditing = true; } - editingSeqs = true; } else { @@ -825,6 +834,21 @@ 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 @@ -843,7 +867,8 @@ 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; /* @@ -1531,9 +1556,10 @@ public class SeqPanel extends JPanel implements MouseListener, */ public void doMousePressedDefineMode(MouseEvent evt) { - int res = findRes(evt); - int seq = findSeq(evt); + final int res = findRes(evt); + final int seq = findSeq(evt); oldSeq = seq; + needOverviewUpdate = false; startWrapBlock = wrappedBlock; @@ -1596,28 +1622,21 @@ public class SeqPanel extends JPanel implements MouseListener, } av.setSelectionGroup(stretchGroup); - } - if (evt.isPopupTrigger()) + if (evt.isPopupTrigger()) // Mac: mousePressed { - List allFeatures = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); - List links = new ArrayList(); - for (SequenceFeature sf : allFeatures) - { - if (sf.links != null) - { - for (String link : sf.links) - { - links.add(link); - } - } - } + showPopupMenu(evt); + return; + } - PopupMenu pop = new PopupMenu(ap, null, links); - pop.show(this, evt.getX(), evt.getY()); + /* + * defer right-mouse click handling to mouseReleased on Windows + * (where isPopupTrigger() will answer true) + * NB isRightMouseButton is also true for Cmd-click on Mac + */ + if (SwingUtilities.isRightMouseButton(evt) && !Platform.isAMac()) + { return; } @@ -1639,7 +1658,6 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); - stretchGroup = sg; if (av.getConservationSelected()) @@ -1671,6 +1689,37 @@ public class SeqPanel extends JPanel implements MouseListener, } /** + * Build and show a pop-up menu at the right-click mouse position + * + * @param evt + * @param res + * @param sequence + */ + void showPopupMenu(MouseEvent evt) + { + final int res = findRes(evt); + final int seq = findSeq(evt); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); + List allFeatures = ap.getFeatureRenderer() + .findFeaturesAtRes(sequence.getDatasetSequence(), + sequence.findPosition(res)); + List links = new ArrayList(); + for (SequenceFeature sf : allFeatures) + { + if (sf.links != null) + { + for (String link : sf.links) + { + links.add(link); + } + } + } + + PopupMenu pop = new PopupMenu(ap, null, links); + pop.show(this, evt.getX(), evt.getY()); + } + + /** * DOCUMENT ME! * * @param evt @@ -1682,9 +1731,10 @@ 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 && av.isSelectionDefinedGroup(); if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1702,8 +1752,8 @@ public class SeqPanel extends JPanel implements MouseListener, } } PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(true); - + ap.paintAlignment(needOverviewUpdate); + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1757,6 +1807,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1764,6 +1815,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1797,6 +1849,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } else { @@ -1806,6 +1859,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1947,28 +2001,28 @@ 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) { - Cache.log.warn("alignviewport av SeqSetId=" - + av.getSequenceSetId() + " ViewId=" + av.getViewId() + 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.isEmpty())) + 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) @@ -2061,7 +2115,6 @@ 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());