X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=3266fabf5631a665138d9e9f7feb574d451a8434;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=903f868c184d890f6636d58e903b5b9791dc2018;hpb=6b929eb6a01039353f35ce94c7606618e8d92284;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 903f868..3266fab 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; @@ -42,6 +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; @@ -54,11 +56,12 @@ 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; /** @@ -509,6 +512,7 @@ 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; @@ -579,6 +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); @@ -599,19 +610,20 @@ public class SeqPanel extends JPanel implements MouseListener, { lastMousePress = evt.getPoint(); - if (javax.swing.SwingUtilities.isMiddleMouseButton(evt)) + if (SwingUtilities.isMiddleMouseButton(evt)) { mouseWheelPressed = true; 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 { @@ -833,7 +845,8 @@ public class SeqPanel extends JPanel implements MouseListener, * 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 + // private boolean editingDefinedGroup = false; // TODO: refactor to + // avcontroller or viewModel /** * Set status message in alignment panel @@ -854,7 +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; /* @@ -1185,8 +1199,7 @@ 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; @@ -1248,7 +1261,7 @@ 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(); @@ -1380,7 +1393,7 @@ 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; @@ -1543,9 +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; @@ -1580,12 +1594,10 @@ 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) @@ -1604,35 +1616,27 @@ public class SeqPanel extends JPanel implements MouseListener, && (allGroups[i].getEndRes() >= res)) { stretchGroup = allGroups[i]; - editingDefinedGroup = true; break; } } } av.setSelectionGroup(stretchGroup); - } - if (javax.swing.SwingUtilities.isRightMouseButton(evt)) + if (evt.isPopupTrigger()) // Mac: mousePressed { - List allFeatures = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); - Vector links = new Vector(); - for (SequenceFeature sf : allFeatures) - { - if (sf.links != null) - { - for (int j = 0; j < sf.links.size(); j++) - { - links.addElement(sf.links.elementAt(j)); - } - } - } + showPopupMenu(evt); + return; + } - jalview.gui.PopupMenu pop = new jalview.gui.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; } @@ -1654,7 +1658,6 @@ public class SeqPanel extends JPanel implements MouseListener, sg.setEndRes(res); sg.addSequence(sequence, false); av.setSelectionGroup(sg); - editingDefinedGroup = false; stretchGroup = sg; if (av.getConservationSelected()) @@ -1686,6 +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 @@ -1700,7 +1734,7 @@ public class SeqPanel extends JPanel implements MouseListener, // 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; + needOverviewUpdate |= vischange && av.isSelectionDefinedGroup(); if (stretchGroup.cs != null) { stretchGroup.cs.alignmentChanged(stretchGroup, @@ -1719,8 +1753,7 @@ public class SeqPanel extends JPanel implements MouseListener, } PaintRefresher.Refresh(this, av.getSequenceSetId()); ap.paintAlignment(needOverviewUpdate); - needOverviewUpdate =false; - editingDefinedGroup = false; + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1774,7 +1807,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); - needOverviewUpdate |= editingDefinedGroup; + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1782,7 +1815,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); - needOverviewUpdate |= editingDefinedGroup; + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1816,7 +1849,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); - needOverviewUpdate |= editingDefinedGroup; + needOverviewUpdate |= av.isSelectionDefinedGroup(); } else { @@ -1826,7 +1859,7 @@ public class SeqPanel extends JPanel implements MouseListener, } stretchGroup.addSequence(nextSeq, false); - needOverviewUpdate |= editingDefinedGroup; + needOverviewUpdate |= av.isSelectionDefinedGroup(); } } @@ -1968,28 +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) { - jalview.bin.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) @@ -2082,7 +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());