X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=fd3ca7687bf01b76c27e9e2a3fa5ea683c278197;hb=f9e86edb330898f638ab3713b9534e9b6364a3d4;hp=d588a32848247f61669f537555e98cb94df7d7f8;hpb=04320d3fca5c5aeb5aa319ccc0481b751da0dab9;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index d588a32..fd3ca76 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -27,13 +27,15 @@ import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; import jalview.datamodel.AlignmentI; import jalview.datamodel.ColumnSelection; +import jalview.datamodel.SearchResultMatchI; import jalview.datamodel.SearchResults; -import jalview.datamodel.SearchResults.Match; +import jalview.datamodel.SearchResultsI; import jalview.datamodel.Sequence; import jalview.datamodel.SequenceFeature; import jalview.datamodel.SequenceGroup; import jalview.datamodel.SequenceI; import jalview.io.SequenceAnnotationReport; +import jalview.renderer.ResidueShaderI; import jalview.schemes.ResidueProperties; import jalview.structure.SelectionListener; import jalview.structure.SelectionSource; @@ -43,6 +45,7 @@ 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; @@ -58,7 +61,6 @@ import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.List; -import javax.swing.JOptionPane; import javax.swing.JPanel; import javax.swing.SwingUtilities; import javax.swing.ToolTipManager; @@ -123,7 +125,7 @@ public class SeqPanel extends JPanel implements MouseListener, private final SequenceAnnotationReport seqARep; - StringBuffer tooltipText = new StringBuffer(); + StringBuilder tooltipText = new StringBuilder(); String tmpString; @@ -131,7 +133,7 @@ public class SeqPanel extends JPanel implements MouseListener, StructureSelectionManager ssm; - SearchResults lastSearchResults; + SearchResultsI lastSearchResults; /** * Creates a new SeqPanel object. @@ -207,7 +209,7 @@ public class SeqPanel extends JPanel implements MouseListener, } wrappedBlock = y / cHeight; - wrappedBlock += av.getStartRes() / cwidth; + wrappedBlock += av.getRanges().getStartRes() / cwidth; res = wrappedBlock * cwidth + x / av.getCharWidth(); @@ -220,11 +222,11 @@ public class SeqPanel extends JPanel implements MouseListener, // right-hand gutter x = seqCanvas.getX() + seqCanvas.getWidth(); } - res = (x / av.getCharWidth()) + av.getStartRes(); - if (res > av.getEndRes()) + res = (x / av.getCharWidth()) + av.getRanges().getStartRes(); + if (res > av.getRanges().getEndRes()) { // moused off right - res = av.getEndRes(); + res = av.getRanges().getEndRes(); } } @@ -260,7 +262,9 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - seq = Math.min((y / av.getCharHeight()) + av.getStartSeq(), av + seq = Math.min((y / av.getCharHeight()) + + av.getRanges().getStartSeq(), + av .getAlignment().getHeight() - 1); } @@ -383,18 +387,18 @@ public class SeqPanel extends JPanel implements MouseListener, } else { - while (seqCanvas.cursorY < av.startSeq) + while (seqCanvas.cursorY < av.getRanges().getStartSeq()) { ap.scrollUp(true); } - while (seqCanvas.cursorY + 1 > av.endSeq) + while (seqCanvas.cursorY + 1 > av.getRanges().getEndSeq()) { ap.scrollUp(false); } if (!av.getWrapAlignment()) { while (seqCanvas.cursorX < av.getColumnSelection() - .adjustForHiddenColumns(av.startRes)) + .adjustForHiddenColumns(av.getRanges().getStartRes())) { if (!ap.scrollRight(false)) { @@ -402,7 +406,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.endRes)) + .adjustForHiddenColumns(av.getRanges().getEndRes())) { if (!ap.scrollRight(true)) { @@ -582,6 +586,13 @@ 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 +619,14 @@ 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 { @@ -667,7 +679,7 @@ public class SeqPanel extends JPanel implements MouseListener, * the start of the highlighted region. */ @Override - public void highlightSequence(SearchResults results) + public void highlightSequence(SearchResultsI results) { if (results == null || results.equals(lastSearchResults)) { @@ -776,7 +788,7 @@ public class SeqPanel extends JPanel implements MouseListener, seqARep.appendFeatures(tooltipText, rpos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } - if (tooltipText.length() == 6) // + if (tooltipText.length() == 6) // { setToolTipText(null); lastTooltip = null; @@ -901,7 +913,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @param results */ - private void setStatusMessage(SearchResults results) + private void setStatusMessage(SearchResultsI results) { AlignmentI al = this.av.getAlignment(); int sequenceIndex = al.findIndex(results); @@ -910,7 +922,7 @@ public class SeqPanel extends JPanel implements MouseListener, return; } SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence(); - for (Match m : results.getResults()) + for (SearchResultMatchI m : results.getResults()) { SequenceI seq = m.getSequence(); if (seq.getDatasetSequence() != null) @@ -932,30 +944,36 @@ public class SeqPanel extends JPanel implements MouseListener, } /** - * DOCUMENT ME! - * - * @param evt - * DOCUMENT ME! + * {@inheritDoc} */ @Override public void mouseDragged(MouseEvent evt) { if (mouseWheelPressed) { + boolean inSplitFrame = ap.av.getCodingComplement() != null; + boolean copyChanges = inSplitFrame && av.isProteinFontAsCdna(); + int oldWidth = av.getCharWidth(); // Which is bigger, left-right or up-down? if (Math.abs(evt.getY() - lastMousePress.getY()) > Math.abs(evt .getX() - lastMousePress.getX())) { + /* + * on drag up or down, decrement or increment font size + */ int fontSize = av.font.getSize(); + boolean fontChanged = false; if (evt.getY() < lastMousePress.getY()) { + fontChanged = true; fontSize--; } else if (evt.getY() > lastMousePress.getY()) { + fontChanged = true; fontSize++; } @@ -964,24 +982,56 @@ public class SeqPanel extends JPanel implements MouseListener, fontSize = 1; } - av.setFont( - new Font(av.font.getName(), av.font.getStyle(), fontSize), - true); - av.setCharWidth(oldWidth); - ap.fontChanged(); + if (fontChanged) + { + Font newFont = new Font(av.font.getName(), av.font.getStyle(), + fontSize); + av.setFont(newFont, true); + av.setCharWidth(oldWidth); + ap.fontChanged(); + if (copyChanges) + { + ap.av.getCodingComplement().setFont(newFont, true); + SplitFrame splitFrame = (SplitFrame) ap.alignFrame + .getSplitViewContainer(); + splitFrame.adjustLayout(); + splitFrame.repaint(); + } + } } else { + /* + * on drag left or right, decrement or increment character width + */ + int newWidth = 0; if (evt.getX() < lastMousePress.getX() && av.getCharWidth() > 1) { - av.setCharWidth(av.getCharWidth() - 1); + newWidth = av.getCharWidth() - 1; + av.setCharWidth(newWidth); } else if (evt.getX() > lastMousePress.getX()) { - av.setCharWidth(av.getCharWidth() + 1); + newWidth = av.getCharWidth() + 1; + av.setCharWidth(newWidth); + } + if (newWidth > 0) + { + ap.paintAlignment(false); + if (copyChanges) + { + /* + * need to ensure newWidth is set on cdna, regardless of which + * panel the mouse drag happened in; protein will compute its + * character width as 1:1 or 3:1 + */ + av.getCodingComplement().setCharWidth(newWidth); + SplitFrame splitFrame = (SplitFrame) ap.alignFrame + .getSplitViewContainer(); + splitFrame.adjustLayout(); + splitFrame.repaint(); + } } - - ap.paintAlignment(false); } FontMetrics fm = getFontMetrics(av.getFont()); @@ -1492,7 +1542,7 @@ public class SeqPanel extends JPanel implements MouseListener, if (features != null && features.size() > 0) { - SearchResults highlight = new SearchResults(); + SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); @@ -1547,8 +1597,8 @@ 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; @@ -1556,10 +1606,10 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getWrapAlignment() && seq > av.getAlignment().getHeight()) { - JOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager + JvOptionPane.showInternalMessageDialog(Desktop.desktop, MessageManager .getString("label.cannot_edit_annotations_in_wrapped_view"), MessageManager.getString("label.wrapped_view_no_edit"), - JOptionPane.WARNING_MESSAGE); + JvOptionPane.WARNING_MESSAGE); return; } @@ -1577,63 +1627,30 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup = av.getSelectionGroup(); - if (stretchGroup == null) + if (stretchGroup == null || !stretchGroup.contains(sequence, res)) { - stretchGroup = av.getAlignment().findGroup(sequence); - - if ((stretchGroup != null) && (res > stretchGroup.getStartRes()) - && (res < stretchGroup.getEndRes())) + stretchGroup = av.getAlignment().findGroup(sequence, res); + if (stretchGroup != null) { + // only update the current selection if the popup menu has a group to + // focus on av.setSelectionGroup(stretchGroup); } - else - { - stretchGroup = null; - } } - else if (!stretchGroup.getSequences(null).contains(sequence) - || (stretchGroup.getStartRes() > res) - || (stretchGroup.getEndRes() < res)) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); - - if (allGroups != null) - { - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - stretchGroup = allGroups[i]; - break; - } - } - } - av.setSelectionGroup(stretchGroup); + if (evt.isPopupTrigger()) // Mac: mousePressed + { + showPopupMenu(evt); + return; } - if (evt.isPopupTrigger()) + /* + * 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()) { - 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()); return; } @@ -1659,15 +1676,16 @@ public class SeqPanel extends JPanel implements MouseListener, if (av.getConservationSelected()) { - SliderPanel.setConservationSlider(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } if (av.getAbovePIDThreshold()) { - SliderPanel.setPIDSliderSource(ap, av.getGlobalColourScheme(), - "Background"); + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); } + // TODO: stretchGroup will always be not null. Is this a merge error ? if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) { // Edit end res position of selected group @@ -1686,6 +1704,37 @@ 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 @@ -1706,20 +1755,20 @@ public class SeqPanel extends JPanel implements MouseListener, stretchGroup.cs.alignmentChanged(stretchGroup, av.getHiddenRepSequences()); + ResidueShaderI groupColourScheme = stretchGroup.getGroupColourScheme(); + String name = stretchGroup.getName(); if (stretchGroup.cs.conservationApplied()) { - SliderPanel.setConservationSlider(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setConservationSlider(ap, groupColourScheme, name); } - else + if (stretchGroup.cs.getThreshold() > 0) { - SliderPanel.setPIDSliderSource(ap, stretchGroup.cs, - stretchGroup.getName()); + SliderPanel.setPIDSliderSource(ap, groupColourScheme, name); } } PaintRefresher.Refresh(this, av.getSequenceSetId()); ap.paintAlignment(needOverviewUpdate); - needOverviewUpdate =false; + needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1763,9 +1812,9 @@ public class SeqPanel extends JPanel implements MouseListener, changeStartRes = true; } - if (res < av.getStartRes()) + if (res < av.getRanges().getStartRes()) { - res = av.getStartRes(); + res = av.getRanges().getStartRes(); } if (changeEndRes) @@ -1899,13 +1948,15 @@ public class SeqPanel extends JPanel implements MouseListener, { if (evt != null) { - if (mouseDragging && (evt.getY() < 0) && (av.getStartSeq() > 0)) + if (mouseDragging && (evt.getY() < 0) + && (av.getRanges().getStartSeq() > 0)) { running = ap.scrollUp(true); } if (mouseDragging && (evt.getY() >= getHeight()) - && (av.getAlignment().getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getRanges() + .getEndSeq())) { running = ap.scrollUp(false); } @@ -1979,8 +2030,8 @@ public class SeqPanel extends JPanel implements MouseListener, { 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; }