X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=1432fcb4e6688b30b4d7259b20ab882e37f1993c;hb=773ac00a0ac2eb882e993e567a650ee4d7df3dda;hp=5b87445e6c7ba060829d46be7009ea53a3d514dc;hpb=d2177decb24a93432ad55175b2123741bb3d8ac7;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 5b87445..1432fcb 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -35,6 +35,7 @@ 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; @@ -58,6 +59,7 @@ import java.awt.event.MouseMotionListener; import java.awt.event.MouseWheelEvent; import java.awt.event.MouseWheelListener; import java.util.ArrayList; +import java.util.Collections; import java.util.List; import javax.swing.JPanel; @@ -208,7 +210,7 @@ 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(); @@ -221,11 +223,11 @@ 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(); } } @@ -261,7 +263,9 @@ 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); } @@ -384,18 +388,18 @@ 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)) { @@ -403,7 +407,7 @@ public class SeqPanel extends JPanel implements MouseListener, } } while (seqCanvas.cursorX > av.getColumnSelection() - .adjustForHiddenColumns(av.endRes)) + .adjustForHiddenColumns(av.getRanges().getEndRes())) { if (!ap.scrollRight(true)) { @@ -1481,6 +1485,11 @@ public class SeqPanel extends JPanel implements MouseListener, } } + /** + * Handler for double-click on a position with one or more sequence features. + * Opens the Amend Features dialog to allow feature details to be amended, or + * the feature deleted. + */ @Override public void mouseClicked(MouseEvent evt) { @@ -1499,20 +1508,23 @@ public class SeqPanel extends JPanel implements MouseListener, .findFeaturesAtRes(sequence.getDatasetSequence(), sequence.findPosition(findRes(evt))); - if (features != null && features.size() > 0) + if (!features.isEmpty()) { + /* + * highlight the first feature at the position on the alignment + */ SearchResultsI highlight = new SearchResults(); highlight.addResult(sequence, features.get(0).getBegin(), features .get(0).getEnd()); seqCanvas.highlightSearchResults(highlight); - } - if (features != null && features.size() > 0) - { - seqCanvas.getFeatureRenderer().amendFeatures( - new SequenceI[] { sequence }, - features.toArray(new SequenceFeature[features.size()]), - false, ap); + /* + * open the Amend Features dialog; clear highlighting afterwards, + * whether changes were made or not + */ + List seqs = Collections.singletonList(sequence); + seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, + ap, null); seqCanvas.highlightSearchResults(null); } } @@ -1586,34 +1598,15 @@ 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, res); - av.setSelectionGroup(stretchGroup); - } - if (stretchGroup == null - || !stretchGroup.getSequences(null).contains(sequence) - || (stretchGroup.getStartRes() > res) - || (stretchGroup.getEndRes() < res)) - { - stretchGroup = null; - - SequenceGroup[] allGroups = av.getAlignment().findAllGroups(sequence); - - if (allGroups != null) + if (stretchGroup != null) { - for (int i = 0; i < allGroups.length; i++) - { - if ((allGroups[i].getStartRes() <= res) - && (allGroups[i].getEndRes() >= res)) - { - stretchGroup = allGroups[i]; - break; - } - } + // only update the current selection if the popup menu has a group to + // focus on + av.setSelectionGroup(stretchGroup); } - - av.setSelectionGroup(stretchGroup); } if (evt.isPopupTrigger()) // Mac: mousePressed @@ -1654,15 +1647,16 @@ 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 @@ -1685,7 +1679,7 @@ public class SeqPanel extends JPanel implements MouseListener, * * @param evt * @param res - * @param sequence + * @param sequences */ void showPopupMenu(MouseEvent evt) { @@ -1732,15 +1726,15 @@ 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()); @@ -1789,9 +1783,9 @@ 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) @@ -1925,13 +1919,15 @@ 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); } @@ -1969,9 +1965,20 @@ public class SeqPanel extends JPanel implements MouseListener, // shared between viewports. boolean iSentTheSelection = (av == source || (source instanceof AlignViewport && ((AlignmentViewport) source) .getSequenceSetId().equals(av.getSequenceSetId()))); - if (iSentTheSelection || !av.followSelection) + + if (iSentTheSelection) { - return; + // respond to our own event by updating dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + + // process further ? + if (!av.followSelection) + { + return; + } } /* @@ -2069,6 +2076,13 @@ public class SeqPanel extends JPanel implements MouseListener, PaintRefresher.Refresh(this, av.getSequenceSetId()); // ap.paintAlignment(false); } + + // lastly, update dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + } /** @@ -2108,6 +2122,12 @@ public class SeqPanel extends JPanel implements MouseListener, av); av.setColumnSelection(cs); + // lastly, update any dependent dialogs + if (ap.getCalculationDialog() != null) + { + ap.getCalculationDialog().validateCalcTypes(); + } + PaintRefresher.Refresh(this, av.getSequenceSetId()); return true;