X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FSeqPanel.java;h=9a61f5fc350998c2a81a637ae530c427b9e5f20b;hb=dc1488c10064504e3919e8b6b24218cc032e3ba3;hp=57bfa685275457b5d0ac2fb68ae708e3b863a222;hpb=2ca31c294c758a1f7e6c314ff671ddd03f937e60;p=jalview.git diff --git a/src/jalview/appletgui/SeqPanel.java b/src/jalview/appletgui/SeqPanel.java index 57bfa68..9a61f5f 100644 --- a/src/jalview/appletgui/SeqPanel.java +++ b/src/jalview/appletgui/SeqPanel.java @@ -54,10 +54,8 @@ import java.awt.event.InputEvent; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; -import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.ListIterator; import java.util.Vector; public class SeqPanel extends Panel implements MouseMotionListener, @@ -337,7 +335,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, sg.addSequence(sequence, false); av.setSelectionGroup(sg); } - ap.paintAlignment(false); + ap.paintAlignment(false, false); av.sendSelection(); } @@ -419,7 +417,6 @@ public class SeqPanel extends Panel implements MouseMotionListener, * alignment column * @param seq * index of sequence in alignment - * @return position of column in sequence or -1 if at gap */ void setStatusMessage(SequenceI sequence, int column, int seq) { @@ -530,7 +527,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < 0 || res < 0) { @@ -566,14 +563,9 @@ public class SeqPanel extends Panel implements MouseMotionListener, av.setSelectionGroup(null); } - int column = findRes(evt); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); - List features = findFeaturesAtRes(sequence, - sequence.findPosition(column)); - if (isGapped) - { - removeAdjacentFeatures(features, column + 1, sequence); - } + int column = findColumn(evt); + List features = findFeaturesAtColumn(sequence, + column + 1); if (!features.isEmpty()) { @@ -583,8 +575,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, seqCanvas.highlightSearchResults(highlight); seqCanvas.getFeatureRenderer().amendFeatures( Collections.singletonList(sequence), features, false, ap); - - seqCanvas.highlightSearchResults(null); + av.setSearchResults(null); // clear highlighting + seqCanvas.repaint(); // draw new/amended features } } } @@ -610,7 +602,14 @@ public class SeqPanel extends Panel implements MouseMotionListener, int wrappedBlock = -1; - int findRes(MouseEvent evt) + /** + * Returns the aligned sequence position (base 0) at the mouse position, or + * the closest visible one + * + * @param evt + * @return + */ + int findColumn(MouseEvent evt) { int res = 0; int x = evt.getX(); @@ -714,7 +713,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { int seq = findSeq(evt); - int res = findRes(evt); + int res = findColumn(evt); if (seq < av.getAlignment().getHeight() && res < av.getAlignment().getSequenceAt(seq).getLength()) @@ -786,7 +785,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, @Override public void mouseMoved(MouseEvent evt) { - final int column = findRes(evt); + final int column = findColumn(evt); int seq = findSeq(evt); if (seq >= av.getAlignment().getHeight() || seq < 0 || column < 0) @@ -869,12 +868,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, */ if (av.isShowSequenceFeatures()) { - List allFeatures = findFeaturesAtRes(sequence, - sequence.findPosition(column)); - if (isGapped) - { - removeAdjacentFeatures(allFeatures, column + 1, sequence); - } + List allFeatures = findFeaturesAtColumn(sequence, + column + 1); for (SequenceFeature sf : allFeatures) { tooltipText.append(sf.getType() + " " + sf.begin + ":" + sf.end); @@ -907,63 +902,18 @@ public class SeqPanel extends Panel implements MouseMotionListener, } /** - * Removes from the list of features any that start after, or end before, the - * given column position. This allows us to retain only those features - * adjacent to a gapped position that straddle the position. Contact features - * that 'straddle' the position are also removed, since they are not 'at' the - * position. + * Returns features at the specified aligned column on the given sequence. + * Non-positional features are not included. If the column has a gap, then + * enclosing features are included (but not contact features). * - * @param features - * @param column - * alignment column (1..) * @param sequence + * @param column + * (1..) + * @return */ - protected void removeAdjacentFeatures(List features, - int column, SequenceI sequence) + List findFeaturesAtColumn(SequenceI sequence, int column) { - // TODO should this be an AlignViewController method (shared by gui)? - ListIterator it = features.listIterator(); - while (it.hasNext()) - { - SequenceFeature sf = it.next(); - if (sf.isContactFeature() - || sequence.findIndex(sf.getBegin()) > column - || sequence.findIndex(sf.getEnd()) < column) - { - it.remove(); - } - } - } - - List findFeaturesAtRes(SequenceI sequence, int res) - { - List result = new ArrayList<>(); - SequenceFeature[] features = sequence.getSequenceFeatures(); - if (features != null) - { - for (int i = 0; i < features.length; i++) - { - if (av.getFeaturesDisplayed() == null || !av.getFeaturesDisplayed() - .isVisible(features[i].getType())) - { - continue; - } - - if (features[i].featureGroup != null && !seqCanvas.fr - .checkGroupVisibility(features[i].featureGroup, false)) - { - continue; - } - - if ((features[i].getBegin() <= res) - && (features[i].getEnd() >= res)) - { - result.add(features[i]); - } - } - } - - return result; + return seqCanvas.getFeatureRenderer().findFeaturesAtColumn(sequence, column); } Tooltip tooltip; @@ -1032,7 +982,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, lastMousePress = evt.getPoint(); - ap.paintAlignment(false); + ap.paintAlignment(false, false); ap.annotationPanel.image = null; return; } @@ -1043,7 +993,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, return; } - int res = findRes(evt); + int res = findColumn(evt); if (res < 0) { @@ -1225,7 +1175,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, // Find the next gap before the end // of the visible region boundary boolean blank = false; - for (fixedRight = fixedRight; fixedRight > lastres; fixedRight--) + for (; fixedRight > lastres; fixedRight--) { blank = true; @@ -1455,7 +1405,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, scrollThread = null; } - int res = findRes(evt); + int column = findColumn(evt); int seq = findSeq(evt); oldSeq = seq; startWrapBlock = wrappedBlock; @@ -1467,16 +1417,16 @@ public class SeqPanel extends Panel implements MouseMotionListener, SequenceI sequence = av.getAlignment().getSequenceAt(seq); - if (sequence == null || res > sequence.getLength()) + if (sequence == null || column > sequence.getLength()) { return; } stretchGroup = av.getSelectionGroup(); - if (stretchGroup == null || !stretchGroup.contains(sequence, res)) + if (stretchGroup == null || !stretchGroup.contains(sequence, column)) { - stretchGroup = av.getAlignment().findGroup(sequence, res); + stretchGroup = av.getAlignment().findGroup(sequence, column); if (stretchGroup != null) { // only update the current selection if the popup menu has a group to @@ -1489,8 +1439,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK) { - List allFeatures = findFeaturesAtRes(sequence, - sequence.findPosition(res)); + List allFeatures = findFeaturesAtColumn(sequence, + sequence.findPosition(column + 1)); Vector links = null; for (SequenceFeature sf : allFeatures) @@ -1501,10 +1451,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, { links = new Vector<>(); } - for (int j = 0; j < sf.links.size(); j++) - { - links.addElement(sf.links.elementAt(j)); - } + links.addAll(sf.links); } } APopupMenu popup = new APopupMenu(ap, null, links); @@ -1515,7 +1462,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, if (av.cursorMode) { - seqCanvas.cursorX = findRes(evt); + seqCanvas.cursorX = findColumn(evt); seqCanvas.cursorY = findSeq(evt); seqCanvas.repaint(); return; @@ -1527,8 +1474,8 @@ public class SeqPanel extends Panel implements MouseMotionListener, { // define a new group here SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); + sg.setStartRes(column); + sg.setEndRes(column); sg.addSequence(sequence, false); av.setSelectionGroup(sg); stretchGroup = sg; @@ -1576,7 +1523,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, } } PaintRefresher.Refresh(ap, av.getSequenceSetId()); - ap.paintAlignment(needOverviewUpdate); + ap.paintAlignment(needOverviewUpdate, needOverviewUpdate); needOverviewUpdate = false; changeEndRes = false; changeStartRes = false; @@ -1586,7 +1533,7 @@ public class SeqPanel extends Panel implements MouseMotionListener, public void doMouseDraggedDefineMode(MouseEvent evt) { - int res = findRes(evt); + int res = findColumn(evt); int y = findSeq(evt); if (wrappedBlock != startWrapBlock)