X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=e11af48ce3d918dfe2c9a355a07fd2961df19c59;hb=refs%2Fheads%2Fbug%2FJAL-2831;hp=056a602768b5debbb85d18bc5de50ad6c7af523e;hpb=3d0101179759ef157b088ea135423cd909512d9f;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 056a602..e11af48 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -62,7 +62,6 @@ import java.awt.event.MouseWheelListener; import java.util.ArrayList; import java.util.Collections; import java.util.List; -import java.util.ListIterator; import javax.swing.JPanel; import javax.swing.SwingUtilities; @@ -85,6 +84,16 @@ public class SeqPanel extends JPanel /** DOCUMENT ME!! */ public AlignmentPanel ap; + /* + * last column position for mouseMoved event + */ + private int lastMouseColumn; + + /* + * last sequence offset for mouseMoved event + */ + private int lastMouseSeq; + protected int lastres; protected int startseq; @@ -171,6 +180,9 @@ public class SeqPanel extends JPanel ssm.addStructureViewerListener(this); ssm.addSelectionListener(this); } + + lastMouseColumn = -1; + lastMouseSeq = -1; } int startWrapBlock = -1; @@ -203,8 +215,8 @@ public class SeqPanel extends JPanel + hgap + seqCanvas.getAnnotationHeight(); int y = evt.getY(); - y -= hgap; - x = Math.max(0, x - seqCanvas.LABEL_WEST); + y = Math.max(0, y - hgap); + x = Math.max(0, x - seqCanvas.getLabelWidthWest()); int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); if (cwidth < 1) @@ -308,13 +320,13 @@ public class SeqPanel extends JPanel void setCursorRow() { seqCanvas.cursorY = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorColumn() { seqCanvas.cursorX = getKeyboardNo1() - 1; - scrollToVisible(); + scrollToVisible(true); } void setCursorRowAndColumn() @@ -327,7 +339,7 @@ public class SeqPanel extends JPanel { seqCanvas.cursorX = getKeyboardNo1() - 1; seqCanvas.cursorY = getKeyboardNo2() - 1; - scrollToVisible(); + scrollToVisible(true); } } @@ -336,7 +348,7 @@ public class SeqPanel extends JPanel SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); seqCanvas.cursorX = sequence.findIndex(getKeyboardNo1()) - 1; - scrollToVisible(); + scrollToVisible(true); } void moveCursor(int dx, int dy) @@ -364,10 +376,16 @@ public class SeqPanel extends JPanel } } - scrollToVisible(); + scrollToVisible(false); } - void scrollToVisible() + /** + * Scroll to make the cursor visible in the viewport. + * + * @param jump + * just jump to the location rather than scrolling + */ + void scrollToVisible(boolean jump) { if (seqCanvas.cursorX < 0) { @@ -388,20 +406,41 @@ public class SeqPanel extends JPanel } endEditing(); - if (av.getWrapAlignment()) + + boolean repaintNeeded = true; + if (jump) { - av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); + // only need to repaint if the viewport did not move, as otherwise it will + // get a repaint + repaintNeeded = !av.getRanges().setViewportLocation(seqCanvas.cursorX, + seqCanvas.cursorY); } else { - av.getRanges().scrollToVisible(seqCanvas.cursorX, seqCanvas.cursorY); + if (av.getWrapAlignment()) + { + av.getRanges().scrollToWrappedVisible(seqCanvas.cursorX); + } + else + { + av.getRanges().scrollToVisible(seqCanvas.cursorX, + seqCanvas.cursorY); + } } - setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), + + if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX)) + { + setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), seqCanvas.cursorX, seqCanvas.cursorY); + } - seqCanvas.repaint(); + if (repaintNeeded) + { + seqCanvas.repaint(); + } } + void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); @@ -472,7 +511,7 @@ public class SeqPanel extends JPanel av.setSelectionGroup(sg); } - ap.paintAlignment(false); + ap.paintAlignment(false, false); av.sendSelection(); } @@ -669,6 +708,8 @@ public class SeqPanel extends JPanel } lastSearchResults = results; + boolean wasScrolled = false; + if (av.isFollowHighlight()) { // don't allow highlight of protein/cDNA to also scroll a complementary @@ -676,14 +717,19 @@ public class SeqPanel extends JPanel // over residue to change abruptly, causing highlighted residue in panel 2 // to change, causing a scroll in panel 1 etc) ap.setToScrollComplementPanel(false); - if (ap.scrollToPosition(results, false)) + wasScrolled = ap.scrollToPosition(results, false); + if (wasScrolled) { seqCanvas.revalidate(); } ap.setToScrollComplementPanel(true); } - setStatusMessage(results); - seqCanvas.highlightSearchResults(results); + + boolean noFastPaint = wasScrolled && av.getWrapAlignment(); + if (seqCanvas.highlightSearchResults(results, noFastPaint)) + { + setStatusMessage(results); + } } @Override @@ -700,10 +746,12 @@ public class SeqPanel extends JPanel } /** - * DOCUMENT ME! + * Action on mouse movement is to update the status bar to show the current + * sequence position, and (if features are shown) to show any features at the + * position in a tooltip. Does nothing if the mouse move does not change + * residue position. * * @param evt - * DOCUMENT ME! */ @Override public void mouseMoved(MouseEvent evt) @@ -716,11 +764,22 @@ public class SeqPanel extends JPanel } final int column = findColumn(evt); - int seq = findSeq(evt); + final int seq = findSeq(evt); + if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight()) { + lastMouseSeq = -1; + return; + } + if (column == lastMouseColumn && seq == lastMouseSeq) + { + /* + * just a pixel move without change of residue + */ return; } + lastMouseColumn = column; + lastMouseSeq = seq; SequenceI sequence = av.getAlignment().getSequenceAt(seq); @@ -771,11 +830,7 @@ public class SeqPanel extends JPanel if (av.isShowSequenceFeatures()) { List features = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), pos); - if (isGapped) - { - removeAdjacentFeatures(features, column + 1, sequence); - } + .findFeaturesAtColumn(sequence, column + 1); seqARep.appendFeatures(tooltipText, pos, features, this.ap.getSeqPanel().seqCanvas.fr.getMinMax()); } @@ -786,45 +841,13 @@ public class SeqPanel extends JPanel } else { - if (lastTooltip == null - || !lastTooltip.equals(tooltipText.toString())) + String textString = tooltipText.toString(); + if (lastTooltip == null || !lastTooltip.equals(textString)) { - String formatedTooltipText = JvSwingUtils.wrapTooltip(true, - tooltipText.toString()); - // String formatedTooltipText = tooltipText.toString(); - setToolTipText(formatedTooltipText); - lastTooltip = tooltipText.toString(); - } - - } - - } - - /** - * 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. - * - * @param features - * @param column - * alignment column (1..) - * @param sequence - */ - protected void removeAdjacentFeatures(List features, - final int column, SequenceI sequence) - { - // TODO should this be an AlignViewController method (and reused by applet)? - 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(); + String formattedTooltipText = JvSwingUtils.wrapTooltip(true, + textString); + setToolTipText(formattedTooltipText); + lastTooltip = textString; } } } @@ -859,11 +882,12 @@ public class SeqPanel extends JPanel /** * 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 + * shading in overviews and structures to be recalculated. this could be + * changed to a something more expressive that indicates what actually has + * changed, so selective redraws can be applied (ie. only structures, only + * overview, etc) */ - private boolean needOverviewUpdate = false; // TODO: refactor to avcontroller + private boolean updateOverviewAndStructs = false; // TODO: refactor to avcontroller /** * set if av.getSelectionGroup() refers to a group that is defined on the @@ -883,19 +907,48 @@ public class SeqPanel extends JPanel * aligned sequence object * @param column * alignment column - * @param seq + * @param seqIndex * index of sequence in alignment * @return sequence position of residue at column, or adjacent residue if at a * gap */ - int setStatusMessage(SequenceI sequence, final int column, int seq) + int setStatusMessage(SequenceI sequence, final int column, int seqIndex) + { + char sequenceChar = sequence.getCharAt(column); + int pos = sequence.findPosition(column); + setStatusMessage(sequence, seqIndex, sequenceChar, pos); + + return pos; + } + + /** + * Builds the status message for the current cursor location and writes it to + * the status bar, for example + * + * 
+   * Sequence 3 ID: FER1_SOLLC
+   * Sequence 5 ID: FER1_PEA Residue: THR (4)
+   * Sequence 5 ID: FER1_PEA Residue: B (3)
+   * Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
+   *
+ * + * @param sequence + * @param seqIndex + * sequence position in the alignment (1..) + * @param sequenceChar + * the character under the cursor + * @param residuePos + * the sequence residue position (if not over a gap) + */ + protected void setStatusMessage(SequenceI sequence, int seqIndex, + char sequenceChar, int residuePos) { StringBuilder text = new StringBuilder(32); /* * Sequence number (if known), and sequence name. */ - String seqno = seq == -1 ? "" : " " + (seq + 1); + String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); text.append("Sequence").append(seqno).append(" ID: ") .append(sequence.getName()); @@ -904,13 +957,12 @@ public class SeqPanel extends JPanel /* * Try to translate the display character to residue name (null for gap). */ - final String displayChar = String.valueOf(sequence.getCharAt(column)); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); - int pos = sequence.findPosition(column); + boolean isGapped = Comparison.isGap(sequenceChar); if (!isGapped) { boolean nucleotide = av.getAlignment().isNucleotide(); + String displayChar = String.valueOf(sequenceChar); if (nucleotide) { residue = ResidueProperties.nucleotideName.get(displayChar); @@ -924,11 +976,9 @@ public class SeqPanel extends JPanel text.append(" ").append(nucleotide ? "Nucleotide" : "Residue") .append(": ").append(residue == null ? displayChar : residue); - text.append(" (").append(Integer.toString(pos)).append(")"); + text.append(" (").append(Integer.toString(residuePos)).append(")"); } ap.alignFrame.statusBar.setText(text.toString()); - - return pos; } /** @@ -956,12 +1006,9 @@ public class SeqPanel extends JPanel if (seq == ds) { - /* - * Convert position in sequence (base 1) to sequence character array - * index (base 0) - */ - int start = m.getStart() - m.getSequence().getStart(); - setStatusMessage(seq, start, sequenceIndex); + int start = m.getStart(); + setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1), + start); return; } } @@ -1041,7 +1088,7 @@ public class SeqPanel extends JPanel } if (newWidth > 0) { - ap.paintAlignment(false); + ap.paintAlignment(false, false); if (copyChanges) { /* @@ -1095,7 +1142,7 @@ public class SeqPanel extends JPanel } mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } @@ -1258,7 +1305,7 @@ public class SeqPanel extends JPanel // 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; @@ -1521,9 +1568,9 @@ public class SeqPanel extends JPanel oldSeq = 0; } - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } } @@ -1542,7 +1589,7 @@ public class SeqPanel extends JPanel return; } - if (mouseDragging) + if (mouseDragging && scrollThread == null) { scrollThread = new ScrollThread(); } @@ -1568,19 +1615,13 @@ public class SeqPanel extends JPanel } int column = findColumn(evt); - boolean isGapped = Comparison.isGap(sequence.getCharAt(column)); /* * find features at the position (if not gapped), or straddling * the position (if at a gap) */ List features = seqCanvas.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(column)); - if (isGapped) - { - removeAdjacentFeatures(features, column, sequence); - } + .findFeaturesAtColumn(sequence, column + 1); if (!features.isEmpty()) { @@ -1588,9 +1629,9 @@ public class SeqPanel extends JPanel * 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); + highlight.addResult(sequence, features.get(0).getBegin(), features + .get(0).getEnd()); + seqCanvas.highlightSearchResults(highlight, false); /* * open the Amend Features dialog; clear highlighting afterwards, @@ -1599,7 +1640,8 @@ public class SeqPanel extends JPanel List seqs = Collections.singletonList(sequence); seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, ap); - seqCanvas.highlightSearchResults(null); + av.setSearchResults(null); // clear highlighting + seqCanvas.repaint(); // draw new/amended features } } } @@ -1615,7 +1657,7 @@ public class SeqPanel extends JPanel av.getRanges().scrollRight(true); } - else if (!av.getWrapAlignment()) + else { av.getRanges().scrollUp(false); } @@ -1626,12 +1668,18 @@ public class SeqPanel extends JPanel { av.getRanges().scrollRight(false); } - else if (!av.getWrapAlignment()) + else { av.getRanges().scrollUp(true); } } - // TODO Update tooltip for new position. + + /* + * update status bar and tooltip for new position + * (need to synthesize a mouse movement to refresh tooltip) + */ + mouseMoved(e); + ToolTipManager.sharedInstance().mouseMoved(e); } /** @@ -1645,7 +1693,7 @@ public class SeqPanel extends JPanel final int res = findColumn(evt); final int seq = findSeq(evt); oldSeq = seq; - needOverviewUpdate = false; + updateOverviewAndStructs = false; startWrapBlock = wrappedBlock; @@ -1710,43 +1758,53 @@ public class SeqPanel extends JPanel if (stretchGroup == null) { - // Only if left mouse button do we want to change group sizes + createStretchGroup(res, sequence); + } - // define a new group here - SequenceGroup sg = new SequenceGroup(); - sg.setStartRes(res); - sg.setEndRes(res); - sg.addSequence(sequence, false); - av.setSelectionGroup(sg); - stretchGroup = sg; + if (stretchGroup != null) + { + stretchGroup.addPropertyChangeListener(seqCanvas); + } - if (av.getConservationSelected()) - { - SliderPanel.setConservationSlider(ap, av.getResidueShading(), - ap.getViewName()); - } + seqCanvas.repaint(); + } - if (av.getAbovePIDThreshold()) - { - 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 - changeEndRes = true; - } - else if ((stretchGroup != null) - && (stretchGroup.getStartRes() == res)) - { - // Edit end res position of selected group - changeStartRes = true; - } - stretchGroup.getWidth(); + private void createStretchGroup(int res, SequenceI sequence) + { + // Only if left mouse button do we want to change group sizes + // define a new group here + SequenceGroup sg = new SequenceGroup(); + sg.setStartRes(res); + sg.setEndRes(res); + sg.addSequence(sequence, false); + av.setSelectionGroup(sg); + stretchGroup = sg; + + if (av.getConservationSelected()) + { + SliderPanel.setConservationSlider(ap, av.getResidueShading(), + ap.getViewName()); } - seqCanvas.repaint(); + if (av.getAbovePIDThreshold()) + { + SliderPanel.setPIDSliderSource(ap, av.getResidueShading(), + ap.getViewName()); + } + // TODO: stretchGroup will always be not null. Is this a merge error ? + // or is there a threading issue here? + if ((stretchGroup != null) && (stretchGroup.getEndRes() == res)) + { + // Edit end res position of selected group + changeEndRes = true; + } + else if ((stretchGroup != null) && (stretchGroup.getStartRes() == res)) + { + // Edit end res position of selected group + changeStartRes = true; + } + stretchGroup.getWidth(); + } /** @@ -1758,12 +1816,11 @@ public class SeqPanel extends JPanel */ void showPopupMenu(MouseEvent evt) { - final int res = findColumn(evt); + final int column = findColumn(evt); final int seq = findSeq(evt); SequenceI sequence = av.getAlignment().getSequenceAt(seq); List allFeatures = ap.getFeatureRenderer() - .findFeaturesAtRes(sequence.getDatasetSequence(), - sequence.findPosition(res)); + .findFeaturesAtColumn(sequence, column + 1); List links = new ArrayList<>(); for (SequenceFeature sf : allFeatures) { @@ -1795,10 +1852,13 @@ public class SeqPanel extends JPanel { return; } + + stretchGroup.removePropertyChangeListener(seqCanvas); + // 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() + updateOverviewAndStructs |= vischange && av.isSelectionDefinedGroup() && afterDrag; if (stretchGroup.cs != null) { @@ -1818,8 +1878,10 @@ public class SeqPanel extends JPanel } } PaintRefresher.Refresh(this, av.getSequenceSetId()); - ap.paintAlignment(needOverviewUpdate); - needOverviewUpdate = false; + // TODO: structure colours only need updating if stretchGroup used to or now + // does contain sequences with structure views + ap.paintAlignment(updateOverviewAndStructs, updateOverviewAndStructs); + updateOverviewAndStructs = false; changeEndRes = false; changeStartRes = false; stretchGroup = null; @@ -1873,7 +1935,7 @@ public class SeqPanel extends JPanel if (res > (stretchGroup.getStartRes() - 1)) { stretchGroup.setEndRes(res); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } else if (changeStartRes) @@ -1881,7 +1943,7 @@ public class SeqPanel extends JPanel if (res < (stretchGroup.getEndRes() + 1)) { stretchGroup.setStartRes(res); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1915,7 +1977,7 @@ public class SeqPanel extends JPanel if (stretchGroup.getSequences(null).contains(nextSeq)) { stretchGroup.deleteSequence(seq, false); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } else { @@ -1925,7 +1987,7 @@ public class SeqPanel extends JPanel } stretchGroup.addSequence(nextSeq, false); - needOverviewUpdate |= av.isSelectionDefinedGroup(); + updateOverviewAndStructs |= av.isSelectionDefinedGroup(); } } @@ -1936,21 +1998,19 @@ public class SeqPanel extends JPanel mouseDragging = true; - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { scrollThread.setEvent(evt); } - - seqCanvas.repaint(); } void scrollCanvas(MouseEvent evt) { if (evt == null) { - if (scrollThread != null) + if ((scrollThread != null) && (scrollThread.isRunning())) { - scrollThread.running = false; + scrollThread.stopScrolling(); scrollThread = null; } mouseDragging = false; @@ -1973,7 +2033,7 @@ public class SeqPanel extends JPanel { MouseEvent evt; - boolean running = false; + private volatile boolean threadRunning = true; public ScrollThread() { @@ -1987,37 +2047,40 @@ public class SeqPanel extends JPanel public void stopScrolling() { - running = false; + threadRunning = false; + } + + public boolean isRunning() + { + return threadRunning; } @Override public void run() { - running = true; - - while (running) + while (threadRunning) { if (evt != null) { if (mouseDragging && (evt.getY() < 0) && (av.getRanges().getStartSeq() > 0)) { - running = av.getRanges().scrollUp(true); + av.getRanges().scrollUp(true); } if (mouseDragging && (evt.getY() >= getHeight()) && (av .getAlignment().getHeight() > av.getRanges().getEndSeq())) { - running = av.getRanges().scrollUp(false); + av.getRanges().scrollUp(false); } if (mouseDragging && (evt.getX() < 0)) { - running = av.getRanges().scrollRight(false); + av.getRanges().scrollRight(false); } else if (mouseDragging && (evt.getX() >= getWidth())) { - running = av.getRanges().scrollRight(true); + av.getRanges().scrollRight(true); } }