X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2caea17d01aabf8bb9af9bd7c6d5935f0486412e;hb=eb3e681d6e82ccdd5d312d1981dfb306e7f479f0;hp=407acd604947876413118cbd9b4df130fb679fc8;hpb=182633dda3eeb2c46366789855e8be509238ba17;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index 407acd6..2caea17 100644 --- a/src/jalview/gui/SeqPanel.java +++ b/src/jalview/gui/SeqPanel.java @@ -25,6 +25,8 @@ import java.awt.Color; import java.awt.Font; import java.awt.FontMetrics; import java.awt.Point; +import java.awt.event.ActionEvent; +import java.awt.event.ActionListener; import java.awt.event.MouseEvent; import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; @@ -34,12 +36,15 @@ import java.util.ArrayList; import java.util.Collections; import java.util.List; +import javax.swing.JLabel; import javax.swing.JPanel; +import javax.swing.JToolTip; import javax.swing.SwingUtilities; +import javax.swing.Timer; import javax.swing.ToolTipManager; import jalview.api.AlignViewportI; -import jalview.bin.Cache; +import jalview.bin.Console; import jalview.commands.EditCommand; import jalview.commands.EditCommand.Action; import jalview.commands.EditCommand.Edit; @@ -132,7 +137,7 @@ public class SeqPanel extends JPanel MousePos o = (MousePos) obj; boolean b = (column == o.column && seqIndex == o.seqIndex && annotationIndex == o.annotationIndex); - // System.out.println(obj + (b ? "= " : "!= ") + this); + // jalview.bin.Console.outPrintln(obj + (b ? "= " : "!= ") + this); return b; } @@ -209,9 +214,19 @@ public class SeqPanel extends JPanel private final SequenceAnnotationReport seqARep; - StringBuilder tooltipText = new StringBuilder(); + /* + * the last tooltip on mousing over the alignment (or annotation in wrapped mode) + * - the tooltip is not set again if unchanged + * - this is the tooltip text _before_ formatting as html + */ + private String lastTooltip; - String tmpString; + /* + * the last tooltip on mousing over the alignment (or annotation in wrapped mode) + * - used to decide where to place the tooltip in getTooltipLocation() + * - this is the tooltip text _after_ formatting as html + */ + private String lastFormattedTooltip; EditCommand editCommand; @@ -231,6 +246,7 @@ public class SeqPanel extends JPanel ToolTipManager.sharedInstance().registerComponent(this); ToolTipManager.sharedInstance().setInitialDelay(0); ToolTipManager.sharedInstance().setDismissDelay(10000); + this.av = viewport; setBackground(Color.white); @@ -258,6 +274,9 @@ public class SeqPanel extends JPanel /** * Computes the column and sequence row (and possibly annotation row when in * wrapped mode) for the given mouse position + *

+ * Mouse position is not set if in wrapped mode with the cursor either between + * sequences, or over the left or right vertical scale. * * @param evt * @return @@ -322,15 +341,39 @@ public class SeqPanel extends JPanel return new MousePos(col, seqIndex, annIndex); } + + /** + * @param evt + * @return absolute column in alignment nearest to the mouse pointer + */ + int findAlignmentColumn(MouseEvent evt) + { + return findNearestColumn(evt, true); + } + /** * Returns the aligned sequence position (base 0) at the mouse position, or * the closest visible one + *

+ * Returns -1 if in wrapped mode with the mouse over either left or right + * vertical scale. * * @param evt * @return */ int findColumn(MouseEvent evt) { + return findNearestColumn(evt, false); + } + + /** + * @param nearestColumn + * when false returns negative values for out of bound positions - -1 + * for scale left/right, <-1 if far to right + * @return nearest absolute column to mouse pointer + */ + private int findNearestColumn(MouseEvent evt, boolean nearestColumn) + { int res = 0; int x = evt.getX(); @@ -354,7 +397,14 @@ public class SeqPanel extends JPanel if (x < 0) { // mouse is over left scale - return -1; + if (!nearestColumn) + { + return -1; + } + else + { + x = 0; + } } int cwidth = seqCanvas.getWrappedCanvasWidth(this.getWidth()); @@ -364,8 +414,15 @@ public class SeqPanel extends JPanel } if (x >= cwidth * charWidth) { - // mouse is over right scale - return -1; + if (!nearestColumn) + { + // mouse is over right scale + return -1; + } + else + { + x = cwidth * charWidth - 1; + } } wrappedBlock = y / cHeight; @@ -382,8 +439,14 @@ public class SeqPanel extends JPanel * rather than right-hand gutter */ x = Math.min(x, seqCanvas.getX() + seqCanvas.getWidth()); + if (nearestColumn) + { + x = Math.max(x, 0); + } + res = (x / charWidth) + startRes; res = Math.min(res, av.getRanges().getEndRes()); + } if (av.hasHiddenColumns()) @@ -460,8 +523,9 @@ public class SeqPanel extends JPanel void moveCursor(int dx, int dy) { - moveCursor(dx, dy,false); + moveCursor(dx, dy, false); } + void moveCursor(int dx, int dy, boolean nextWord) { HiddenColumns hidden = av.getAlignment().getHiddenColumns(); @@ -469,11 +533,13 @@ public class SeqPanel extends JPanel if (nextWord) { int maxWidth = av.getAlignment().getWidth(); - int maxHeight=av.getAlignment().getHeight(); - SequenceI seqAtRow = av.getAlignment().getSequenceAt(seqCanvas.cursorY); + int maxHeight = av.getAlignment().getHeight(); + SequenceI seqAtRow = av.getAlignment() + .getSequenceAt(seqCanvas.cursorY); // look for next gap or residue - boolean isGap = Comparison.isGap(seqAtRow.getCharAt(seqCanvas.cursorX)); - int p = seqCanvas.cursorX,lastP,r=seqCanvas.cursorY,lastR; + boolean isGap = Comparison + .isGap(seqAtRow.getCharAt(seqCanvas.cursorX)); + int p = seqCanvas.cursorX, lastP, r = seqCanvas.cursorY, lastR; do { lastP = p; @@ -494,19 +560,23 @@ public class SeqPanel extends JPanel p = nextVisible(hidden, maxWidth, p, dx); } while ((dx != 0 ? p != lastP : r != lastR) && isGap == Comparison.isGap(seqAtRow.getCharAt(p))); - seqCanvas.cursorX=p; - seqCanvas.cursorY=r; - } else { + seqCanvas.cursorX = p; + seqCanvas.cursorY = r; + } + else + { int maxWidth = av.getAlignment().getWidth(); - seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, dx); + seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX, + dx); seqCanvas.cursorY += dy; } scrollToVisible(false); } - private int nextVisible(HiddenColumns hidden,int maxWidth, int original, int dx) + private int nextVisible(HiddenColumns hidden, int maxWidth, int original, + int dx) { - int newCursorX=original+dx; + int newCursorX = original + dx; if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX)) { int visx = hidden.absoluteToVisibleColumn(newCursorX - dx); @@ -527,13 +597,13 @@ public class SeqPanel extends JPanel } } newCursorX = (newCursorX < 0) ? 0 : newCursorX; - if (newCursorX >= maxWidth - || !hidden.isVisible(newCursorX)) + if (newCursorX >= maxWidth || !hidden.isVisible(newCursorX)) { newCursorX = original; } return newCursorX; } + /** * Scroll to make the cursor visible in the viewport. * @@ -589,7 +659,7 @@ public class SeqPanel extends JPanel if (av.getAlignment().getHiddenColumns().isVisible(seqCanvas.cursorX)) { setStatusMessage(av.getAlignment().getSequenceAt(seqCanvas.cursorY), - seqCanvas.cursorX, seqCanvas.cursorY); + seqCanvas.cursorX, seqCanvas.cursorY); } if (repaintNeeded) @@ -598,7 +668,6 @@ public class SeqPanel extends JPanel } } - void setSelectionAreaAtCursor(boolean topLeft) { SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY); @@ -852,7 +921,7 @@ public class SeqPanel extends JPanel if (lastMessage == null || !lastMessage.equals(tmp)) { - // System.err.println("mouseOver Sequence: "+tmp); + // jalview.bin.Console.errPrintln("mouseOver Sequence: "+tmp); ssm.mouseOverSequence(sequence, index, pos, av); } lastMessage = tmp; @@ -890,13 +959,12 @@ public class SeqPanel extends JPanel ap.setToScrollComplementPanel(true); } - boolean noFastPaint = wasScrolled && av.getWrapAlignment(); - if (seqCanvas.highlightSearchResults(results, noFastPaint)) + boolean fastPaint = !(wasScrolled && av.getWrapAlignment()); + if (seqCanvas.highlightSearchResults(results, fastPaint)) { setStatusMessage(results); } - // JAL-3303 feature suppressed for now pending review - return null; // results.isEmpty() ? null : getHighlightInfo(results); + return results.isEmpty() ? null : getHighlightInfo(results); } /** @@ -926,19 +994,19 @@ public class SeqPanel extends JPanel AlignFrame af = Desktop.getAlignFrameFor(complement); FeatureRendererModel fr2 = af.getFeatureRenderer(); - int j = results.getSize(); + List matches = results.getResults(); + int j = matches.size(); List infos = new ArrayList<>(); for (int i = 0; i < j; i++) { - SearchResultMatchI match = results.getResults().get(i); + SearchResultMatchI match = matches.get(i); int pos = match.getStart(); if (pos == match.getEnd()) { SequenceI seq = match.getSequence(); SequenceI ds = seq.getDatasetSequence() == null ? seq : seq.getDatasetSequence(); - MappedFeatures mf = fr2 - .findComplementFeaturesAtResidue(ds, pos); + MappedFeatures mf = fr2.findComplementFeaturesAtResidue(ds, pos); if (mf != null) { for (SequenceFeature sf : mf.features) @@ -978,7 +1046,7 @@ public class SeqPanel extends JPanel @Override public void updateColours(SequenceI seq, int index) { - System.out.println("update the seqPanel colours"); + jalview.bin.Console.outPrintln("update the seqPanel colours"); // repaint(); } @@ -1006,8 +1074,10 @@ public class SeqPanel extends JPanel /* * just a pixel move without change of 'cell' */ + moveTooltip = false; return; } + moveTooltip = true; lastMousePosition = mousePos; if (mousePos.isOverAnnotation()) @@ -1023,6 +1093,7 @@ public class SeqPanel extends JPanel lastMousePosition = null; setToolTipText(null); lastTooltip = null; + lastFormattedTooltip = null; ap.alignFrame.setStatus(""); return; } @@ -1044,7 +1115,7 @@ public class SeqPanel extends JPanel mouseOverSequence(sequence, column, pos); } - tooltipText.setLength(6); // Cuts the buffer back to + StringBuilder tooltipText = new StringBuilder(64); SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence); if (groups != null) @@ -1078,9 +1149,8 @@ public class SeqPanel extends JPanel { List features = ap.getFeatureRenderer() .findFeaturesAtColumn(sequence, column + 1); - unshownFeatures = seqARep.appendFeatures(tooltipText, pos, - features, this.ap.getSeqPanel().seqCanvas.fr, - MAX_TOOLTIP_LENGTH); + unshownFeatures = seqARep.appendFeatures(tooltipText, pos, features, + this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH); /* * add features in CDS/protein complement at the corresponding @@ -1098,13 +1168,13 @@ public class SeqPanel extends JPanel pos); if (mf != null) { - unshownFeatures = seqARep.appendFeatures(tooltipText, - pos, mf, fr2, MAX_TOOLTIP_LENGTH); + unshownFeatures += seqARep.appendFeatures(tooltipText, pos, mf, + fr2, MAX_TOOLTIP_LENGTH); } } } } - if (tooltipText.length() == 6) // "" + if (tooltipText.length() == 0) // nothing added { setToolTipText(null); lastTooltip = null; @@ -1124,12 +1194,11 @@ public class SeqPanel extends JPanel .append(""); } String textString = tooltipText.toString(); - if (lastTooltip == null || !lastTooltip.equals(textString)) + if (!textString.equals(lastTooltip)) { - String formattedTooltipText = JvSwingUtils.wrapTooltip(true, - textString); - setToolTipText(formattedTooltipText); lastTooltip = textString; + lastFormattedTooltip = JvSwingUtils.wrapTooltip(true, textString); + setToolTipText(lastFormattedTooltip); } } } @@ -1146,6 +1215,7 @@ public class SeqPanel extends JPanel final int column = pos.column; final int rowIndex = pos.annotationIndex; + // TODO - get yOffset for annotation, too if (column < 0 || !av.getWrapAlignment() || !av.isShowAnnotation() || rowIndex < 0) { @@ -1154,16 +1224,37 @@ public class SeqPanel extends JPanel AlignmentAnnotation[] anns = av.getAlignment().getAlignmentAnnotation(); String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column, - anns); - setToolTipText(tooltip); - lastTooltip = tooltip; + anns, 0, av, ap); + if (tooltip == null ? tooltip != lastTooltip + : !tooltip.equals(lastTooltip)) + { + lastTooltip = tooltip; + lastFormattedTooltip = tooltip == null ? null + : JvSwingUtils.wrapTooltip(true, tooltip); + setToolTipText(lastFormattedTooltip); + } String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column, - anns[rowIndex]); + anns[rowIndex], 0, av); ap.alignFrame.setStatus(msg); } - private Point lastp = null; + /* + * if Shift key is held down while moving the mouse, + * the tooltip location is not changed once shown + */ + private Point lastTooltipLocation = null; + + /* + * this flag is false for pixel moves within a residue, + * to reduce tooltip flicker + */ + private boolean moveTooltip = true; + + /* + * a dummy tooltip used to estimate where to position tooltips + */ + private JToolTip tempTip = new JLabel().createToolTip(); /* * (non-Javadoc) @@ -1173,29 +1264,31 @@ public class SeqPanel extends JPanel @Override public Point getToolTipLocation(MouseEvent event) { - if (tooltipText == null || tooltipText.length() <= 6) + // BH 2018 + + if (lastTooltip == null || !moveTooltip) { - lastp = null; return null; } - int x = event.getX(); - int w = getWidth(); - // switch sides when tooltip is too close to edge - int wdth = (w - x < 200) ? -(w / 2) : 5; - Point p = lastp; - if (!event.isShiftDown() || p == null) + if (lastTooltipLocation != null && event.isShiftDown()) { - p = new Point(event.getX() + wdth, event.getY() - 20); - lastp = p; + return lastTooltipLocation; } - /* - * TODO: try to set position so region is not obscured by tooltip - */ - return p; - } - String lastTooltip; + int x = event.getX(); + int y = event.getY(); + int w = getWidth(); + + tempTip.setTipText(lastFormattedTooltip); + int tipWidth = (int) tempTip.getPreferredSize().getWidth(); + + // was x += (w - x < 200) ? -(w / 2) : 5; + x = (x + tipWidth < w ? x + 10 : w - tipWidth); + Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20? + + return lastTooltipLocation = p; + } /** * set when the current UI interaction has resulted in a change that requires @@ -1204,7 +1297,8 @@ public class SeqPanel extends JPanel * changed, so selective redraws can be applied (ie. only structures, only * overview, etc) */ - private boolean updateOverviewAndStructs = 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 @@ -1266,8 +1360,7 @@ public class SeqPanel extends JPanel * Sequence number (if known), and sequence name. */ String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1); - text.append("Sequence").append(seqno).append(" ID: ") - .append(seqName); + text.append("Sequence").append(seqno).append(" ID: ").append(seqName); String residue = null; @@ -1526,12 +1619,12 @@ public class SeqPanel extends JPanel String label = null; if (groupEditing) { - message.append("Edit group:"); + message.append("Edit group:"); label = MessageManager.getString("action.edit_group"); } else { - message.append("Edit sequence: " + seq.getName()); + message.append("Edit sequence: " + seq.getName()); label = seq.getName(); if (label.length() > 10) { @@ -1723,8 +1816,7 @@ public class SeqPanel extends JPanel { for (int j = 0; j < startres - editLastRes; j++) { - if (!Comparison - .isGap(groupSeqs[g].getCharAt(fixedRight - j))) + if (!Comparison.isGap(groupSeqs[g].getCharAt(fixedRight - j))) { blank = false; break; @@ -2072,7 +2164,7 @@ public class SeqPanel extends JPanel if (mouseDragging && scrollThread == null) { - scrollThread = new ScrollThread(); + startScrolling(e.getPoint()); } } @@ -2116,19 +2208,15 @@ 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, false); + highlight.addResult(sequence, features.get(0).getBegin(), + features.get(0).getEnd()); + seqCanvas.highlightSearchResults(highlight, true); /* - * open the Amend Features dialog; clear highlighting afterwards, - * whether changes were made or not + * open the Amend Features dialog */ - List seqs = Collections.singletonList(sequence); - seqCanvas.getFeatureRenderer().amendFeatures(seqs, features, false, - ap); - av.setSearchResults(null); // clear highlighting - seqCanvas.repaint(); // draw new/amended features + new FeatureEditor(ap, Collections.singletonList(sequence), features, + false).showDialog(); } } } @@ -2210,19 +2298,19 @@ public class SeqPanel extends JPanel } } - if (evt.isPopupTrigger()) // Mac: mousePressed - { - showPopupMenu(evt, pos); - return; - } - /* * 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()) + if (Platform.isWinRightButton(evt)) + { + return; + } + + if (evt.isPopupTrigger()) // Mac: mousePressed { + showPopupMenu(evt, pos); return; } @@ -2385,7 +2473,7 @@ public class SeqPanel extends JPanel return; } - res = Math.min(res, av.getAlignment().getWidth()-1); + res = Math.min(res, av.getAlignment().getWidth() - 1); if (stretchGroup.getEndRes() == res) { @@ -2518,29 +2606,73 @@ public class SeqPanel extends JPanel /** * Starts a thread to scroll the alignment, towards a given mouse position - * outside the panel bounds + * outside the panel bounds, unless the alignment is in wrapped mode * * @param mousePos */ void startScrolling(Point mousePos) { - if (scrollThread == null) + /* + * set this.mouseDragging in case this was called from + * a drag in ScalePanel or AnnotationPanel + */ + mouseDragging = true; + if (!av.getWrapAlignment() && scrollThread == null) { scrollThread = new ScrollThread(); + scrollThread.setMousePosition(mousePos); + if (Platform.isJS()) + { + /* + * Javascript - run every 20ms until scrolling stopped + * or reaches the limit of scrollable alignment + */ + Timer t = new Timer(20, new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (scrollThread != null) + { + // if (!scrollOnce() {t.stop();}) gives compiler error :-( + scrollThread.scrollOnce(); + } + } + }); + t.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + if (scrollThread == null) + { + // SeqPanel.stopScrolling called + t.stop(); + } + } + }); + t.start(); + } + else + { + /* + * Java - run in a new thread + */ + scrollThread.start(); + } } - - mouseDragging = true; - scrollThread.setMousePosition(mousePos); } /** - * Performs scrolling of the visible alignment left, right, up or down + * Performs scrolling of the visible alignment left, right, up or down, until + * scrolling is stopped by calling stopScrolling, mouse drag is ended, or the + * limit of the alignment is reached */ class ScrollThread extends Thread { private Point mousePos; - private volatile boolean threadRunning = true; + private volatile boolean keepRunning = true; /** * Constructor @@ -2548,12 +2680,14 @@ public class SeqPanel extends JPanel public ScrollThread() { setName("SeqPanel$ScrollThread"); - start(); } /** * Sets the position of the mouse that determines the direction of the - * scroll to perform + * scroll to perform. If this is called as the mouse moves, scrolling should + * respond accordingly. For example, if the mouse is dragged right, scroll + * right should start; if the drag continues down, scroll down should also + * happen. * * @param p */ @@ -2567,7 +2701,7 @@ public class SeqPanel extends JPanel */ public void stopScrolling() { - threadRunning = false; + keepRunning = false; } /** @@ -2578,48 +2712,12 @@ public class SeqPanel extends JPanel @Override public void run() { - while (threadRunning && mouseDragging) + while (keepRunning) { if (mousePos != null) { - boolean scrolled = false; - ViewportRanges ranges = SeqPanel.this.av.getRanges(); - - /* - * scroll up or down - */ - if (mousePos.y < 0) - { - // mouse is above this panel - try scroll up - scrolled = ranges.scrollUp(true); - } - else if (mousePos.y >= getHeight()) - { - // mouse is below this panel - try scroll down - scrolled = ranges.scrollUp(false); - } - - /* - * scroll left or right - */ - if (mousePos.x < 0) - { - scrolled |= ranges.scrollRight(false); - } - else if (mousePos.x >= getWidth()) - { - scrolled |= ranges.scrollRight(true); - } - if (!scrolled) - { - /* - * we have reached the limit of the visible alignment - quit - */ - threadRunning = false; - SeqPanel.this.ap.repaint(); - } + keepRunning = scrollOnce(); } - try { Thread.sleep(20); @@ -2627,6 +2725,60 @@ public class SeqPanel extends JPanel { } } + SeqPanel.this.scrollThread = null; + } + + /** + * Scrolls + *

+ * Answers true if a scroll was performed, false if not - meaning either + * that the mouse position is within the panel, or the edge of the alignment + * has been reached. + */ + boolean scrollOnce() + { + /* + * quit after mouseUp ensures interrupt in JalviewJS + */ + if (!mouseDragging) + { + return false; + } + + boolean scrolled = false; + ViewportRanges ranges = SeqPanel.this.av.getRanges(); + + /* + * scroll up or down + */ + if (mousePos.y < 0) + { + // mouse is above this panel - try scroll up + scrolled = ranges.scrollUp(true); + } + else if (mousePos.y >= getHeight()) + { + // mouse is below this panel - try scroll down + scrolled = ranges.scrollUp(false); + } + + /* + * scroll left or right + */ + if (mousePos.x < 0) + { + scrolled |= ranges.scrollRight(false); + } + else if (mousePos.x >= getWidth()) + { + scrolled |= ranges.scrollRight(true); + } + return scrolled; } } @@ -2694,7 +2846,7 @@ public class SeqPanel extends JPanel { if (av.getAlignment() == null) { - Cache.log.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + Console.warn("alignviewport av SeqSetId=" + av.getSequenceSetId() + " ViewId=" + av.getViewId() + " 's alignment is NULL! returning immediately."); return; @@ -2749,7 +2901,7 @@ public class SeqPanel extends JPanel if (copycolsel && av.hasHiddenColumns() && (av.getAlignment().getHiddenColumns() == null)) { - System.err.println("Bad things"); + jalview.bin.Console.errPrintln("Bad things"); } if (repaint) // always true! { @@ -2819,6 +2971,8 @@ public class SeqPanel extends JPanel * if hidden column selection has changed */ ap.paintAlignment(hiddenChanged, hiddenChanged); + // propagate any selection changes + PaintRefresher.Refresh(ap, av.getSequenceSetId()); return true; }