X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=845004bdb05d1391565f86889238045bd45eb59a;hb=5640ec0623c6d1205e62f9fe15292f32bfdab7d9;hp=bb85948a7a2c9ece090e6414da9cbe7cd390ba81;hpb=af259f508805faf2da90585ee9a67cd7853bf5aa;p=jalview.git diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java index bb85948..845004b 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);
}
/**
@@ -938,8 +1006,7 @@ public class SeqPanel extends JPanel
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)
@@ -979,7 +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();
}
@@ -1007,8 +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())
@@ -1024,6 +1093,7 @@ public class SeqPanel extends JPanel
lastMousePosition = null;
setToolTipText(null);
lastTooltip = null;
+ lastFormattedTooltip = null;
ap.alignFrame.setStatus("");
return;
}
@@ -1045,7 +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)
@@ -1079,9 +1149,8 @@ public class SeqPanel extends JPanel
{
List
+ *
+ * Note that this method may also be fired by scrolling with a gesture on a
+ * trackpad.
+ */
@Override
public void mouseWheelMoved(MouseWheelEvent e)
{
e.consume();
double wheelRotation = e.getPreciseWheelRotation();
+
+ /*
+ * scroll more for large (fast) mouse movements
+ */
+ int size = 1 + (int) Math.abs(wheelRotation);
+
if (wheelRotation > 0)
{
if (e.isShiftDown())
{
- av.getRanges().scrollRight(true);
-
+ /*
+ * scroll right
+ * stop trying to scroll right when limit is reached (saves
+ * expensive calls to Alignment.getWidth())
+ */
+ while (size-- > 0 && !ap.isScrolledFullyRight())
+ {
+ if (!av.getRanges().scrollRight(true))
+ {
+ break;
+ }
+ }
}
else
{
- av.getRanges().scrollUp(false);
+ /*
+ * scroll down
+ */
+ while (size-- > 0)
+ {
+ if (!av.getRanges().scrollUp(false))
+ {
+ break;
+ }
+ }
}
}
else if (wheelRotation < 0)
{
if (e.isShiftDown())
{
- av.getRanges().scrollRight(false);
+ /*
+ * scroll left
+ */
+ while (size-- > 0)
+ {
+ if (!av.getRanges().scrollRight(false))
+ {
+ break;
+ }
+ }
}
else
{
- av.getRanges().scrollUp(true);
+ /*
+ * scroll up
+ */
+ while (size-- > 0)
+ {
+ if (!av.getRanges().scrollUp(true))
+ {
+ break;
+ }
+ }
}
}
@@ -2211,19 +2351,19 @@ 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;
}
@@ -2386,7 +2526,7 @@ 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)
{
@@ -2519,29 +2659,73 @@ 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
@@ -2549,12 +2733,14 @@ 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
*/
@@ -2568,7 +2754,7 @@ public class SeqPanel extends JPanel
*/
public void stopScrolling()
{
- threadRunning = false;
+ keepRunning = false;
}
/**
@@ -2579,48 +2765,12 @@ 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);
@@ -2628,6 +2778,60 @@ 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;
}
}
@@ -2695,7 +2899,7 @@ 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;
@@ -2750,7 +2954,7 @@ 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!
{
@@ -2820,6 +3024,8 @@ 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;
}