X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=2caea17d01aabf8bb9af9bd7c6d5935f0486412e;hb=afe4b88500a5d61bc8d312909cfdde2b7cdd53df;hp=27ceb278145ee65200c20ff1c244827ebd1a4a16;hpb=c53cc5969e41f96099d2a81400353c3b39f164b7;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 27ceb27..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;
}
@@ -207,13 +212,21 @@ public class SeqPanel extends JPanel
StringBuffer keyboardNo2;
- java.net.URL linkImageURL;
-
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;
@@ -229,11 +242,11 @@ public class SeqPanel extends JPanel
*/
public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
{
- linkImageURL = getClass().getResource("/images/link.gif");
- seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+ seqARep = new SequenceAnnotationReport(true);
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
+
this.av = viewport;
setBackground(Color.white);
@@ -261,6 +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
@@ -325,15 +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();
@@ -357,7 +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());
@@ -367,8 +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;
@@ -385,8 +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())
@@ -463,45 +523,85 @@ public class SeqPanel extends JPanel
void moveCursor(int dx, int dy)
{
- seqCanvas.cursorX += dx;
- seqCanvas.cursorY += dy;
+ moveCursor(dx, dy, false);
+ }
+ void moveCursor(int dx, int dy, boolean nextWord)
+ {
HiddenColumns hidden = av.getAlignment().getHiddenColumns();
- if (av.hasHiddenColumns() && !hidden.isVisible(seqCanvas.cursorX))
+ if (nextWord)
{
- int original = seqCanvas.cursorX - dx;
int maxWidth = av.getAlignment().getWidth();
-
- if (!hidden.isVisible(seqCanvas.cursorX))
- {
- int visx = hidden.absoluteToVisibleColumn(seqCanvas.cursorX - dx);
- int[] region = hidden.getRegionWithEdgeAtRes(visx);
-
- if (region != null) // just in case
+ 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;
+ do
+ {
+ lastP = p;
+ lastR = r;
+ if (dy != 0)
{
- if (dx == 1)
+ r += dy;
+ if (r < 0)
{
- // moving right
- seqCanvas.cursorX = region[1] + 1;
+ r = 0;
}
- else if (dx == -1)
+ if (r >= maxHeight)
{
- // moving left
- seqCanvas.cursorX = region[0] - 1;
+ r = maxHeight - 1;
}
+ seqAtRow = av.getAlignment().getSequenceAt(r);
}
- seqCanvas.cursorX = (seqCanvas.cursorX < 0) ? 0 : seqCanvas.cursorX;
- }
+ 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
+ {
+ int maxWidth = av.getAlignment().getWidth();
+ seqCanvas.cursorX = nextVisible(hidden, maxWidth, seqCanvas.cursorX,
+ dx);
+ seqCanvas.cursorY += dy;
+ }
+ scrollToVisible(false);
+ }
+
+ private int nextVisible(HiddenColumns hidden, int maxWidth, int original,
+ int dx)
+ {
+ int newCursorX = original + dx;
+ if (av.hasHiddenColumns() && !hidden.isVisible(newCursorX))
+ {
+ int visx = hidden.absoluteToVisibleColumn(newCursorX - dx);
+ int[] region = hidden.getRegionWithEdgeAtRes(visx);
- if (seqCanvas.cursorX >= maxWidth
- || !hidden.isVisible(seqCanvas.cursorX))
+ if (region != null) // just in case
{
- seqCanvas.cursorX = original;
+ if (dx == 1)
+ {
+ // moving right
+ newCursorX = region[1] + 1;
+ }
+ else if (dx == -1)
+ {
+ // moving left
+ newCursorX = region[0] - 1;
+ }
}
}
-
- scrollToVisible(false);
+ newCursorX = (newCursorX < 0) ? 0 : newCursorX;
+ if (newCursorX >= maxWidth || !hidden.isVisible(newCursorX))
+ {
+ newCursorX = original;
+ }
+ return newCursorX;
}
/**
@@ -559,7 +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)
@@ -568,7 +668,6 @@ public class SeqPanel extends JPanel
}
}
-
void setSelectionAreaAtCursor(boolean topLeft)
{
SequenceI sequence = av.getAlignment().getSequenceAt(seqCanvas.cursorY);
@@ -822,7 +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;
@@ -860,8 +959,8 @@ 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);
}
@@ -895,19 +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)
@@ -947,7 +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();
}
@@ -975,8 +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())
@@ -992,6 +1093,7 @@ public class SeqPanel extends JPanel
lastMousePosition = null;
setToolTipText(null);
lastTooltip = null;
+ lastFormattedTooltip = null;
ap.alignFrame.setStatus("");
return;
}
@@ -1013,7 +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)
@@ -1047,8 +1149,7 @@ public class SeqPanel extends JPanel
{
List features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
- unshownFeatures = seqARep.appendFeaturesLengthLimit(tooltipText, pos,
- features,
+ unshownFeatures = seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr, MAX_TOOLTIP_LENGTH);
/*
@@ -1067,14 +1168,13 @@ public class SeqPanel extends JPanel
pos);
if (mf != null)
{
- unshownFeatures = seqARep.appendFeaturesLengthLimit(
- 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;
@@ -1094,12 +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);
}
}
}
@@ -1116,6 +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)
{
@@ -1124,16 +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)
@@ -1143,29 +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
@@ -1174,7 +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
@@ -1203,7 +1327,7 @@ public class SeqPanel extends JPanel
{
char sequenceChar = sequence.getCharAt(column);
int pos = sequence.findPosition(column);
- setStatusMessage(sequence, seqIndex, sequenceChar, pos);
+ setStatusMessage(sequence.getName(), seqIndex, sequenceChar, pos);
return pos;
}
@@ -1219,7 +1343,7 @@ public class SeqPanel extends JPanel
* Sequence 6 ID: O.niloticus.3 Nucleotide: Uracil (2)
*
*
- * @param sequence
+ * @param seqName
* @param seqIndex
* sequence position in the alignment (1..)
* @param sequenceChar
@@ -1227,7 +1351,7 @@ public class SeqPanel extends JPanel
* @param residuePos
* the sequence residue position (if not over a gap)
*/
- protected void setStatusMessage(SequenceI sequence, int seqIndex,
+ protected void setStatusMessage(String seqName, int seqIndex,
char sequenceChar, int residuePos)
{
StringBuilder text = new StringBuilder(32);
@@ -1236,8 +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(sequence.getName());
+ text.append("Sequence").append(seqno).append(" ID: ").append(seqName);
String residue = null;
@@ -1282,7 +1405,8 @@ public class SeqPanel extends JPanel
{
return;
}
- SequenceI ds = al.getSequenceAt(sequenceIndex).getDatasetSequence();
+ SequenceI alignedSeq = al.getSequenceAt(sequenceIndex);
+ SequenceI ds = alignedSeq.getDatasetSequence();
for (SearchResultMatchI m : results.getResults())
{
SequenceI seq = m.getSequence();
@@ -1294,8 +1418,8 @@ public class SeqPanel extends JPanel
if (seq == ds)
{
int start = m.getStart();
- setStatusMessage(seq, sequenceIndex, seq.getCharAt(start - 1),
- start);
+ setStatusMessage(alignedSeq.getName(), sequenceIndex,
+ seq.getCharAt(start - 1), start);
return;
}
}
@@ -1495,12 +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)
{
@@ -1692,8 +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;
@@ -2041,7 +2164,7 @@ public class SeqPanel extends JPanel
if (mouseDragging && scrollThread == null)
{
- scrollThread = new ScrollThread();
+ startScrolling(e.getPoint());
}
}
@@ -2085,19 +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();
}
}
}
@@ -2179,19 +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;
}
@@ -2354,7 +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)
{
@@ -2487,29 +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
@@ -2517,12 +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
*/
@@ -2536,7 +2701,7 @@ public class SeqPanel extends JPanel
*/
public void stopScrolling()
{
- threadRunning = false;
+ keepRunning = false;
}
/**
@@ -2547,48 +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);
@@ -2596,6 +2725,60 @@ public class SeqPanel extends JPanel
{
}
}
+ SeqPanel.this.scrollThread = null;
+ }
+
+ /**
+ * Scrolls
+ *
+ * - one row up, if the mouse is above the panel
+ * - one row down, if the mouse is below the panel
+ * - one column left, if the mouse is left of the panel
+ * - one column right, if the mouse is right of the panel
+ *
+ * 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;
}
}
@@ -2663,7 +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;
@@ -2718,7 +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!
{
@@ -2788,6 +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;
}