X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=fdb75a45da75fa023787a8f4da47aabc5e4971f5;hb=0751c58086542f9e0466201b624f84d1efd547bb;hp=08c74e8ac761a79cc912e438bc20eec5eb05e957;hpb=c9b03515daddb7666215ef3d0f19026aa601534b;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 08c74e8..fdb75a4 100644
--- a/src/jalview/gui/SeqPanel.java
+++ b/src/jalview/gui/SeqPanel.java
@@ -20,6 +20,29 @@
*/
package jalview.gui;
+import java.awt.BorderLayout;
+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;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+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.commands.EditCommand;
@@ -29,6 +52,7 @@ import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.AlignmentI;
import jalview.datamodel.ColumnSelection;
import jalview.datamodel.HiddenColumns;
+import jalview.datamodel.MappedFeatures;
import jalview.datamodel.SearchResultMatchI;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResultsI;
@@ -50,23 +74,7 @@ import jalview.util.MessageManager;
import jalview.util.Platform;
import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Font;
-import java.awt.FontMetrics;
-import java.awt.Point;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.MouseMotionListener;
-import java.awt.event.MouseWheelEvent;
-import java.awt.event.MouseWheelListener;
-import java.util.Collections;
-import java.util.List;
-
-import javax.swing.JPanel;
-import javax.swing.SwingUtilities;
-import javax.swing.ToolTipManager;
+import jalview.viewmodel.seqfeatures.FeatureRendererModel;
/**
* DOCUMENT ME!
@@ -79,6 +87,7 @@ public class SeqPanel extends JPanel
SequenceListener, SelectionListener
{
/*
+ *
* a class that holds computed mouse position
* - column of the alignment (0...)
* - sequence offset (0...)
@@ -204,13 +213,21 @@ 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;
@@ -226,11 +243,13 @@ public class SeqPanel extends JPanel
*/
public SeqPanel(AlignViewport viewport, AlignmentPanel alignPanel)
{
- linkImageURL = getClass().getResource("/images/link.gif");
- seqARep = new SequenceAnnotationReport(linkImageURL.toString());
+ setName("SeqPanel");
+ seqARep = new SequenceAnnotationReport(true);
ToolTipManager.sharedInstance().registerComponent(this);
ToolTipManager.sharedInstance().setInitialDelay(0);
ToolTipManager.sharedInstance().setDismissDelay(10000);
+
+
this.av = viewport;
setBackground(Color.white);
@@ -255,11 +274,6 @@ public class SeqPanel extends JPanel
int wrappedBlock = -1;
- MousePos findMousePosition(MouseEvent evt)
- {
- return findMousePosition(evt, false);
- }
-
/**
* Computes the column and sequence row (and possibly annotation row when in
* wrapped mode) for the given mouse position
@@ -267,26 +281,18 @@ public class SeqPanel extends JPanel
* @param evt
* @return
*/
- MousePos findMousePosition(MouseEvent evt, boolean debug)
+ MousePos findMousePosition(MouseEvent evt)
{
- int col = findColumn(evt, debug);
+ int col = findColumn(evt);
int seqIndex = -1;
int annIndex = -1;
int y = evt.getY();
int charHeight = av.getCharHeight();
int alignmentHeight = av.getAlignment().getHeight();
- if (debug)
- {
- System.out.println(String.format(
- "charHeight %d alHeight %d canvasWidth %d canvasHeight %d",
- charHeight, alignmentHeight, seqCanvas.getWidth(),
- seqCanvas.getHeight()));
- }
if (av.getWrapAlignment())
{
- seqCanvas.calculateWrappedGeometry(seqCanvas.getWidth(),
- seqCanvas.getHeight());
+ seqCanvas.calculateWrappedGeometry();
/*
* yPos modulo height of repeating width
@@ -343,11 +349,6 @@ public class SeqPanel extends JPanel
*/
int findColumn(MouseEvent evt)
{
- return findColumn(evt, true);
- }
-
- int findColumn(MouseEvent evt, boolean debug)
- {
int res = 0;
int x = evt.getX();
@@ -368,12 +369,6 @@ public class SeqPanel extends JPanel
int y = evt.getY();
y = Math.max(0, y - hgap);
x -= seqCanvas.getLabelWidthWest();
- if (debug)
- {
- System.out.println(
- String.format("findColumn: x %d labelWest %d charWidth %d ",
- x, seqCanvas.getLabelWidthWest(), charWidth));
- }
if (x < 0)
{
// mouse is over left scale
@@ -387,10 +382,6 @@ public class SeqPanel extends JPanel
}
if (x >= cwidth * charWidth)
{
- if (debug)
- {
- System.out.println("findColumn: cwidth = " + cwidth);
- }
// mouse is over right scale
return -1;
}
@@ -433,8 +424,7 @@ public class SeqPanel extends JPanel
if (editCommand != null && editCommand.getSize() > 0)
{
ap.alignFrame.addHistoryItem(editCommand);
- av.firePropertyChange("alignment", null,
- av.getAlignment().getSequences());
+ ap.av.notifyAlignment();
}
} finally
{
@@ -859,11 +849,11 @@ public class SeqPanel extends JPanel
* the start of the highlighted region.
*/
@Override
- public void highlightSequence(SearchResultsI results)
+ public String highlightSequence(SearchResultsI results)
{
if (results == null || results.equals(lastSearchResults))
{
- return;
+ return null;
}
lastSearchResults = results;
@@ -884,11 +874,82 @@ 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);
}
+ return results.isEmpty() ? null : getHighlightInfo(results);
+ }
+
+ /**
+ * temporary hack: answers a message suitable to show on structure hover
+ * label. This is normally null. It is a peptide variation description if
+ *
+ * - results are a single residue in a protein alignment
+ * - there is a mapping to a coding sequence (codon)
+ * - there are one or more SNP variant features on the codon
+ *
+ * in which case the answer is of the format (e.g.) "p.Glu388Asp"
+ *
+ * @param results
+ * @return
+ */
+ private String getHighlightInfo(SearchResultsI results)
+ {
+ /*
+ * ideally, just find mapped CDS (as we don't care about render style here);
+ * for now, go via split frame complement's FeatureRenderer
+ */
+ AlignViewportI complement = ap.getAlignViewport().getCodingComplement();
+ if (complement == null)
+ {
+ return null;
+ }
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+
+ int j = results.getSize();
+ List infos = new ArrayList<>();
+ for (int i = 0; i < j; i++)
+ {
+ SearchResultMatchI match = results.getResults().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);
+ if (mf != null)
+ {
+ for (SequenceFeature sf : mf.features)
+ {
+ String pv = mf.findProteinVariants(sf);
+ if (pv.length() > 0 && !infos.contains(pv))
+ {
+ infos.add(pv);
+ }
+ }
+ }
+ }
+ }
+
+ if (infos.isEmpty())
+ {
+ return null;
+ }
+ StringBuilder sb = new StringBuilder();
+ for (String info : infos)
+ {
+ if (sb.length() > 0)
+ {
+ sb.append("|");
+ }
+ sb.append(info);
+ }
+ return sb.toString();
}
@Override
@@ -928,8 +989,10 @@ public class SeqPanel extends JPanel
/*
* just a pixel move without change of 'cell'
*/
+ moveTooltip = false;
return;
}
+ moveTooltip = true;
lastMousePosition = mousePos;
if (mousePos.isOverAnnotation())
@@ -945,6 +1008,7 @@ public class SeqPanel extends JPanel
lastMousePosition = null;
setToolTipText(null);
lastTooltip = null;
+ lastFormattedTooltip = null;
ap.alignFrame.setStatus("");
return;
}
@@ -966,7 +1030,7 @@ 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)
@@ -995,32 +1059,63 @@ public class SeqPanel extends JPanel
* add features that straddle the gap (pos may be the residue before or
* after the gap)
*/
+ int unshownFeatures = 0;
if (av.isShowSequenceFeatures())
{
List features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
- seqARep.appendFeatures(tooltipText, pos, features,
- this.ap.getSeqPanel().seqCanvas.fr);
+ unshownFeatures = seqARep.appendFeatures(tooltipText, pos,
+ features, this.ap.getSeqPanel().seqCanvas.fr,
+ MAX_TOOLTIP_LENGTH);
+
+ /*
+ * add features in CDS/protein complement at the corresponding
+ * position if configured to do so
+ */
+ if (av.isShowComplementFeatures())
+ {
+ if (!Comparison.isGap(sequence.getCharAt(column)))
+ {
+ AlignViewportI complement = ap.getAlignViewport()
+ .getCodingComplement();
+ AlignFrame af = Desktop.getAlignFrameFor(complement);
+ FeatureRendererModel fr2 = af.getFeatureRenderer();
+ MappedFeatures mf = fr2.findComplementFeaturesAtResidue(sequence,
+ pos);
+ if (mf != null)
+ {
+ unshownFeatures = seqARep.appendFeatures(tooltipText,
+ pos, mf, fr2, MAX_TOOLTIP_LENGTH);
+ }
+ }
+ }
}
- if (tooltipText.length() == 6) //
+ if (tooltipText.length() == 0) // nothing added
{
setToolTipText(null);
lastTooltip = null;
}
else
{
- if (tooltipText.length() > MAX_TOOLTIP_LENGTH) // constant
+ if (tooltipText.length() > MAX_TOOLTIP_LENGTH)
{
tooltipText.setLength(MAX_TOOLTIP_LENGTH);
tooltipText.append("...");
}
+ if (unshownFeatures > 0)
+ {
+ tooltipText.append("
").append("... ").append("")
+ .append(MessageManager.formatMessage(
+ "label.features_not_shown", unshownFeatures))
+ .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);
}
}
}
@@ -1046,15 +1141,36 @@ public class SeqPanel extends JPanel
String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
anns);
- setToolTipText(tooltip);
- lastTooltip = tooltip;
+ boolean tooltipChanged = tooltip == null ? lastTooltip != null : !tooltip.equals(lastTooltip);
+ if (tooltipChanged)
+ {
+ lastTooltip = tooltip;
+ lastFormattedTooltip = tooltip == null ? null
+ : JvSwingUtils.wrapTooltip(true, tooltip);
+ setToolTipText(lastFormattedTooltip);
+ }
String msg = AnnotationPanel.getStatusMessage(av.getAlignment(), column,
anns[rowIndex]);
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)
@@ -1064,29 +1180,31 @@ 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
@@ -1124,7 +1242,7 @@ 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;
}
@@ -1140,7 +1258,7 @@ 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
@@ -1148,7 +1266,7 @@ 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);
@@ -1158,7 +1276,7 @@ public class SeqPanel extends JPanel
*/
String seqno = seqIndex == -1 ? "" : " " + (seqIndex + 1);
text.append("Sequence").append(seqno).append(" ID: ")
- .append(sequence.getName());
+ .append(seqName);
String residue = null;
@@ -1203,7 +1321,8 @@ 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();
@@ -1215,8 +1334,8 @@ 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;
}
}
@@ -1962,7 +2081,7 @@ public class SeqPanel extends JPanel
if (mouseDragging && scrollThread == null)
{
- scrollThread = new ScrollThread();
+ startScrolling(e.getPoint());
}
}
@@ -1981,7 +2100,7 @@ public class SeqPanel extends JPanel
return;
}
- if (evt.getClickCount() > 1)
+ if (evt.getClickCount() > 1 && av.isShowSequenceFeatures())
{
sg = av.getSelectionGroup();
if (sg != null && sg.getSize() == 1
@@ -2008,17 +2127,13 @@ public class SeqPanel extends JPanel
SearchResultsI highlight = new SearchResults();
highlight.addResult(sequence, features.get(0).getBegin(), features
.get(0).getEnd());
- seqCanvas.highlightSearchResults(highlight, false);
+ 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();
}
}
}
@@ -2100,22 +2215,22 @@ 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;
+ }
+
if (av.cursorMode)
{
seqCanvas.cursorX = res;
@@ -2186,11 +2301,11 @@ public class SeqPanel extends JPanel
final int column = pos.column;
final int seq = pos.seqIndex;
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- List features = ap.getFeatureRenderer()
- .findFeaturesAtColumn(sequence, column + 1);
-
- PopupMenu pop = new PopupMenu(ap, null, features);
- pop.show(this, evt.getX(), evt.getY());
+ if (sequence != null)
+ {
+ PopupMenu pop = new PopupMenu(ap, sequence, column);
+ pop.show(this, evt.getX(), evt.getY());
+ }
}
/**
@@ -2408,29 +2523,73 @@ 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
@@ -2438,12 +2597,14 @@ 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
*/
@@ -2457,7 +2618,7 @@ public class SeqPanel extends JPanel
*/
public void stopScrolling()
{
- threadRunning = false;
+ keepRunning = false;
}
/**
@@ -2468,48 +2629,12 @@ 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);
@@ -2517,6 +2642,60 @@ 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;
}
}
@@ -2684,7 +2863,7 @@ public class SeqPanel extends JPanel
* Map sequence selection
*/
SequenceGroup sg = MappingUtils.mapSequenceGroup(seqsel, sourceAv, av);
- av.setSelectionGroup(sg);
+ av.setSelectionGroup(sg != null && sg.getSize() > 0 ? sg : null);
av.isSelectionGroupChanged(true);
/*
@@ -2721,4 +2900,45 @@ public class SeqPanel extends JPanel
{
return lastSearchResults;
}
+
+ /**
+ * scroll to the given row/column - or nearest visible location
+ *
+ * @param row
+ * @param column
+ */
+ public void scrollTo(int row, int column)
+ {
+
+ row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+ column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+ ap.scrollTo(column, column, row, true, true);
+ }
+
+ /**
+ * scroll to the given row - or nearest visible location
+ *
+ * @param row
+ */
+ public void scrollToRow(int row)
+ {
+
+ row = row < 0 ? ap.av.getRanges().getStartSeq() : row;
+ ap.scrollTo(ap.av.getRanges().getStartRes(),
+ ap.av.getRanges().getStartRes(), row, true, true);
+ }
+
+ /**
+ * scroll to the given column - or nearest visible location
+ *
+ * @param column
+ */
+ public void scrollToColumn(int column)
+ {
+
+ column = column < 0 ? ap.av.getRanges().getStartRes() : column;
+ ap.scrollTo(column, column, ap.av.getRanges().getStartSeq(), true,
+ true);
+ }
+
}