X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=inline;f=src%2Fjalview%2Fgui%2FSeqPanel.java;h=163ae25fd3a45a152283f246e93560bfa0eac21d;hb=bed0c230be450b16213e30ee1dcaf3e76ddfc669;hp=18e9365b22044442d15f06396ec96e58ceb27a65;hpb=1f54b227847c46fefbe0bfbe923c08fb22bab52d;p=jalview.git
diff --git a/src/jalview/gui/SeqPanel.java b/src/jalview/gui/SeqPanel.java
index 18e9365..163ae25 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;
@@ -53,29 +76,6 @@ import jalview.viewmodel.AlignmentViewport;
import jalview.viewmodel.ViewportRanges;
import jalview.viewmodel.seqfeatures.FeatureRendererModel;
-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;
-
/**
* DOCUMENT ME!
*
@@ -212,13 +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;
@@ -234,8 +242,7 @@ 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);
@@ -268,6 +275,9 @@ 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
@@ -335,6 +345,9 @@ public class SeqPanel extends JPanel
/**
* 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
@@ -822,8 +835,6 @@ public class SeqPanel extends JPanel
String lastMessage;
- private String formattedTooltipText;
-
@Override
public void mouseOverSequence(SequenceI sequence, int index, int pos)
{
@@ -904,11 +915,12 @@ 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())
{
@@ -984,8 +996,10 @@ public class SeqPanel extends JPanel
/*
* just a pixel move without change of 'cell'
*/
+ moveTooltip = false;
return;
}
+ moveTooltip = true;
lastMousePosition = mousePos;
if (mousePos.isOverAnnotation())
@@ -1001,6 +1015,7 @@ public class SeqPanel extends JPanel
lastMousePosition = null;
setToolTipText(null);
lastTooltip = null;
+ lastFormattedTooltip = null;
ap.alignFrame.setStatus("");
return;
}
@@ -1022,7 +1037,7 @@ public class SeqPanel extends JPanel
mouseOverSequence(sequence, column, pos);
}
- tooltipText.setLength(6); // ""
+ StringBuilder tooltipText = new StringBuilder(64);
SequenceGroup[] groups = av.getAlignment().findAllGroups(sequence);
if (groups != null)
@@ -1056,9 +1071,9 @@ public class SeqPanel extends JPanel
{
List features = ap.getFeatureRenderer()
.findFeaturesAtColumn(sequence, column + 1);
- unshownFeatures = seqARep.appendFeaturesLengthLimit(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
@@ -1076,14 +1091,13 @@ 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;
@@ -1103,12 +1117,12 @@ public class SeqPanel extends JPanel
.append("");
}
String textString = tooltipText.toString();
- if (lastTooltip == null || !lastTooltip.equals(textString))
+ if (!textString.equals(lastTooltip))
{
- formattedTooltipText = JvSwingUtils.wrapTooltip(true,
- textString);
- setToolTipText(formattedTooltipText);
lastTooltip = textString;
+ lastFormattedTooltip = JvSwingUtils.wrapTooltip(true,
+ textString);
+ setToolTipText(lastFormattedTooltip);
}
}
}
@@ -1134,16 +1148,34 @@ public class SeqPanel extends JPanel
String tooltip = AnnotationPanel.buildToolTip(anns[rowIndex], column,
anns);
- setToolTipText(tooltip);
- lastTooltip = tooltip;
+ if (!tooltip.equals(lastTooltip))
+ {
+ 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();
/*
@@ -1156,33 +1188,30 @@ public class SeqPanel extends JPanel
{
// BH 2018
- if (tooltipText == null || tooltipText.length() <= 6)
+ if (lastTooltip == null || !moveTooltip)
{
return null;
}
- if (lastp != null && event.isShiftDown())
+ if (lastTooltipLocation != null && event.isShiftDown())
{
- return lastp;
+ return lastTooltipLocation;
}
- Point p = lastp;
int x = event.getX();
int y = event.getY();
int w = getWidth();
- tempTip.setTipText(formattedTooltipText);
+ 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);
- p = new Point(x, y + 20); // BH 2018 was - 20?
+ Point p = new Point(x, y + av.getCharHeight()); // BH 2018 was - 20?
- return lastp = p;
+ return lastTooltipLocation = p;
}
- String lastTooltip;
-
/**
* set when the current UI interaction has resulted in a change that requires
* shading in overviews and structures to be recalculated. this could be
@@ -1219,7 +1248,7 @@ 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;
}
@@ -1235,7 +1264,7 @@ 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
@@ -1243,7 +1272,7 @@ 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);
@@ -1253,7 +1282,7 @@ 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;
@@ -1298,7 +1327,8 @@ 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();
@@ -1310,8 +1340,8 @@ 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;
}
}