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JAL-2526 removed redundant call to Sequence.findPosition()
author
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 19 May 2017 15:59:48 +0000
(16:59 +0100)
committer
gmungoc
<g.m.carstairs@dundee.ac.uk>
Fri, 19 May 2017 15:59:48 +0000
(16:59 +0100)
src/jalview/gui/SeqPanel.java
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diff --git
a/src/jalview/gui/SeqPanel.java
b/src/jalview/gui/SeqPanel.java
index
de44aa0
..
7dfac5e
100644
(file)
--- a/
src/jalview/gui/SeqPanel.java
+++ b/
src/jalview/gui/SeqPanel.java
@@
-183,7
+183,7
@@
public class SeqPanel extends JPanel implements MouseListener,
* @param evt
* @return
*/
* @param evt
* @return
*/
- int findRes(MouseEvent evt)
+ int findColumn(MouseEvent evt)
{
int res = 0;
int x = evt.getX();
{
int res = 0;
int x = evt.getX();
@@
-642,7
+642,7
@@
public class SeqPanel extends JPanel implements MouseListener,
}
int seq = findSeq(evt);
}
int seq = findSeq(evt);
- int res = findRes(evt);
+ int res = findColumn(evt);
if (seq < 0 || res < 0)
{
if (seq < 0 || res < 0)
{
@@
-741,25
+741,27
@@
public class SeqPanel extends JPanel implements MouseListener,
mouseDragged(evt);
}
mouseDragged(evt);
}
- int res = findRes(evt);
+ final int column = findColumn(evt);
int seq = findSeq(evt);
int seq = findSeq(evt);
- int pos;
- if (res < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
+ if (column < 0 || seq < 0 || seq >= av.getAlignment().getHeight())
{
return;
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
{
return;
}
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
- if (res >= sequence.getLength())
+ if (column >= sequence.getLength())
{
return;
}
{
return;
}
- pos = setStatusMessage(sequence, res, seq);
+ /*
+ * set status bar message, returning residue position in sequence
+ */
+ final int pos = setStatusMessage(sequence, column, seq);
if (ssm != null && pos > -1)
{
if (ssm != null && pos > -1)
{
- mouseOverSequence(sequence, res, pos);
+ mouseOverSequence(sequence, column, pos);
}
tooltipText.setLength(6); // Cuts the buffer back to <html>
}
tooltipText.setLength(6); // Cuts the buffer back to <html>
@@
-769,7
+771,8
@@
public class SeqPanel extends JPanel implements MouseListener,
{
for (int g = 0; g < groups.length; g++)
{
{
for (int g = 0; g < groups.length; g++)
{
- if (groups[g].getStartRes() <= res && groups[g].getEndRes() >= res)
+ if (groups[g].getStartRes() <= column
+ && groups[g].getEndRes() >= column)
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
{
if (!groups[g].getName().startsWith("JTreeGroup")
&& !groups[g].getName().startsWith("JGroup"))
@@
-785,14
+788,11
@@
public class SeqPanel extends JPanel implements MouseListener,
}
}
}
}
- // use aa to see if the mouse pointer is on a
if (av.isShowSequenceFeatures())
{
if (av.isShowSequenceFeatures())
{
- int rpos;
List<SequenceFeature> features = ap.getFeatureRenderer()
List<SequenceFeature> features = ap.getFeatureRenderer()
- .findFeaturesAtRes(sequence.getDatasetSequence(),
- rpos = sequence.findPosition(res));
- seqARep.appendFeatures(tooltipText, rpos, features,
+ .findFeaturesAtRes(sequence.getDatasetSequence(), pos);
+ seqARep.appendFeatures(tooltipText, pos, features,
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
if (tooltipText.length() == 6) // <html>
this.ap.getSeqPanel().seqCanvas.fr.getMinMax());
}
if (tooltipText.length() == 6) // <html>
@@
-859,17
+859,19
@@
public class SeqPanel extends JPanel implements MouseListener,
// avcontroller or viewModel
/**
// avcontroller or viewModel
/**
- * Set status message in alignment panel
+ * Sets the status message in alignment panel, showing the sequence number
+ * (index) and id, residue and residue position for the given sequence and
+ * column position. Returns the calculated residue position in the sequence.
*
* @param sequence
* aligned sequence object
*
* @param sequence
* aligned sequence object
- * @param res
+ * @param column
* alignment column
* @param seq
* index of sequence in alignment
* @return position of res in sequence
*/
* alignment column
* @param seq
* index of sequence in alignment
* @return position of res in sequence
*/
- int setStatusMessage(SequenceI sequence, int res, int seq)
+ int setStatusMessage(SequenceI sequence, final int column, int seq)
{
StringBuilder text = new StringBuilder(32);
{
StringBuilder text = new StringBuilder(32);
@@
-884,7
+886,7
@@
public class SeqPanel extends JPanel implements MouseListener,
/*
* Try to translate the display character to residue name (null for gap).
*/
/*
* Try to translate the display character to residue name (null for gap).
*/
- final String displayChar = String.valueOf(sequence.getCharAt(res));
+ final String displayChar = String.valueOf(sequence.getCharAt(column));
if (av.getAlignment().isNucleotide())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
if (av.getAlignment().isNucleotide())
{
residue = ResidueProperties.nucleotideName.get(displayChar);
@@
-905,9
+907,9
@@
public class SeqPanel extends JPanel implements MouseListener,
}
int pos = -1;
}
int pos = -1;
+ pos = sequence.findPosition(column);
if (residue != null)
{
if (residue != null)
{
- pos = sequence.findPosition(res);
text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
text.append(" (").append(Integer.toString(pos)).append(")");
}
ap.alignFrame.statusBar.setText(text.toString());
@@
-1055,7
+1057,7
@@
public class SeqPanel extends JPanel implements MouseListener,
return;
}
return;
}
- int res = findRes(evt);
+ int res = findColumn(evt);
if (res < 0)
{
if (res < 0)
{
@@
-1552,7
+1554,7
@@
public class SeqPanel extends JPanel implements MouseListener,
List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(),
List<SequenceFeature> features = seqCanvas.getFeatureRenderer()
.findFeaturesAtRes(sequence.getDatasetSequence(),
- sequence.findPosition(findRes(evt)));
+ sequence.findPosition(findColumn(evt)));
if (!features.isEmpty())
{
if (!features.isEmpty())
{
@@
-1614,7
+1616,7
@@
public class SeqPanel extends JPanel implements MouseListener,
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
*/
public void doMousePressedDefineMode(MouseEvent evt)
{
- final int res = findRes(evt);
+ final int res = findColumn(evt);
final int seq = findSeq(evt);
oldSeq = seq;
needOverviewUpdate = false;
final int seq = findSeq(evt);
oldSeq = seq;
needOverviewUpdate = false;
@@
-1673,7
+1675,7
@@
public class SeqPanel extends JPanel implements MouseListener,
if (av.cursorMode)
{
if (av.cursorMode)
{
- seqCanvas.cursorX = findRes(evt);
+ seqCanvas.cursorX = findColumn(evt);
seqCanvas.cursorY = findSeq(evt);
seqCanvas.repaint();
return;
seqCanvas.cursorY = findSeq(evt);
seqCanvas.repaint();
return;
@@
-1729,7
+1731,7
@@
public class SeqPanel extends JPanel implements MouseListener,
*/
void showPopupMenu(MouseEvent evt)
{
*/
void showPopupMenu(MouseEvent evt)
{
- final int res = findRes(evt);
+ final int res = findColumn(evt);
final int seq = findSeq(evt);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
final int seq = findSeq(evt);
SequenceI sequence = av.getAlignment().getSequenceAt(seq);
List<SequenceFeature> allFeatures = ap.getFeatureRenderer()
@@
-1800,7
+1802,7
@@
public class SeqPanel extends JPanel implements MouseListener,
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
*/
public void doMouseDraggedDefineMode(MouseEvent evt)
{
- int res = findRes(evt);
+ int res = findColumn(evt);
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)
int y = findSeq(evt);
if (wrappedBlock != startWrapBlock)