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Merge branch 'develop' into imp/JAL-2775
[jalview.git]
/
src
/
jalview
/
gui
/
AnnotationLabels.java
diff --git
a/src/jalview/gui/AnnotationLabels.java
b/src/jalview/gui/AnnotationLabels.java
index
3e4ec98
..
b94a615
100755
(executable)
--- a/
src/jalview/gui/AnnotationLabels.java
+++ b/
src/jalview/gui/AnnotationLabels.java
@@
-52,7
+52,6
@@
import java.awt.image.BufferedImage;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.List;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
@@
-68,8
+67,8
@@
import javax.swing.ToolTipManager;
* @author $author$
* @version $Revision$
*/
* @author $author$
* @version $Revision$
*/
-public class AnnotationLabels extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel
+ implements MouseListener, MouseMotionListener, ActionListener
{
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
{
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
@@
-268,7
+267,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
new AnnotationExporter().exportAnnotations(ap,
- new AlignmentAnnotation[] { aa[selectedRow] });
+ new AlignmentAnnotation[]
+ { aa[selectedRow] });
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
@@
-440,9
+440,9
@@
public class AnnotationLabels extends JPanel implements MouseListener,
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
// av and sequencegroup need to implement same interface for
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .isIgnoreGapsConsensus());
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef.getIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addActionListener(new ActionListener()
{
@@
-453,8
+453,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
{
// TODO: pass on reference to ap so the view can be updated.
aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
- ap.getAnnotationPanel().paint(
- ap.getAnnotationPanel().getGraphics());
+ ap.getAnnotationPanel()
+ .paint(ap.getAnnotationPanel().getGraphics());
}
else
{
}
else
{
@@
-700,12
+700,12
@@
public class AnnotationLabels extends JPanel implements MouseListener,
if ((d.height - dif) > 20)
{
if ((d.height - dif) > 20)
{
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
+ ap.annotationScroller
+ .setPreferredSize(new Dimension(d.width, d.height - dif));
d = ap.annotationSpaceFillerHolder.getPreferredSize();
d = ap.annotationSpaceFillerHolder.getPreferredSize();
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- d.width, d.height - dif));
- ap.paintAlignment(true);
+ ap.annotationSpaceFillerHolder
+ .setPreferredSize(new Dimension(d.width, d.height - dif));
+ ap.paintAlignment(true, false);
}
ap.addNotify();
}
ap.addNotify();
@@
-729,8
+729,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
getSelectedRow(evt.getY() - getScrollOffset());
getSelectedRow(evt.getY() - getScrollOffset());
- if (selectedRow > -1
- && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ if (selectedRow > -1 && ap.av.getAlignment()
+ .getAlignmentAnnotation().length > selectedRow)
{
AlignmentAnnotation aa = ap.av.getAlignment()
.getAlignmentAnnotation()[selectedRow];
{
AlignmentAnnotation aa = ap.av.getAlignment()
.getAlignmentAnnotation()[selectedRow];
@@
-744,8
+744,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
// tooltips
desc.append(aa.getDescription(true).trim());
// check to see if the description is an html fragment.
// tooltips
desc.append(aa.getDescription(true).trim());
// check to see if the description is an html fragment.
- if (desc.length() < 6
- || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
+ if (desc.length() < 6 || (desc.substring(0, 6).toLowerCase()
+ .indexOf("<html>") < 0))
{
// clean the description ready for embedding in html
desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
{
// clean the description ready for embedding in html
desc = new StringBuffer(LEFT_ANGLE_BRACKET_PATTERN.matcher(desc)
@@
-819,17
+819,16
@@
public class AnnotationLabels extends JPanel implements MouseListener,
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
// process modifiers
SequenceGroup sg = ap.av.getSelectionGroup();
ap.getSeqPanel().ap.getIdPanel().highlightSearchResults(null);
// process modifiers
SequenceGroup sg = ap.av.getSelectionGroup();
- if (sg == null
- || sg == aa[selectedRow].groupRef
- || !(jalview.util.Platform.isControlDown(evt) || evt
- .isShiftDown()))
+ if (sg == null || sg == aa[selectedRow].groupRef
+ || !(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
if (jalview.util.Platform.isControlDown(evt)
|| evt.isShiftDown())
{
// clone a new selection group from the associated group
{
if (jalview.util.Platform.isControlDown(evt)
|| evt.isShiftDown())
{
// clone a new selection group from the associated group
- ap.av.setSelectionGroup(new SequenceGroup(
- aa[selectedRow].groupRef));
+ ap.av.setSelectionGroup(
+ new SequenceGroup(aa[selectedRow].groupRef));
}
else
{
}
else
{
@@
-856,7
+855,7
@@
public class AnnotationLabels extends JPanel implements MouseListener,
}
}
}
}
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
@@
-871,10
+870,9
@@
public class AnnotationLabels extends JPanel implements MouseListener,
{
if (evt.getClickCount() == 1)
{
{
if (evt.getClickCount() == 1)
{
- ap.getSeqPanel().ap
- .getIdPanel()
- .highlightSearchResults(
- Arrays.asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ ap.getSeqPanel().ap.getIdPanel()
+ .highlightSearchResults(Arrays.asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
}
else if (evt.getClickCount() >= 2)
{
@@
-885,8
+883,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
// we make a copy rather than edit the current selection if no
// modifiers pressed
// see Enhancement JAL-1557
// we make a copy rather than edit the current selection if no
// modifiers pressed
// see Enhancement JAL-1557
- if (!(jalview.util.Platform.isControlDown(evt) || evt
- .isShiftDown()))
+ if (!(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
{
sg = new SequenceGroup(sg);
sg.clear();
@@
-914,7
+912,7
@@
public class AnnotationLabels extends JPanel implements MouseListener,
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
sg.addSequence(aa[selectedRow].sequenceRef, false);
}
ap.av.setSelectionGroup(sg);
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
@@
-948,18
+946,16
@@
public class AnnotationLabels extends JPanel implements MouseListener,
if (av.hasHiddenColumns())
{
omitHidden = av.getAlignment().getHiddenColumns()
if (av.hasHiddenColumns())
{
omitHidden = av.getAlignment().getHiddenColumns()
- .getVisibleSequenceStrings(0,
- sq.getLength(), seqs);
+ .getVisibleSequenceStrings(0, sq.getLength(), seqs);
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
}
int[] alignmentStartEnd = new int[] { 0, ds.getWidth() - 1 };
- List<int[]> hiddenCols = av.getAlignment().getHiddenColumns()
- .getListOfCols();
- if (hiddenCols != null)
+ if (av.hasHiddenColumns())
{
{
- alignmentStartEnd = av.getAlignment().getVisibleStartAndEndIndex(
- hiddenCols);
+ alignmentStartEnd = av.getAlignment().getHiddenColumns()
+ .getVisibleStartAndEndIndex(av.getAlignment().getWidth());
}
}
+
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
seqs, omitHidden, alignmentStartEnd);
String output = new FormatAdapter().formatSequences(FileFormat.Fasta,
seqs, omitHidden, alignmentStartEnd);
@@
-967,14
+963,11
@@
public class AnnotationLabels extends JPanel implements MouseListener,
.setContents(new StringSelection(output), Desktop.instance);
ArrayList<int[]> hiddenColumns = null;
.setContents(new StringSelection(output), Desktop.instance);
ArrayList<int[]> hiddenColumns = null;
+
if (av.hasHiddenColumns())
{
if (av.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<int[]>();
- for (int[] region : av.getAlignment().getHiddenColumns()
- .getListOfCols())
- {
- hiddenColumns.add(new int[] { region[0], region[1] });
- }
+ hiddenColumns = av.getAlignment().getHiddenColumns()
+ .getHiddenColumnsCopy();
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
@@
-1070,8
+1063,9
@@
public class AnnotationLabels extends JPanel implements MouseListener,
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
int ofontH = fontHeight;
int sOffset = 0;
int visHeight = 0;
- int[] visr = (ap != null && ap.getAnnotationPanel() != null) ? ap
- .getAnnotationPanel().getVisibleVRange() : null;
+ int[] visr = (ap != null && ap.getAnnotationPanel() != null)
+ ? ap.getAnnotationPanel().getVisibleVRange()
+ : null;
if (clip && visr != null)
{
sOffset = visr[0];
if (clip && visr != null)
{
sOffset = visr[0];
@@
-1114,8
+1108,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
{
if (debugRedraw)
{
{
if (debugRedraw)
{
- System.out.println("Scroll offset: " + sOffset
- + " after vis: " + i);
+ System.out.println(
+ "Scroll offset: " + sOffset + " after vis: " + i);
}
after = true;
}
}
after = true;
}
@@
-1153,7
+1147,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
}
if (groupSize * (fontHeight + 8) < aa[i].height)
{
}
if (groupSize * (fontHeight + 8) < aa[i].height)
{
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
else
{
}
else
{
@@
-1167,11
+1162,12
@@
public class AnnotationLabels extends JPanel implements MouseListener,
{
fontHeight = -8 + (int) h;
s = ((float) fontHeight) / (float) ofontH;
{
fontHeight = -8 + (int) h;
s = ((float) fontHeight) / (float) ofontH;
- Font f = baseFont.deriveFont(AffineTransform
- .getScaleInstance(s, s));
+ Font f = baseFont
+ .deriveFont(AffineTransform.getScaleInstance(s, s));
g.setFont(f);
fm = g.getFontMetrics();
g.setFont(f);
fm = g.getFontMetrics();
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
}
if (visible)
}
}
if (visible)
@@
-1188,8
+1184,8
@@
public class AnnotationLabels extends JPanel implements MouseListener,
g.setColor(aa[gg]._linecolour);
g.drawLine(x, y - graphExtras + 3,
g.setColor(aa[gg]._linecolour);
g.drawLine(x, y - graphExtras + 3,
- x + fm.stringWidth(aa[gg].label), y - graphExtras
- + 3);
+ x + fm.stringWidth(aa[gg].label),
+ y - graphExtras + 3);
}
g.setColor(Color.black);
}
g.setColor(Color.black);