import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import java.awt.event.MouseMotionListener;
import java.awt.geom.AffineTransform;
import java.awt.image.BufferedImage;
-import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collections;
-import java.util.List;
+import java.util.Iterator;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
* @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("<");
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))
{
// 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()
{
{
// 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
{
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();
- 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();
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];
// 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)
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
- ap.av.setSelectionGroup(new SequenceGroup(
- aa[selectedRow].groupRef));
+ ap.av.setSelectionGroup(
+ new SequenceGroup(aa[selectedRow].groupRef));
}
else
{
}
}
- ap.paintAlignment(false);
+ ap.paintAlignment(false, false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
ap.av.sendSelection();
}
{
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)
{
// 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.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();
}
Alignment ds = new Alignment(dseqs);
if (av.hasHiddenColumns())
{
- omitHidden = av.getAlignment().getHiddenColumns()
- .getVisibleSequenceStrings(0,
- sq.getLength(), seqs);
+ Iterator<int[]> it = av.getAlignment().getHiddenColumns()
+ .getVisContigsIterator(0, sq.getLength(), false);
+ omitHidden = new String[] { sq.getSequenceStringFromIterator(it) };
}
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);
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
- ArrayList<int[]> hiddenColumns = null;
+ HiddenColumns hiddenColumns = null;
+
if (av.hasHiddenColumns())
{
- hiddenColumns = new ArrayList<int[]>();
- for (int[] region : av.getAlignment().getHiddenColumns()
- .getListOfCols())
- {
- hiddenColumns.add(new int[] { region[0], region[1] });
- }
+ hiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
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 (debugRedraw)
{
- System.out.println("Scroll offset: " + sOffset
- + " after vis: " + i);
+ System.out.println(
+ "Scroll offset: " + sOffset + " after vis: " + i);
}
after = true;
}
}
if (groupSize * (fontHeight + 8) < aa[i].height)
{
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
else
{
{
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();
- graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8)))
+ / 2;
}
}
if (visible)
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);
git://source.jalview.org / jalview.git / blobdiff