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.FontMetrics;
import java.awt.Graphics;
import java.awt.Graphics2D;
-import java.awt.Image;
-import java.awt.MediaTracker;
import java.awt.RenderingHints;
import java.awt.Toolkit;
import java.awt.datatransfer.StringSelection;
import java.awt.event.MouseListener;
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.Iterator;
import java.util.regex.Pattern;
import javax.swing.JCheckBoxMenuItem;
public class AnnotationLabels extends JPanel
implements MouseListener, MouseMotionListener, ActionListener
{
- // width in pixels within which height adjuster arrows are shown and active
+ /**
+ * width in pixels within which height adjuster arrows are shown and active
+ */
private static final int HEIGHT_ADJUSTER_WIDTH = 50;
+ /**
+ * height in pixels for allowing height adjuster to be active
+ */
+ private static int HEIGHT_ADJUSTER_HEIGHT = 10;
+
private static final Pattern LEFT_ANGLE_BRACKET_PATTERN = Pattern
.compile("<");
private static final String COPYCONS_SEQ = MessageManager
.getString("label.copy_consensus_sequence");
- private static Image adjusterImage;
-
- private static int adjusterImageHeight;
-
private final boolean debugRedraw = false;
private AlignmentPanel ap;
av = ap.av;
ToolTipManager.sharedInstance().registerComponent(this);
- if (adjusterImage == null)
- {
- loadAdjusterImage();
- }
-
addMouseListener(this);
addMouseMotionListener(this);
addMouseWheelListener(ap.getAnnotationPanel());
}
/**
- * Loads the gif for the panel height adjustment
- */
- protected void loadAdjusterImage()
- {
- java.net.URL url = getClass().getResource("/images/idwidth.gif");
- Image temp = null;
-
- if (url != null)
- {
- temp = Toolkit.getDefaultToolkit().createImage(url);
- }
-
- try
- {
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(temp, 0);
- mt.waitForID(0);
- } catch (Exception ex)
- {
- }
-
- BufferedImage bi = new BufferedImage(temp.getHeight(this),
- temp.getWidth(this), BufferedImage.TYPE_INT_RGB);
- Graphics2D g = (Graphics2D) bi.getGraphics();
- g.rotate(Math.toRadians(90));
- g.drawImage(temp, 0, -bi.getWidth(this), this);
- adjusterImage = bi;
- adjusterImageHeight = bi.getHeight();
- }
-
- /**
* DOCUMENT ME!
*
* @param y
if (!ann.groupRef.isUseInfoLetterHeight())
{
ann.groupRef.setIgnoreBelowBackground(cbmi.getState());
+ // todo and recompute group annotation
}
}
else if (!ap.av.isInfoLetterHeight())
{
ap.av.setIgnoreBelowBackground(cbmi.getState(), ap);
+ // todo and recompute annotation
}
- ap.alignmentChanged();
+ ap.alignmentChanged(); // todo not like this
}
});
pop.add(cbmi);
{
ann.groupRef.setInfoLetterHeight((letterHeight.getState()));
ann.groupRef.setIgnoreBelowBackground(true);
+ // todo and recompute group annotation
}
else
{
ap.av.setInfoLetterHeight(letterHeight.getState(), ap);
ap.av.setIgnoreBelowBackground(true, ap);
+ // todo and recompute annotation
}
ap.alignmentChanged();
}
@Override
public void actionPerformed(ActionEvent e)
{
- ann.groupRef.setshowHMMSequenceLogo(cprofl.getState());
+ ann.groupRef.setShowHMMSequenceLogo(cprofl.getState());
ap.repaint();
}
});
ann.groupRef
.setNormaliseHMMSequenceLogo(cproflnorm.getState());
// automatically enable logo display if we're clicked
- ann.groupRef.setshowHMMSequenceLogo(true);
+ ann.groupRef.setShowHMMSequenceLogo(true);
ap.repaint();
}
});
@Override
public void actionPerformed(ActionEvent e)
{
- av.updateInformation(ap);
av.setShowHMMSequenceLogo(cprof.getState());
ap.repaint();
}
{
// begin the tooltip's html fragment
desc.append("<html>");
- if (aa.hasScore())
- {
- // TODO: limit precision of score to avoid noise from imprecise
- // doubles
- // (64.7 becomes 64.7+/some tiny value).
- desc.append(" Score: " + aa.score);
- }
}
+
+ if (aa.hasScore())
+ {
+ // TODO: limit precision of score to avoid noise from imprecise
+ // doubles
+ // (64.7 becomes 64.7+/some tiny value).
+ desc.append(" Score: " + aa.score);
+ }
+
if (desc.length() > 6)
{
desc.append("</html>");
protected void showOrHideAdjuster(MouseEvent evt)
{
boolean was = resizePanel;
- resizePanel = evt.getY() < adjusterImageHeight && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
if (resizePanel != was)
{
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 };
Toolkit.getDefaultToolkit().getSystemClipboard()
.setContents(new StringSelection(output), Desktop.instance);
- ArrayList<int[]> hiddenColumns = null;
+ HiddenColumns hiddenColumns = null;
if (av.hasHiddenColumns())
{
-
- hiddenColumns = av.getAlignment().getHiddenColumns()
- .getHiddenColumnsCopy();
+ hiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
}
Desktop.jalviewClipboard = new Object[] { seqs, ds, // what is the dataset
}
}
- if (resizePanel)
- {
- // g.drawImage(adjusterImage, 2, 0 - getScrollOffset(), this);
- }
- else if (dragEvent != null && aa != null)
+ if (!resizePanel && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
git://source.jalview.org / jalview.git / blobdiff