import jalview.analysis.AlignmentUtils;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.Annotation;
+import jalview.datamodel.HiddenColumns;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.util.MessageManager;
import java.awt.Checkbox;
import java.awt.CheckboxMenuItem;
import java.awt.Color;
+import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.FlowLayout;
import java.awt.FontMetrics;
import java.awt.event.MouseMotionListener;
import java.util.Arrays;
import java.util.Collections;
-import java.util.Vector;
-public class AnnotationLabels extends Panel implements ActionListener,
- MouseListener, MouseMotionListener
+public class AnnotationLabels extends Panel
+ implements ActionListener, MouseListener, MouseMotionListener
{
Image image;
+ /**
+ * 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;
+
boolean active = false;
AlignmentPanel ap;
this.ap = ap;
this.av = ap.av;
setLayout(null);
-
- /**
- * this retrieves the adjustable height glyph from resources. we don't use
- * it at the moment. java.net.URL url =
- * getClass().getResource("/images/idwidth.gif"); Image temp = null;
- *
- * if (url != null) { temp =
- * java.awt.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); image = (Image) bi;
- */
addMouseListener(this);
addMouseMotionListener(this);
}
return row;
}
+ @Override
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
ap.alignFrame);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
- + " - " + aa[selectedRow].label, 500, 100);
+ jalview.bin.JalviewLite.addFrame(frame,
+ ap.alignFrame.getTitle() + " - " + aa[selectedRow].label, 500,
+ 100);
cap.setText(aa[selectedRow].toString());
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- SequenceI cons = av.getConsensusSeq();
+ SequenceGroup group = aa[selectedRow].groupRef;
+ SequenceI cons = group == null ? av.getConsensusSeq()
+ : group.getConsensusSeq();
if (cons != null)
{
copy_annotseqtoclipboard(cons);
ap.annotationPanel.adjustPanelHeight();
setSize(getSize().width, ap.annotationPanel.getSize().height);
ap.validate();
- ap.paintAlignment(true);
+ // TODO: only paint if we needed to
+ ap.paintAlignment(true, true);
}
boolean editLabelDescription(AlignmentAnnotation annotation)
{
- Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
- + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+ Checkbox padGaps = new Checkbox(
+ "Fill Empty Gaps With \"" + ap.av.getGapCharacter() + "\"",
+ annotation.padGaps);
EditNameDialog dialog = new EditNameDialog(annotation.label,
annotation.description, " Annotation Label",
boolean resizePanel = false;
+ @Override
public void mouseMoved(MouseEvent evt)
{
- resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ resizePanel = evt.getY() < HEIGHT_ADJUSTER_HEIGHT
+ && evt.getX() < HEIGHT_ADJUSTER_WIDTH;
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
int row = getSelectedRow(evt.getY() + scrollOffset);
if (row > -1)
dragCancelled = true;
}
+ @Override
public void mouseDragged(MouseEvent evt)
{
if (dragCancelled)
if (resizePanel)
{
- Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
- .getSize(), f = ap.seqPanelHolder.getSize();
+ Dimension d = ap.annotationPanelHolder.getSize(),
+ e = ap.annotationSpaceFillerHolder.getSize(),
+ f = ap.seqPanelHolder.getSize();
int dif = evt.getY() - oldY;
dif /= ap.av.getCharHeight();
{
ap.annotationPanel.setSize(d.width, d.height - dif);
setSize(new Dimension(e.width, d.height - dif));
- ap.annotationSpaceFillerHolder.setSize(new Dimension(e.width,
- d.height - dif));
- ap.annotationPanelHolder.setSize(new Dimension(d.width, d.height
- - dif));
+ ap.annotationSpaceFillerHolder
+ .setSize(new Dimension(e.width, d.height - dif));
+ ap.annotationPanelHolder
+ .setSize(new Dimension(d.width, d.height - dif));
ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
av.calcPanelHeight());
f.height += dif;
ap.seqPanelHolder.setPreferredSize(f);
- ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+ ap.setScrollValues(av.getRanges().getStartRes(),
+ av.getRanges().getStartSeq());
ap.validate();
// ap.paintAlignment(true);
ap.addNotify();
}
}
+ @Override
public void mouseClicked(MouseEvent evt)
{
}
+ @Override
public void mouseReleased(MouseEvent evt)
{
if (!resizePanel && !dragCancelled)
resizePanel = false;
dragEvent = null;
dragCancelled = false;
+ setCursor(Cursor.getPredefinedCursor(Cursor.DEFAULT_CURSOR));
repaint();
ap.annotationPanel.repaint();
}
+ @Override
public void mouseEntered(MouseEvent evt)
{
if (evt.getY() < 10 && evt.getX() < 14)
resizePanel = true;
repaint();
}
+ setCursor(Cursor.getPredefinedCursor(
+ resizePanel ? Cursor.S_RESIZE_CURSOR : Cursor.DEFAULT_CURSOR));
}
+ @Override
public void mouseExited(MouseEvent evt)
{
dragCancelled = false;
repaint();
}
+ @Override
public void mousePressed(MouseEvent evt)
{
oldY = evt.getY();
.getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
- if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
+ if ((evt.getModifiersEx()
+ & InputEvent.BUTTON3_DOWN_MASK) == InputEvent.BUTTON3_DOWN_MASK)
{
PopupMenu popup = new PopupMenu(
popup.addSeparator();
final CheckboxMenuItem cbmi = new CheckboxMenuItem(
MessageManager.getString("label.ignore_gaps_consensus"),
- (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
- .getIgnoreGapsConsensus() : ap.av
- .isIgnoreGapsConsensus());
+ (aa[selectedRow].groupRef != null)
+ ? aa[selectedRow].groupRef
+ .isIgnoreGapsConsensus()
+ : ap.av.isIgnoreGapsConsensus());
final AlignmentAnnotation aaa = aa[selectedRow];
cbmi.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
if (aaa.groupRef != null)
{
ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
}
- ap.paintAlignment(true);
+ ap.paintAlignment(true, true);
}
});
popup.add(cbmi);
aa[selectedRow].groupRef.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
aa[selectedRow].groupRef.isShowSequenceLogo());
cprofl.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
aa[selectedRow].groupRef.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
av.isShowConsensusHistogram());
chist.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
// can be
// updated.
av.setShowConsensusHistogram(chist.getState());
- ap.alignFrame.showConsensusHistogram.setState(chist
- .getState()); // TODO: implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for applet
+ ap.alignFrame.showConsensusHistogram
+ .setState(chist.getState()); // TODO: implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for applet
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
}
av.isShowSequenceLogo());
cprof.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
av.isNormaliseSequenceLogo());
cprofn.addItemListener(new ItemListener()
{
+ @Override
public void itemStateChanged(ItemEvent e)
{
// TODO: pass on reference
// can be
// updated.
av.setShowSequenceLogo(true);
- ap.alignFrame.normSequenceLogo.setState(cprofn.getState()); // TODO:
- // implement
- // ap.updateGUI()/alignFrame.updateGUI
- // for
- // applet
+ ap.alignFrame.normSequenceLogo
+ .setState(cprofn.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
av.setNormaliseSequenceLogo(cprofn.getState());
ap.repaint();
// ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
// todo: make the ap scroll to the selection - not necessary, first
// click highlights/scrolls, second selects
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- ap.av.setSelectionGroup(// new SequenceGroup(
- aa[selectedRow].groupRef); // );
- ap.av.sendSelection();
- ap.paintAlignment(false);
+ // process modifiers
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ 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));
+ }
+ else
+ {
+ // set selection to the associated group so it can be edited
+ ap.av.setSelectionGroup(aa[selectedRow].groupRef);
+ }
+ }
+ else
+ {
+ // modify current selection with associated group
+ int remainToAdd = aa[selectedRow].groupRef.getSize();
+ for (SequenceI sgs : aa[selectedRow].groupRef.getSequences())
+ {
+ if (jalview.util.Platform.isControlDown(evt))
+ {
+ sg.addOrRemove(sgs, --remainToAdd == 0);
+ }
+ else
+ {
+ // notionally, we should also add intermediate sequences from
+ // last added sequence ?
+ sg.addSequence(sgs, --remainToAdd == 0);
+ }
+ }
+ }
+ ap.paintAlignment(false, false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
}
else
{
- ap.seqPanel.ap.idPanel
- .highlightSearchResults(aa[selectedRow].groupRef
- .getSequences(null));
+ ap.seqPanel.ap.idPanel.highlightSearchResults(
+ aa[selectedRow].groupRef.getSequences(null));
}
return;
}
if (evt.getClickCount() == 1)
{
ap.seqPanel.ap.idPanel
- .highlightSearchResults(Arrays
- .asList(new SequenceI[] { aa[selectedRow].sequenceRef }));
+ .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 (!(evt.isControlDown() || evt.isShiftDown()))
+ if (!(jalview.util.Platform.isControlDown(evt)
+ || evt.isShiftDown()))
{
sg = new SequenceGroup(sg);
sg.clear();
}
else
{
- if (evt.isControlDown())
+ if (jalview.util.Platform.isControlDown(evt))
{
sg.addOrRemove(aa[selectedRow].sequenceRef, true);
}
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();
}
return;
}
jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
- jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
- + sq.getStart() + "\t" + sq.getEnd() + "\t"
- + sq.getSequenceAsString() + "\n");
+ jalview.appletgui.AlignFrame.copiedSequences
+ .append(sq.getName() + "\t" + sq.getStart() + "\t" + sq.getEnd()
+ + "\t" + sq.getSequenceAsString() + "\n");
if (av.hasHiddenColumns())
{
- jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
- for (int[] region : av.getColumnSelection().getHiddenColumns())
- {
- jalview.appletgui.AlignFrame.copiedHiddenColumns
- .addElement(new int[] { region[0], region[1] });
- }
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new HiddenColumns(
+ av.getAlignment().getHiddenColumns());
}
}
+ @Override
public void update(Graphics g)
{
paint(g);
}
+ @Override
public void paint(Graphics g)
{
int w = getSize().width;
}
}
g.translate(0, +scrollOffset);
- if (resizePanel)
- {
- g.setColor(Color.red);
- g.setPaintMode();
- g.drawLine(2, 8, 5, 2);
- g.drawLine(5, 2, 8, 8);
- }
- else if (!dragCancelled && dragEvent != null && aa != null)
+
+ if (!resizePanel && !dragCancelled && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
git://source.jalview.org / jalview.git / blobdiff