/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
- * Copyright (C) 2010 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
*
* This file is part of Jalview.
*
import java.awt.image.BufferedImage;
import jalview.datamodel.*;
+import jalview.util.ParseHtmlBodyAndLinks;
public class AnnotationLabels extends Panel implements ActionListener,
MouseListener, MouseMotionListener
this.av = ap.av;
setLayout(null);
- 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;
-
+ /**
+ * 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);
}
public void mouseMoved(MouseEvent evt)
{
- resizePanel = evt.getY() < 10;
-
+ resizePanel = evt.getY() < 10 && evt.getX() < 14;
int row = getSelectedRow(evt.getY() + scrollOffset);
if (row > -1)
{
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(av.alignment.getAlignmentAnnotation()[row].getDescription(true), true, "\n");
if (tooltip == null)
{
- tooltip = new Tooltip(
- ap.av.alignment.getAlignmentAnnotation()[row]
- .getDescription(true),
- this);
+ tooltip = new Tooltip(phb.getNonHtmlContent(), this);
}
else
{
- tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row]
- .getDescription(true));
+ tooltip.setTip(phb.getNonHtmlContent());
}
}
else if (tooltip != null)
{
tooltip.setTip("");
}
-
}
+ /**
+ * curent drag position
+ */
MouseEvent dragEvent = null;
+ /**
+ * flag to indicate drag events should be ignored
+ */
+ private boolean dragCancelled = false;
+
+ /**
+ * clear any drag events in progress
+ */
+ public void cancelDrag()
+ {
+ dragEvent = null;
+ dragCancelled = true;
+ }
+
public void mouseDragged(MouseEvent evt)
{
+ if (dragCancelled)
+ {
+ return;
+ }
+ ;
dragEvent = evt;
if (resizePanel)
{
- Dimension d = ap.annotationPanelHolder.getSize(),e = ap.annotationSpaceFillerHolder.getSize();;
+ Dimension d = ap.annotationPanelHolder.getSize(), e = ap.annotationSpaceFillerHolder
+ .getSize(), f = ap.seqPanelHolder.getSize();
int dif = evt.getY() - oldY;
dif /= ap.av.charHeight;
dif *= ap.av.charHeight;
- if ((d.height - dif) > 20)
+ if ((d.height - dif) > 20 && (f.height + dif) > 20)
{
-
- setPreferredSize(new Dimension(e.width,d.height-dif));
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(e.width, d.height - dif));
- ap.annotationPanelHolder.setPreferredSize(new Dimension(d.width, d.height - dif));
- ap.apvscroll.setValues(ap.apvscroll.getValue(), d.height-dif, 0, ap.annotationPanel.adjustPanelHeight(false));
-
+ 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.apvscroll.setValues(ap.apvscroll.getValue(), d.height - dif, 0,
+ ap.annotationPanel.calcPanelHeight());
+ f.height += dif;
+ ap.seqPanelHolder.setPreferredSize(f);
+ ap.setScrollValues(av.getStartRes(), av.getStartSeq());
ap.validate();
- //ap.paintAlignment(true);
+ // ap.paintAlignment(true);
+ ap.addNotify();
}
- ap.addNotify();
}
else
{
+ int diff;
+ if ((diff = 6 - evt.getY()) > 0)
+ {
+ // nudge scroll up
+ ap.apvscroll.setValue(ap.apvscroll.getValue() - diff);
+ ap.adjustmentValueChanged(null);
+
+ }
+ else if ((0 < (diff = 6
+ - ap.annotationSpaceFillerHolder.getSize().height
+ + evt.getY())))
+ {
+ // nudge scroll down
+ ap.apvscroll.setValue(ap.apvscroll.getValue() + diff);
+ ap.adjustmentValueChanged(null);
+ }
repaint();
}
}
public void mouseReleased(MouseEvent evt)
{
+ if (!resizePanel && !dragCancelled)
+ {
+ int start = selectedRow;
+
+ int end = getSelectedRow(evt.getY() + scrollOffset);
+
+ if (start>-1 && start != end)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.alignment
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.alignment
+ .getAlignmentAnnotation()[end];
+
+ ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+ ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+ }
+ }
resizePanel = false;
dragEvent = null;
+ dragCancelled = false;
repaint();
ap.annotationPanel.repaint();
}
public void mouseEntered(MouseEvent evt)
{
- if (evt.getY() < 10)
+ if (evt.getY() < 10 && evt.getX() < 14)
{
resizePanel = true;
repaint();
public void mouseExited(MouseEvent evt)
{
+ dragCancelled = false;
if (dragEvent == null)
{
public void mousePressed(MouseEvent evt)
{
oldY = evt.getY();
+ if (resizePanel)
+ {
+ return;
+ }
+ dragCancelled=false;
// todo: move below to mouseClicked ?
selectedRow = getSelectedRow(evt.getY() + scrollOffset);
item = new MenuItem(OUTPUT_TEXT);
item.addActionListener(this);
popup.add(item);
-
- if (aa[selectedRow] == ap.av.consensus)
+ if (selectedRow < aa.length)
{
- popup.addSeparator();
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
-
- cbmi.addItemListener(new ItemListener()
+ if (aa[selectedRow].autoCalculated)
{
- public void itemStateChanged(ItemEvent e)
+ if (aa[selectedRow].label.indexOf("Consensus") > -1)
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.paintAlignment(true);
+ popup.addSeparator();
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+ "Ignore Gaps In Consensus",
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .getIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState());
+ }
+ ap.paintAlignment(true);
+ }
+ });
+ popup.add(cbmi);
+ if (aaa.groupRef != null)
+ {
+ final CheckboxMenuItem chist = new CheckboxMenuItem(
+ "Show Group Histogram",
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(chist);
+ final CheckboxMenuItem cprofl = new CheckboxMenuItem(
+ "Show Group Logo",
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(cprofl.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofl);
+ }
+ else
+ {
+ final CheckboxMenuItem chist = new CheckboxMenuItem(
+ "Show Histogram", av.isShowConsensusHistogram());
+ chist.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(chist);
+ final CheckboxMenuItem cprof = new CheckboxMenuItem(
+ "Show Logo", av.isShowSequenceLogo());
+ cprof.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(cprof.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprof);
+ }
+
+ item = new MenuItem(COPYCONS_SEQ);
+ item.addActionListener(this);
+ popup.add(item);
}
- });
- popup.add(cbmi);
- item = new MenuItem(COPYCONS_SEQ);
- item.addActionListener(this);
- popup.add(item);
+ }
}
-
popup.show(this, evt.getX(), evt.getY());
}
else
public void paint(Graphics g)
{
int w = getSize().width;
- if (image == null || w != image.getWidth(this))
+ int h = getSize().height;
+ if (image == null || w != image.getWidth(this) || h!=image.getHeight(this) )
{
image = createImage(w, ap.annotationPanel.getSize().height);
}
g.drawLine(2, 8, 5, 2);
g.drawLine(5, 2, 8, 8);
}
- else if (dragEvent != null && aa != null)
+ else if (!dragCancelled && dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
g.drawString("to add annotation", 2, 18);
}
}
-
}
git://source.jalview.org / jalview.git / blobdiff