/*
- * 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 2.8.2b1)
+ * Copyright (C) 2014 The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
- * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
- *
+ * as published by the Free Software Foundation, either version 3
+ * of the License, or (at your option) any later version.
+ *
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
- * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * You should have received a copy of the GNU General Public License
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.appletgui;
import java.util.*;
-
import java.awt.*;
import java.awt.event.*;
import jalview.datamodel.*;
+import jalview.util.MessageManager;
+import jalview.util.ParseHtmlBodyAndLinks;
public class AnnotationLabels extends Panel implements ActionListener,
MouseListener, MouseMotionListener
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);
}
this.av = av;
}
- public void setScrollOffset(int y)
+ public void setScrollOffset(int y, boolean repaint)
{
scrollOffset = y;
- repaint();
+ if (repaint)
+ {
+ repaint();
+ }
}
/**
int getSelectedRow(int y)
{
int row = -2;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (aa == null)
{
public void actionPerformed(ActionEvent evt)
{
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
- new Annotation[ap.av.alignment.getWidth()]);
+ new Annotation[ap.av.getAlignment().getWidth()]);
if (!editLabelDescription(newAnnotation))
{
return;
}
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
}
else if (evt.getActionCommand().equals(EDITNAME))
{
}
+ boolean resizePanel = false;
+
public void mouseMoved(MouseEvent evt)
{
- int row = getSelectedRow(evt.getY() - scrollOffset);
+ resizePanel = evt.getY() < 10 && evt.getX() < 14;
+ int row = getSelectedRow(evt.getY() + scrollOffset);
if (row > -1)
{
+ ParseHtmlBodyAndLinks phb = new ParseHtmlBodyAndLinks(
+ av.getAlignment().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(), f = ap.seqPanelHolder.getSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.charHeight;
+ dif *= ap.av.charHeight;
+
+ if ((d.height - dif) > 20 && (f.height + dif) > 20)
+ {
+ 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,
+ av.calcPanelHeight());
+ f.height += dif;
+ ap.seqPanelHolder.setPreferredSize(f);
+ ap.setScrollValues(av.getStartRes(), av.getStartSeq());
+ ap.validate();
+ // ap.paintAlignment(true);
+ 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 mouseClicked(MouseEvent evt)
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.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
+ {
+ end = ap.av.getAlignment().getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[end];
+
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
+ }
+ }
+ resizePanel = false;
+ dragEvent = null;
+ dragCancelled = false;
+ repaint();
+ ap.annotationPanel.repaint();
}
public void mouseEntered(MouseEvent evt)
{
+ if (evt.getY() < 10 && evt.getX() < 14)
+ {
+ resizePanel = true;
+ repaint();
+ }
}
public void mouseExited(MouseEvent evt)
{
+ dragCancelled = false;
+
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ }
+ else
+ {
+ if (!resizePanel)
+ {
+ dragEvent = null;
+ }
+ }
+ repaint();
}
public void mousePressed(MouseEvent evt)
{
- selectedRow = getSelectedRow(evt.getY() - scrollOffset);
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ oldY = evt.getY();
+ if (resizePanel)
+ {
+ return;
+ }
+ dragCancelled = false;
+ // todo: move below to mouseClicked ?
+ selectedRow = getSelectedRow(evt.getY() + scrollOffset);
+
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
// DETECT RIGHT MOUSE BUTTON IN AWT
if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
+ PopupMenu popup = new PopupMenu(
+ MessageManager.getString("label.annotations"));
- PopupMenu popup = new PopupMenu("Annotations");
-
- MenuItem item = new MenuItem(ADDNEW);
- item.addActionListener(this);
- popup.add(item);
- if (selectedRow < 0)
- {
- // this never happens at moment: - see comment on JAL-563
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow < 0)
+ {
+ // this never happens at moment: - see comment on JAL-563
+ if (hasHiddenRows)
+ {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ // add the rest if there are actually rows to show
+ item = new MenuItem(EDITNAME);
+ item.addActionListener(this);
+ popup.add(item);
+ item = new MenuItem(HIDE);
+ item.addActionListener(this);
+ popup.add(item);
if (hasHiddenRows)
{
item = new MenuItem(SHOWALL);
popup.add(item);
}
this.add(popup);
- popup.show(this, evt.getX(), evt.getY());
- return;
- }
- // add the rest if there are actually rows to show
- item = new MenuItem(EDITNAME);
- item.addActionListener(this);
- popup.add(item);
- item = new MenuItem(HIDE);
- item.addActionListener(this);
- popup.add(item);
- if (hasHiddenRows)
- {
- item = new MenuItem(SHOWALL);
+ item = new MenuItem(OUTPUT_TEXT);
item.addActionListener(this);
popup.add(item);
- }
- this.add(popup);
- item = new MenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- popup.add(item);
-
- if (aa[selectedRow] == ap.av.consensus)
- {
- popup.addSeparator();
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
-
- cbmi.addItemListener(new ItemListener()
+ if (selectedRow < aa.length)
{
- public void itemStateChanged(ItemEvent e)
+ if (aa[selectedRow].autoCalculated)
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.paintAlignment(true);
+ if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ popup.addSeparator();
+ final CheckboxMenuItem cbmi = new CheckboxMenuItem(
+ MessageManager.getString("label.ignore_gaps_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(
+ MessageManager.getString("label.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(
+ MessageManager.getString("label.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);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ MessageManager.getString("label.normalise_group_logo"),
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setshowSequenceLogo(true);
+ aaa.groupRef.setNormaliseSequenceLogo(cprofn.getState());
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprofn);
+ }
+ else
+ {
+ final CheckboxMenuItem chist = new CheckboxMenuItem(
+ MessageManager.getString("label.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.alignFrame.showConsensusHistogram.setState(chist
+ .getState()); // TODO: implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for applet
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(chist);
+ final CheckboxMenuItem cprof = new CheckboxMenuItem(
+ MessageManager.getString("label.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.alignFrame.showSequenceLogo.setState(cprof.getState()); // TODO:
+ // implement
+ // ap.updateGUI()/alignFrame.updateGUI
+ // for
+ // applet
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ popup.add(cprof);
+ final CheckboxMenuItem cprofn = new CheckboxMenuItem(
+ MessageManager.getString("label.normalise_logo"), av.isNormaliseSequenceLogo());
+ cprofn.addItemListener(new ItemListener()
+ {
+ public void itemStateChanged(ItemEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ 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());
+ }
+ });
+ popup.add(cprofn);
+ }
+
+ 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());
}
-
- popup.show(this, evt.getX(), evt.getY());
- } else {
+ else
+ {
// selection action.
if (selectedRow > -1 && selectedRow < aa.length)
{
{
if (evt.getClickCount() >= 2)
{
- // todo: make the ap scroll to the selection - not necessary, first click highlights/scrolls, second selects
+ // 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); // );
}
else if (aa[selectedRow].sequenceRef != null)
{
- Vector sr = new Vector();
- sr.addElement(aa[selectedRow].sequenceRef);
if (evt.getClickCount() == 1)
{
- ap.seqPanel.ap.idPanel.highlightSearchResults(sr);
+ ap.seqPanel.ap.idPanel.highlightSearchResults(Arrays
+ .asList(new SequenceI[]
+ { aa[selectedRow].sequenceRef }));
}
else if (evt.getClickCount() >= 2)
{
ap.seqPanel.ap.idPanel.highlightSearchResults(null);
- SequenceGroup sg = new SequenceGroup();
- sg.addSequence(aa[selectedRow].sequenceRef, false);
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ if (sg!=null)
+ {
+ // we make a copy rather than edit the current selection if no modifiers pressed
+ // see Enhancement JAL-1557
+ if (!(evt.isControlDown() || evt.isShiftDown()))
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ } else {
+ if (evt.isControlDown())
+ {
+ sg.addOrRemove(aa[selectedRow].sequenceRef, true);
+ } else {
+ // notionally, we should also add intermediate sequences from last added sequence ?
+ sg.addSequence(aa[selectedRow].sequenceRef, true);
+ }
+ }
+ } else {
+ sg = new SequenceGroup();
+ sg.setStartRes(0);
+ sg.setEndRes(ap.av.getAlignment().getWidth()-1);
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ }
ap.av.setSelectionGroup(sg);
ap.paintAlignment(false);
PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+ sq.getStart() + "\t" + sq.getEnd() + "\t"
+ sq.getSequenceAsString() + "\n");
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
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.setColor(Color.white);
g.fillRect(0, 0, getSize().width, getSize().height);
- g.translate(0, scrollOffset);
+ g.translate(0, -scrollOffset);
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int y = 0, fy = g.getFont().getSize();
int x = 0, offset;
g.drawString(aa[i].label, x, y + offset);
}
}
- }
+ 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)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY());
+ }
+ if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ {
+ g.setColor(Color.black);
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff