/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * This program 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 2
- * of the License, or (at your option) any later version.
- *
- * This program 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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.
+ *
+ * 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/>.
*/
-
package jalview.appletgui;
import java.util.*;
import java.awt.*;
import java.awt.event.*;
+import java.awt.image.BufferedImage;
import jalview.datamodel.*;
+import jalview.util.ParseHtmlBodyAndLinks;
-public class AnnotationLabels
- extends Panel implements ActionListener, MouseListener, MouseMotionListener
+public class AnnotationLabels extends Panel implements ActionListener,
+ MouseListener, MouseMotionListener
{
Image image;
+
boolean active = false;
+
AlignmentPanel ap;
+
AlignViewport av;
+
boolean resizing = false;
+
int oldY, mouseX;
static String ADDNEW = "Add New Row";
+
static String EDITNAME = "Edit Label/Description";
+
static String HIDE = "Hide This Row";
+
static String SHOWALL = "Show All Hidden Rows";
+
static String OUTPUT_TEXT = "Show Values In Textbox";
+
static String COPYCONS_SEQ = "Copy Consensus Sequence";
int scrollOffset = 0;
+
int selectedRow = -1;
Tooltip tooltip;
+ private boolean hasHiddenRows;
+
public AnnotationLabels(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);
}
repaint();
}
+ /**
+ *
+ * @param y
+ * @return -2 if no rows are visible at all, -1 if no visible rows were
+ * selected
+ */
int getSelectedRow(int y)
{
- int row = -1;
+ int row = -2;
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
if (aa == null)
{
return row;
}
-
int height = 0;
for (int i = 0; i < aa.length; i++)
{
+ row = -1;
if (!aa[i].visible)
{
continue;
}
-
height += aa[i].height;
if (y < height)
{
if (evt.getActionCommand().equals(ADDNEW))
{
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation("",
- null,
- new Annotation[ap.av.alignment.getWidth()]);
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+ new Annotation[ap.av.alignment.getWidth()]);
if (!editLabelDescription(newAnnotation))
{
{
for (int i = 0; i < aa.length; i++)
{
- aa[i].visible = (aa[i].annotations==null) ? false : true;
+ aa[i].visible = (aa[i].annotations == null) ? false : true;
}
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+ 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))
boolean editLabelDescription(AlignmentAnnotation annotation)
{
Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
- +ap.av.getGapCharacter()+"\"",
- annotation.padGaps);
-
- EditNameDialog dialog = new EditNameDialog(
- annotation.label,
- annotation.description,
- " Annotation Label",
- "Annotation Description",
- ap.alignFrame,
- "Edit Annotation Name / Description",
- 500, 180, false);
+ + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description, " Annotation Label",
+ "Annotation Description", ap.alignFrame,
+ "Edit Annotation Name / Description", 500, 180, false);
Panel empty = new Panel(new FlowLayout());
empty.add(padGaps);
}
+ 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.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(), 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,
+ ap.annotationPanel.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.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 && 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);
+ oldY = evt.getY();
+ if (resizePanel)
+ {
+ return;
+ }
+ dragCancelled=false;
+ // todo: move below to mouseClicked ?
+ selectedRow = getSelectedRow(evt.getY() + scrollOffset);
AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- PopupMenu popup = new PopupMenu("Annotations");
-
- MenuItem item = new MenuItem(ADDNEW);
- item.addActionListener(this);
- popup.add(item);
- item = new MenuItem(EDITNAME);
- item.addActionListener(this);
- popup.add(item);
- item = new MenuItem(HIDE);
- item.addActionListener(this);
- popup.add(item);
- item = new MenuItem(SHOWALL);
- 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)
+ // DETECT RIGHT MOUSE BUTTON IN AWT
+ if ((evt.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
{
- popup.addSeparator();
- final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus",
- ap.av.getIgnoreGapsConsensus());
- cbmi.addItemListener(new ItemListener()
+ PopupMenu popup = new PopupMenu("Annotations");
+
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow < 0)
{
- public void itemStateChanged(ItemEvent e)
+ // this never happens at moment: - see comment on JAL-563
+ if (hasHiddenRows)
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.paintAlignment(true);
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
}
- });
- popup.add(cbmi);
- item = new MenuItem(COPYCONS_SEQ);
+ 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.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ item = new MenuItem(OUTPUT_TEXT);
item.addActionListener(this);
popup.add(item);
+ if (selectedRow < aa.length)
+ {
+ if (aa[selectedRow].autoCalculated)
+ {
+ if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ 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.show(this, evt.getX(), evt.getY());
}
+ else
+ {
+ // selection action.
+ if (selectedRow > -1 && selectedRow < aa.length)
+ {
+ if (aa[selectedRow].groupRef != null)
+ {
+ if (evt.getClickCount() >= 2)
+ {
+ // 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);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ }
+ else
+ {
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(aa[selectedRow].groupRef
+ .getSequences(null));
+ }
+ return;
+ }
+ 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);
+ }
+ else if (evt.getClickCount() >= 2)
+ {
+ ap.seqPanel.ap.idPanel.highlightSearchResults(null);
+ SequenceGroup sg = new SequenceGroup();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ ap.av.setSelectionGroup(sg);
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
- popup.show(this, evt.getX(), evt.getY());
+ }
+ }
+ }
}
/**
* DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
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 i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
{
- int[] region = (int[])
- av.getColumnSelection().getHiddenColumns().elementAt(i);
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(i);
- jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]
- {region[0],
- region[1]});
+ jalview.appletgui.AlignFrame.copiedHiddenColumns
+ .addElement(new int[]
+ { region[0], region[1] });
}
}
}
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();
- int y = g.getFont().getSize();
- int x = 0;
+ int y = 0, fy = g.getFont().getSize();
+ int x = 0, offset;
if (aa != null)
{
+ hasHiddenRows = false;
for (int i = 0; i < aa.length; i++)
{
if (!aa[i].visible)
{
+ hasHiddenRows = true;
continue;
}
x = width - fm.stringWidth(aa[i].label) - 3;
- if (aa[i].graph > 0)
- {
- y += (aa[i].height / 3);
- }
+ y += aa[i].height;
+ offset = -(aa[i].height - fy) / 2;
- g.drawString(aa[i].label, x, y);
-
- if (aa[i].graph > 0)
- {
- y += (2 * aa[i].height / 3);
- }
- else
- {
- y += aa[i].height;
- }
+ 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 ((aa == null) || (aa.length < 1))
+ {
+ g.setColor(Color.black);
+ g.drawString("Right click", 2, 8);
+ g.drawString("to add annotation", 2, 18);
+ }
+ }
}
git://source.jalview.org / jalview.git / blobdiff