/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2006 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
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8.2)
+ * 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.
- *
- * 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.
- *
+ *
+ * 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 this program; if not, write to the Free Software
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import jalview.datamodel.*;
-import jalview.io.FormatAdapter;
+import java.util.*;
+import java.util.regex.Pattern;
import java.awt.*;
-import java.awt.datatransfer.StringSelection;
+import java.awt.datatransfer.*;
import java.awt.event.*;
+import java.awt.geom.AffineTransform;
import java.awt.image.*;
-import java.util.Vector;
-
import javax.swing.*;
+import jalview.datamodel.*;
+import jalview.io.*;
+import jalview.util.MessageManager;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
public class AnnotationLabels extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener
+ MouseMotionListener, ActionListener
{
- static String ADDNEW = "Add New Row";
- static String EDITNAME="Edit Label/Description";
- static String HIDE = "Hide This Row";
- static String DELETE = "Delete This Row";
- static String SHOWALL = "Show All Hidden Rows";
- static String OUTPUT_TEXT = "Export Annotation";
- static String COPYCONS_SEQ = "Copy Consensus Sequence";
- boolean resizePanel = false;
- Image image;
- AlignmentPanel ap;
- AlignViewport av;
- boolean resizing = false;
- MouseEvent dragEvent;
- int oldY;
- int selectedRow;
- int scrollOffset = 0;
- Font font = new Font("Arial", Font.PLAIN, 11);
-
-
- /**
- * Creates a new AnnotationLabels object.
- *
- * @param ap DOCUMENT ME!
- */
- public AnnotationLabels(AlignmentPanel ap)
- {
- this.ap = ap;
- av = ap.av;
- ToolTipManager.sharedInstance().registerComponent(this);
-
- java.net.URL url = getClass().getResource("/images/idwidth.gif");
- Image temp = null;
-
- if (url != null)
- {
- temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
- }
+ String TOGGLE_LABELSCALE = MessageManager.getString("label.scale_label_to_column");
- try
- {
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(temp, 0);
- mt.waitForID(0);
- }
- catch (Exception ex)
- {
- }
+ String ADDNEW = MessageManager.getString("label.add_new_row");
- 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;
+ String EDITNAME = MessageManager.getString("label.edit_label_description");
- addMouseListener(this);
- addMouseMotionListener(this);
- }
+ String HIDE = MessageManager.getString("label.hide_row");
+
+ String DELETE = MessageManager.getString("label.delete_row");
+
+ String SHOWALL = MessageManager.getString("label.show_all_hidden_rows");
+
+ String OUTPUT_TEXT = MessageManager.getString("label.export_annotation");
+
+ String COPYCONS_SEQ = MessageManager.getString("label.copy_consensus_sequence");
+
+ boolean resizePanel = false;
+
+ Image image;
+
+ AlignmentPanel ap;
+
+ AlignViewport av;
- public AnnotationLabels(AlignViewport av)
+ boolean resizing = false;
+
+ MouseEvent dragEvent;
+
+ int oldY;
+
+ int selectedRow;
+
+ int scrollOffset = 0;
+
+ Font font = new Font("Arial", Font.PLAIN, 11);
+
+ private boolean hasHiddenRows;
+
+ /**
+ * Creates a new AnnotationLabels object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ */
+ public AnnotationLabels(AlignmentPanel ap)
+ {
+ this.ap = ap;
+ av = ap.av;
+ ToolTipManager.sharedInstance().registerComponent(this);
+
+ java.net.URL url = getClass().getResource("/images/idwidth.gif");
+ Image temp = null;
+
+ if (url != null)
{
- this.av = av;
+ temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
}
- /**
- * DOCUMENT ME!
- *
- * @param y DOCUMENT ME!
- */
- public void setScrollOffset(int y)
+ try
+ {
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(temp, 0);
+ mt.waitForID(0);
+ } catch (Exception ex)
{
- scrollOffset = y;
- repaint();
}
- void getSelectedRow(int y)
+ 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);
+ addMouseWheelListener(ap.annotationPanel);
+ }
+
+ public AnnotationLabels(AlignViewport av)
+ {
+ this.av = av;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param y
+ * DOCUMENT ME!
+ */
+ public void setScrollOffset(int y)
+ {
+ scrollOffset = y;
+ repaint();
+ }
+
+ /**
+ * sets selectedRow to -2 if no annotation preset, -1 if no visible row is at
+ * y
+ *
+ * @param y
+ * coordinate position to search for a row
+ */
+ void getSelectedRow(int y)
+ {
+ int height = 0;
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ selectedRow = -2;
+ if (aa != null)
{
- int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- if(aa!=null)
+ for (int i = 0; i < aa.length; i++)
{
- for (int i = 0; i < aa.length; i++)
+ selectedRow = -1;
+ if (!aa[i].visible)
{
- if (!aa[i].visible)
- {
- continue;
- }
+ continue;
+ }
- height += aa[i].height;
+ height += aa[i].height;
- if (y < height)
- {
- selectedRow = i;
+ if (y < height)
+ {
+ selectedRow = i;
- break;
- }
+ break;
}
}
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void actionPerformed(ActionEvent evt)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+
+ if (evt.getActionCommand().equals(ADDNEW))
{
- int dif = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- if (evt.getActionCommand().equals(ADDNEW))
- {
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
- null,
- new Annotation[ap.av.alignment.getWidth()]);
-
- if(!editLabelDescription(newAnnotation))
- return;
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
- if (aa != null)
- dif = aa[aa.length - 1].height;
- }
- else if(evt.getActionCommand().equals(EDITNAME))
- {
- editLabelDescription(aa[selectedRow]);
- repaint();
- }
- else if (evt.getActionCommand().equals(HIDE))
- {
- aa[selectedRow].visible = false;
-
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.quality = null;
- }
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
- dif = aa[selectedRow].height * -1;
- }
- else if (evt.getActionCommand().equals(DELETE))
- {
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
- dif = aa[selectedRow].height * -1;
- }
- else if (evt.getActionCommand().equals(SHOWALL))
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ repaint();
+ }
+ else if (evt.getActionCommand().equals(HIDE))
+ {
+ aa[selectedRow].visible = false;
+ }
+ else if (evt.getActionCommand().equals(DELETE))
+ {
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
+ }
+ else if (evt.getActionCommand().equals(SHOWALL))
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ if (!aa[i].visible && aa[i].annotations != null)
{
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- dif += aa[i].height;
- aa[i].visible = true;
- }
- }
+ aa[i].visible = true;
}
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
- {
- new AnnotationExporter().exportAnnotations(
- ap,
+ }
+ }
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
+ {
+ new AnnotationExporter().exportAnnotations(ap,
new AlignmentAnnotation[]
- {aa[selectedRow]},
- null
- );
- }
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))
- {
- SequenceI cons=av.getConsensusSeq();
- if (cons!=null)
- copy_annotseqtoclipboard(cons);
-
- }
-
- ap.annotationPanel.adjustPanelHeight();
- ap.annotationScroller.validate();
- ap.repaint();
+ { aa[selectedRow] }, null, null);
}
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- boolean editLabelDescription(AlignmentAnnotation annotation)
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- EditNameDialog dialog = new EditNameDialog(annotation.label,
- annotation.description,
- " Annotation Name ",
- "Annotation Description ",
- "Edit Annotation Name/Description");
-
- if (!dialog.accept)
+ SequenceI cons = null;
+ if (aa[selectedRow].groupRef != null)
{
- return false;
+ cons = aa[selectedRow].groupRef.getConsensusSeq();
+ }
+ else
+ {
+ cons = av.getConsensusSeq();
+ }
+ if (cons != null)
+ {
+ copy_annotseqtoclipboard(cons);
}
- annotation.label = dialog.getName();
-
- String text = dialog.getDescription();
- if(text.length()==0)
- text = null;
- annotation.description = text;
-
- return true;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
+ else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
{
- getSelectedRow(evt.getY() - scrollOffset);
- oldY = evt.getY();
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
+ ap.validateAnnotationDimensions(false);
+ ap.addNotify();
+ ap.repaint();
+ // validate();
+ // ap.paintAlignment(true);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ boolean editLabelDescription(AlignmentAnnotation annotation)
+ {
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description, " Annotation Name ",
+ "Annotation Description ", "Edit Annotation Name/Description",
+ ap.alignFrame);
+
+ if (!dialog.accept)
{
- int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
- int end = selectedRow;
-
- if(start!=end)
- {
- //Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+ return false;
+ }
+ annotation.label = dialog.getName();
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
- }
-
- resizePanel = false;
- dragEvent = null;
- repaint();
- ap.annotationPanel.repaint();
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
+ {
+ text = null;
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
+ annotation.description = text;
+
+ return true;
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mousePressed(MouseEvent evt)
+ {
+ getSelectedRow(evt.getY() - scrollOffset);
+ oldY = evt.getY();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseReleased(MouseEvent evt)
+ {
+ int start = selectedRow;
+ getSelectedRow(evt.getY() - scrollOffset);
+ int end = selectedRow;
+
+ if (start != end)
{
- if(evt.getY()<10)
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.getAlignment()
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
{
- resizePanel = true;
- repaint();
+ 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;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.annotationPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10)
{
- if(dragEvent == null)
- {
- resizePanel = false;
- repaint();
- }
+ resizePanel = true;
+ repaint();
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent evt)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseExited(MouseEvent evt)
+ {
+ if (dragEvent == null)
+ {
+ resizePanel = false;
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseDragged(MouseEvent evt)
+ {
+ dragEvent = evt;
+
+ if (resizePanel)
{
- dragEvent = evt;
+ Dimension d = ap.annotationScroller.getPreferredSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.charHeight;
+ dif *= ap.av.charHeight;
- if (resizePanel)
+ if ((d.height - dif) > 20)
{
- Dimension d = ap.annotationScroller.getPreferredSize();
- int dif = evt.getY() - oldY;
+ ap.annotationScroller.setPreferredSize(new Dimension(d.width,
+ d.height - dif));
+ d = ap.annotationSpaceFillerHolder.getPreferredSize();
+ ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
+ d.width, d.height - dif));
+ ap.paintAlignment(true);
+ }
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ ap.addNotify();
+ }
+ else
+ {
+ repaint();
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
+
+ getSelectedRow(evt.getY() - scrollOffset);
+
+ if (selectedRow > -1
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
+ {
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .getAlignmentAnnotation()[selectedRow];
- if ( (d.height - dif) > 20)
+ StringBuffer desc = new StringBuffer();
+ if (aa.description != null
+ && !aa.description.equals("New description"))
+ {
+ // TODO: we could refactor and merge this code with the code in
+ // jalview.gui.SeqPanel.mouseMoved(..) that formats sequence feature
+ // tooltips
+ desc.append(aa.getDescription(true).trim());
+ // check to see if the description is an html fragment.
+ if (desc.length() < 6
+ || (desc.substring(0, 6).toLowerCase().indexOf("<html>") < 0))
{
- ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
- d = ap.annotationSpaceFillerHolder.getPreferredSize();
- ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- d.width, d.height - dif));
- ap.repaint();
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(Pattern.compile("<").matcher(desc)
+ .replaceAll("<"));
+ desc.insert(0, "<html>");
+ }
+ else
+ {
+ // remove terminating html if any
+ int i = desc.substring(desc.length() - 7).toLowerCase()
+ .lastIndexOf("</html>");
+ if (i > -1)
+ {
+ desc.setLength(desc.length() - 7 + i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("<br/>");
}
- ap.addNotify();
}
else
- repaint();
- }
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
- {
- resizePanel = evt.getY()<10;
-
- getSelectedRow(evt.getY() - scrollOffset);
-
- if(selectedRow>-1)
{
- String desc = ap.av.alignment.
- getAlignmentAnnotation()[selectedRow].description;
-
- if (desc != null && !desc.equals("New Description"))
- setToolTipText(ap.av.alignment.
- getAlignmentAnnotation()[selectedRow].description);
+ // 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 (desc.length() > 6)
+ {
+ desc.append("</html>");
+ this.setToolTipText(desc.toString());
}
- repaint();
+ else
+ this.setToolTipText(null);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent evt)
+ {
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (SwingUtilities.isLeftMouseButton(evt))
{
- if(!SwingUtilities.isRightMouseButton(evt))
- return;
-
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
-
- if ((aa == null) || (aa.length == 0))
+ if (selectedRow > -1 && selectedRow < aa.length)
+ {
+ if (aa[selectedRow].groupRef != null)
{
- JPopupMenu pop = new JPopupMenu("Annotations");
- JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
- pop.add(item);
- pop.show(this, evt.getX(), evt.getY());
-
- return;
+ 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.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ ap.av.sendSelection();
+ }
+ else
+ {
+ ap.seqPanel.ap.idPanel
+ .highlightSearchResults(aa[selectedRow].groupRef
+ .getSequences(null));
+ }
+ return;
}
+ else if (aa[selectedRow].sequenceRef != null)
+ {
+ if (evt.getClickCount() == 1)
+ {
+ 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 = ap.av.getSelectionGroup();
+ if (sg!=null)
+ {
+ sg = new SequenceGroup(sg);
+ sg.clear();
+ sg.addSequence(aa[selectedRow].sequenceRef, false);
+ } 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.av.sendSelection();
+ ap.paintAlignment(false);
+ PaintRefresher.Refresh(ap, ap.av.getSequenceSetId());
+ }
+ }
+ }
+ }
+ if (!SwingUtilities.isRightMouseButton(evt))
+ {
+ return;
+ }
- JPopupMenu pop = new JPopupMenu("Annotations");
- JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(EDITNAME);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(HIDE);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(DELETE);
- item.addActionListener(this);
- pop.add(item);
+ JPopupMenu pop = new JPopupMenu(
+ MessageManager.getString("label.annotations"));
+ JMenuItem item = new JMenuItem(ADDNEW);
+ item.addActionListener(this);
+ pop.add(item);
+ if (selectedRow < 0)
+ {
+ if (hasHiddenRows)
+ { // let the user make everything visible again
item = new JMenuItem(SHOWALL);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(OUTPUT_TEXT);
- item.addActionListener(this);
- pop.add(item);
- // annotation object should be typed
- if (aa[selectedRow]==ap.av.consensus)
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ item = new JMenuItem(EDITNAME);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(HIDE);
+ item.addActionListener(this);
+ pop.add(item);
+ item = new JMenuItem(DELETE);
+ item.addActionListener(this);
+ pop.add(item);
+ if (hasHiddenRows)
+ {
+ item = new JMenuItem(SHOWALL);
+ item.addActionListener(this);
+ pop.add(item);
+ }
+ item = new JMenuItem(OUTPUT_TEXT);
+ item.addActionListener(this);
+ pop.add(item);
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
+ if (selectedRow < aa.length)
+ {
+ if (!aa[selectedRow].autoCalculated)
+ {
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
+ // display formatting settings for this row.
pop.addSeparator();
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- "Ignore Gaps In Consensus",
- ap.av.getIgnoreGapsConsensus());
- cbmi.addActionListener(new ActionListener()
- {public void actionPerformed(ActionEvent e)
- {
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
- }
- });
- pop.add(cbmi);
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
+ // av and sequencegroup need to implement same interface for
+ item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+ aa[selectedRow].scaleColLabel);
+ item.addActionListener(this);
+ pop.add(item);
}
-
- pop.show(this, evt.getX(), evt.getY());
- }
- /**
- * do a single sequence copy to jalview and the system clipboard
- *
- * @param sq sequence to be copied to clipboard
- */
- protected void copy_annotseqtoclipboard(SequenceI sq)
- {
- SequenceI [] seqs = new SequenceI[] { sq };
- String[] omitHidden = null;
- SequenceI [] dseqs=new SequenceI[] { sq.getDatasetSequence()};
- if (dseqs[0]==null) {
- dseqs[0] = new Sequence(sq);
- dseqs[0].setSequence(
- jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- sq.getSequenceAsString()));
-
- sq.setDatasetSequence(dseqs[0]);
- }
- Alignment ds=new Alignment(dseqs);
- if (av.hasHiddenColumns)
- {
- omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs);
}
-
- String output = new FormatAdapter().formatSequences(
- "Fasta",
- seqs,
- omitHidden);
-
-
- Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(output), Desktop.instance);
-
- Vector hiddenColumns = null;
- if(av.hasHiddenColumns)
+ else if (aa[selectedRow].label.indexOf("Consensus") > -1)
{
- hiddenColumns =new Vector();
- for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
+ "Ignore Gaps In Consensus",
+ (aa[selectedRow].groupRef != null) ? aa[selectedRow].groupRef
+ .getIgnoreGapsConsensus() : ap.av
+ .getIgnoreGapsConsensus());
+ final AlignmentAnnotation aaa = aa[selectedRow];
+ cbmi.addActionListener(new ActionListener()
{
- int[] region = (int[])
- av.getColumnSelection().getHiddenColumns().elementAt(i);
+ public void actionPerformed(ActionEvent e)
+ {
+ if (aaa.groupRef != null)
+ {
+ // TODO: pass on reference to ap so the view can be updated.
+ aaa.groupRef.setIgnoreGapsConsensus(cbmi.getState());
+ ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ else
+ {
+ ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ }
+ }
+ });
+ pop.add(cbmi);
+ // av and sequencegroup need to implement same interface for
+ if (aaa.groupRef != null)
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "Show Group Histogram",
+ aa[selectedRow].groupRef.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent 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());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprofl = new JCheckBoxMenuItem(
+ "Show Group Logo",
+ aa[selectedRow].groupRef.isShowSequenceLogo());
+ cprofl.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent 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());
+ }
+ });
+ pop.add(cprofl);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ "Normalise Group Logo",
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
- hiddenColumns.addElement(new int[]{region[0],
- region[1]});
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ aaa.groupRef.setNormaliseSequenceLogo(cproflnorm.getState());
+ // automatically enable logo display if we're clicked
+ aaa.groupRef.setshowSequenceLogo(true);
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cproflnorm);
+ }
+ else
+ {
+ final JCheckBoxMenuItem chist = new JCheckBoxMenuItem(
+ "Show Histogram", av.isShowConsensusHistogram());
+ chist.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowConsensusHistogram(chist.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(chist);
+ final JCheckBoxMenuItem cprof = new JCheckBoxMenuItem(
+ "Show Logo", av.isShowSequenceLogo());
+ cprof.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(cprof.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ final JCheckBoxMenuItem cprofnorm = new JCheckBoxMenuItem(
+ "Normalise Logo", av.isNormaliseSequenceLogo());
+ cprofnorm.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // TODO: pass on reference
+ // to ap
+ // so the
+ // view
+ // can be
+ // updated.
+ av.setShowSequenceLogo(true);
+ av.setNormaliseSequenceLogo(cprofnorm.getState());
+ ap.alignFrame.setMenusForViewport();
+ ap.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprofnorm);
}
+ final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
+ consclipbrd.addActionListener(this);
+ pop.add(consclipbrd);
}
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ }
+
+ /**
+ * do a single sequence copy to jalview and the system clipboard
+ *
+ * @param sq
+ * sequence to be copied to clipboard
+ */
+ protected void copy_annotseqtoclipboard(SequenceI sq)
+ {
+ SequenceI[] seqs = new SequenceI[]
+ { sq };
+ String[] omitHidden = null;
+ SequenceI[] dseqs = new SequenceI[]
+ { sq.getDatasetSequence() };
+ if (dseqs[0] == null)
+ {
+ dseqs[0] = new Sequence(sq);
+ dseqs[0].setSequence(jalview.analysis.AlignSeq.extractGaps(
+ jalview.util.Comparison.GapChars, sq.getSequenceAsString()));
- Desktop.jalviewClipboard = new Object[]{ seqs,
- ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
- hiddenColumns};
+ sq.setDatasetSequence(dseqs[0]);
}
- /**
- * DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
- */
- public void paintComponent(Graphics g)
+ Alignment ds = new Alignment(dseqs);
+ if (av.hasHiddenColumns())
{
+ omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
+ sq.getLength(), seqs);
+ }
- int width = getWidth();
- if(width==0)
- width = ap.calculateIdWidth().width + 4;
+ String output = new FormatAdapter().formatSequences("Fasta", seqs,
+ omitHidden);
- Graphics2D g2 = (Graphics2D) g;
- if(av.antiAlias)
- g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
- drawComponent(g2, width);
+ Vector hiddenColumns = null;
+ if (av.hasHiddenColumns())
+ {
+ hiddenColumns = new Vector();
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
+ {
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(i);
+ hiddenColumns.addElement(new int[]
+ { region[0], region[1] });
+ }
}
- /**
- * DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
- */
- public void drawComponent(Graphics g, int width)
+ Desktop.jalviewClipboard = new Object[]
+ { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+ // sequence as special.
+ hiddenColumns };
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param g1
+ * DOCUMENT ME!
+ */
+ public void paintComponent(Graphics g)
+ {
+
+ int width = getWidth();
+ if (width == 0)
{
- if(av.getFont().getSize()<10)
- g.setFont(font);
- else
- g.setFont(av.getFont());
+ width = ap.calculateIdWidth().width + 4;
+ }
+
+ Graphics2D g2 = (Graphics2D) g;
+ if (av.antiAlias)
+ {
+ g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
+ RenderingHints.VALUE_ANTIALIAS_ON);
+ }
+
+ drawComponent(g2, true, width);
+
+ }
+
+ /**
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param width
+ * Width for scaling labels
+ *
+ */
+ public void drawComponent(Graphics g, int width)
+ {
+ drawComponent(g, false, width);
+ }
+
+ private final boolean debugRedraw = false;
+
+ /**
+ * Draw the full set of annotation Labels for the alignment at the given
+ * cursor
+ *
+ * @param g
+ * Graphics2D instance (needed for font scaling)
+ * @param clip
+ * - true indicates that only current visible area needs to be
+ * rendered
+ * @param width
+ * Width for scaling labels
+ */
+ public void drawComponent(Graphics g, boolean clip, int width)
+ {
+ if (av.getFont().getSize() < 10)
+ {
+ g.setFont(font);
+ }
+ else
+ {
+ g.setFont(av.getFont());
+ }
- FontMetrics fm = g.getFontMetrics(g.getFont());
- g.setColor(Color.white);
- g.fillRect(0, 0, getWidth(), getHeight());
+ FontMetrics fm = g.getFontMetrics(g.getFont());
+ g.setColor(Color.white);
+ g.fillRect(0, 0, getWidth(), getHeight());
+
+ g.translate(0, scrollOffset);
+ g.setColor(Color.black);
+
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
+ int fontHeight = g.getFont().getSize();
+ int y = 0;
+ int x = 0;
+ int graphExtras = 0;
+ int offset = 0;
+ Font baseFont = g.getFont();
+ FontMetrics baseMetrics = fm;
+ int ofontH = fontHeight;
+ int sOffset = 0;
+ int visHeight = 0;
+ int[] visr = (ap != null && ap.annotationPanel != null) ? ap.annotationPanel
+ .getVisibleVRange() : null;
+ if (clip && visr != null)
+ {
+ sOffset = visr[0];
+ visHeight = visr[1];
+ }
+ boolean visible = true, before = false, after = false;
+ if (aa != null)
+ {
+ hasHiddenRows = false;
+ int olY = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ visible = true;
+ if (!aa[i].visible)
+ {
+ hasHiddenRows = true;
+ continue;
+ }
+ olY = y;
+ y += aa[i].height;
+ if (clip)
+ {
+ if (y < sOffset)
+ {
+ if (!before)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("before vis: " + i);
+ }
+ before = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ if (olY > visHeight)
+ {
- g.translate(0, scrollOffset);
+ if (!after)
+ {
+ if (debugRedraw)
+ {
+ System.out.println("Scroll offset: " + sOffset
+ + " after vis: " + i);
+ }
+ after = true;
+ }
+ // don't draw what isn't visible
+ continue;
+ }
+ }
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int fontHeight = g.getFont().getSize();
- int y = fontHeight;
- int x = 0;
- int graphExtras = 0;
+ offset = -aa[i].height / 2;
+ if (aa[i].hasText)
+ {
+ offset += fm.getHeight() / 2;
+ offset -= fm.getDescent();
+ }
+ else
+ offset += fm.getDescent();
+ x = width - fm.stringWidth(aa[i].label) - 3;
- if (aa != null)
+ if (aa[i].graphGroup > -1)
{
- for (int i = 0; i < aa.length; i++)
+ int groupSize = 0;
+ // TODO: JAL-1291 revise rendering model so the graphGroup map is
+ // computed efficiently for all visible labels
+ for (int gg = 0; gg < aa.length; gg++)
+ {
+ if (aa[gg].graphGroup == aa[i].graphGroup)
{
- if (!aa[i].visible)
- {
- continue;
- }
-
- x = width - fm.stringWidth(aa[i].label) - 3;
+ groupSize++;
+ }
+ }
+ if (groupSize * (fontHeight + 8) < aa[i].height)
+ {
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ }
+ else
+ {
+ // scale font to fit
+ float h = aa[i].height / (float) groupSize, s;
+ if (h < 9)
+ {
+ visible = false;
+ }
+ else
+ {
+ fontHeight = -8 + (int) h;
+ s = ((float) fontHeight) / (float) ofontH;
+ Font f = baseFont.deriveFont(AffineTransform
+ .getScaleInstance(s, s));
+ g.setFont(f);
+ fm = g.getFontMetrics();
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ }
+ }
+ if (visible)
+ {
+ for (int gg = 0; gg < aa.length; gg++)
+ {
+ if (aa[gg].graphGroup == aa[i].graphGroup)
+ {
+ x = width - fm.stringWidth(aa[gg].label) - 3;
+ g.drawString(aa[gg].label, x, y - graphExtras);
- if (aa[i].graph>0 && aa[i].graphHeight>0)
+ if (aa[gg]._linecolour != null)
{
- graphExtras = y;
-
- y += (aa[i].height / 3);
- if(aa[i].graphGroup<0)
- graphExtras = y + fontHeight;
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras
+ + 3);
}
- if(aa[i].graphGroup>-1)
- {
- int groupSize = 0;
- for (int gg = 0; gg < aa.length; gg++)
- {
- if (aa[gg].graphGroup == aa[i].graphGroup)
- groupSize++;
- }
-
- if(groupSize * (fontHeight+8) < aa[i].height)
- graphExtras += (aa[i].height -( groupSize * (fontHeight+8)) )/2;
-
- for(int gg=0; gg<aa.length; gg++)
- {
- if(aa[gg].graphGroup==aa[i].graphGroup)
- {
- x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x, graphExtras );
- if(aa[gg].annotations[0]!=null)
- g.setColor(aa[gg].annotations[0].colour);
-
- g.drawLine( x, graphExtras+3,
- x+fm.stringWidth(aa[gg].label),
- graphExtras+3);
-
- g.setColor(Color.black);
- graphExtras += fontHeight+8;
- }
- }
- }
- else
- g.drawString(aa[i].label, x, y);
-
- if (aa[i].graph>0)
- {
- /* if (aa[i].graphLines != null)
- {
- for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
- {
- x = width - fm.stringWidth(aa[i].getGraphLine(gl).label) - 3;
- g.drawString(aa[i].getGraphLine(gl).label, x, graphExtras);
- g.setColor(aa[i].getGraphLine(gl).colour);
- Graphics2D g2 = (Graphics2D) g;
- g2.setStroke(new BasicStroke(1,
- BasicStroke.CAP_SQUARE,
- BasicStroke.JOIN_ROUND, 3f,
- new float[]
- {5f, 3f}, 0f));
-
- graphExtras += 3;
-
- g.drawLine(x, graphExtras,
- x+fm.stringWidth(aa[i].label),
- graphExtras);
- g2.setStroke(new BasicStroke());
- }
- }*/
- y += ((2 * aa[i].height) / 3);
- }
- else
- {
- y += aa[i].height;
- }
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
}
+ }
+ g.setFont(baseFont);
+ fm = baseMetrics;
+ fontHeight = ofontH;
}
-
- if (resizePanel)
- {
- g.drawImage(image, 2, 0 - scrollOffset, this);
- }
- else if (dragEvent != null && aa!=null)
+ else
{
- g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(), dragEvent.getY() - scrollOffset);
+ g.drawString(aa[i].label, x, y + offset);
}
+ }
+ }
+ if (resizePanel)
+ {
+ g.drawImage(image, 2, 0 - scrollOffset, this);
+ }
+ else if (dragEvent != null && aa != null)
+ {
+ g.setColor(Color.lightGray);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(),
+ dragEvent.getY() - scrollOffset);
+ }
- if ((aa == null) || (aa.length < 1))
- {
- g.drawString("Right click", 2, 8);
- g.drawString("to add annotation", 2, 18);
- }
+ if (!av.wrapAlignment && ((aa == null) || (aa.length < 1)))
+ {
+ g.drawString(MessageManager.getString("label.right_click"), 2, 8);
+ g.drawString(MessageManager.getString("label.to_add_annotation"), 2,
+ 18);
}
+ }
}