X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=ff3b0cddd72c6de52c372992de30cd726c084525;hb=a45774ee31d9f35d4eff46d54d7deab719afb092;hp=4268353fb37e3d585a97f778ac9e8ec8c78f3199;hpb=1f705b7d5fb0920573037631b810aac3262ee190;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 4268353..ff3b0cd 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,591 +1,878 @@
/*
- * 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
- * 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, 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 .
*/
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.image.*;
-import java.util.Vector;
-
import javax.swing.*;
+import jalview.datamodel.*;
+import jalview.io.*;
/**
* 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 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;
-
- java.net.URL url = getClass().getResource("/images/idwidth.gif");
- Image temp = null;
-
- if (url != null)
- {
- temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
- }
+ static String TOGGLE_LABELSCALE = "Scale Label to Column";
- try
- {
- MediaTracker mt = new MediaTracker(this);
- mt.addImage(temp, 0);
- mt.waitForID(0);
- }
- catch (Exception ex)
- {
- }
+ static String ADDNEW = "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;
+ static String EDITNAME = "Edit Label/Description";
- addMouseListener(this);
- addMouseMotionListener(this);
- }
+ static String HIDE = "Hide This Row";
- public AnnotationLabels(AlignViewport av)
- {
- this.av = av;
- }
+ static String DELETE = "Delete This Row";
- /**
- * DOCUMENT ME!
- *
- * @param y DOCUMENT ME!
- */
- public void setScrollOffset(int y)
- {
- scrollOffset = y;
- repaint();
- }
+ static String SHOWALL = "Show All Hidden Rows";
- void getSelectedRow(int y)
- {
- int height = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ static String OUTPUT_TEXT = "Export Annotation";
- if(aa!=null)
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- continue;
- }
+ static String COPYCONS_SEQ = "Copy Consensus Sequence";
- height += aa[i].height;
+ boolean resizePanel = false;
- if (y < height)
- {
- selectedRow = i;
+ Image image;
- break;
- }
- }
- }
- }
+ AlignmentPanel ap;
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void actionPerformed(ActionEvent evt)
- {
- int dif = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignViewport av;
- if (evt.getActionCommand().equals(ADDNEW))
- {
- String label = JOptionPane.showInputDialog(this,
- "Label for annotation");
+ boolean resizing = false;
- if (label == null)
- {
- label = "";
- }
+ MouseEvent dragEvent;
- AlignmentAnnotation newAnnotation = new AlignmentAnnotation(label,
- "New description",
- new Annotation[ap.av.alignment.getWidth()]);
+ int oldY;
- 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(HIDE))
- {
- aa[selectedRow].visible = false;
+ int selectedRow;
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.quality = null;
- }
+ int scrollOffset = 0;
- 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))
- {
- for (int i = 0; i < aa.length; i++)
- {
- if (!aa[i].visible)
- {
- dif += aa[i].height;
- aa[i].visible = true;
- }
- }
- }
- else if (evt.getActionCommand().equals(OUTPUT_TEXT))
- {
- new AnnotationExporter().exportAnnotations(
- ap,
- new AlignmentAnnotation[]
- {aa[selectedRow]}
- );
- }
- else if (evt.getActionCommand().equals(COPYCONS_SEQ))
- {
- SequenceI cons=av.getConsensusSeq();
- if (cons!=null)
- copy_annotseqtoclipboard(cons);
+ Font font = new Font("Arial", Font.PLAIN, 11);
- }
+ private boolean hasHiddenRows;
- ap.annotationPanel.adjustPanelHeight();
- ap.annotationScroller.validate();
- ap.repaint();
- }
+ /**
+ * 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;
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mousePressed(MouseEvent evt)
+ if (url != null)
{
- getSelectedRow(evt.getY() - scrollOffset);
- oldY = evt.getY();
+ temp = java.awt.Toolkit.getDefaultToolkit().createImage(url);
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseReleased(MouseEvent evt)
+ try
{
- int start = selectedRow;
- getSelectedRow(evt.getY() - scrollOffset);
- int end = selectedRow;
+ MediaTracker mt = new MediaTracker(this);
+ mt.addImage(temp, 0);
+ mt.waitForID(0);
+ } catch (Exception ex)
+ {
+ }
- if(start!=end)
+ 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 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.alignment.getAlignmentAnnotation();
+ selectedRow = -2;
+ if (aa != null)
+ {
+ for (int i = 0; i < aa.length; i++)
+ {
+ selectedRow = -1;
+ if (!aa[i].visible)
{
- //Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[start];
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
+ continue;
+ }
+ height += aa[i].height;
- ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
- }
+ if (y < height)
+ {
+ selectedRow = i;
- resizePanel = false;
- dragEvent = null;
- repaint();
- ap.annotationPanel.repaint();
+ break;
+ }
+ }
}
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void actionPerformed(ActionEvent evt)
+ {
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ if (evt.getActionCommand().equals(ADDNEW))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
+ null, new Annotation[ap.av.alignment.getWidth()]);
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseEntered(MouseEvent evt)
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ ap.av.alignment.addAnnotation(newAnnotation);
+ ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ repaint();
+ }
+ else if (evt.getActionCommand().equals(HIDE))
{
- if(evt.getY()<10)
+ aa[selectedRow].visible = false;
+ }
+ else if (evt.getActionCommand().equals(DELETE))
+ {
+ ap.av.alignment.deleteAnnotation(aa[selectedRow]);
+ }
+ else if (evt.getActionCommand().equals(SHOWALL))
+ {
+ for (int i = 0; i < aa.length; i++)
{
- resizePanel = true;
- repaint();
+ if (!aa[i].visible && aa[i].annotations != null)
+ {
+ aa[i].visible = true;
+ }
}
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseExited(MouseEvent evt)
+ else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
- if(dragEvent == null)
+ new AnnotationExporter().exportAnnotations(ap,
+ new AlignmentAnnotation[]
+ { aa[selectedRow] }, null, null);
+ }
+ else if (evt.getActionCommand().equals(COPYCONS_SEQ))
+ {
+ SequenceI cons = null;
+ if (aa[selectedRow].groupRef != null)
+ {
+ cons = aa[selectedRow].groupRef.getConsensusSeq();
+ }
+ else
+ {
+ cons = av.getConsensusSeq();
+ }
+ if (cons != null)
{
- resizePanel = false;
- repaint();
+ copy_annotseqtoclipboard(cons);
}
+
+ }
+ else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+ {
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
}
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseDragged(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)
{
- dragEvent = evt;
+ return false;
+ }
+
+ annotation.label = dialog.getName();
- if (resizePanel)
+ String text = dialog.getDescription();
+ if (text != null && text.length() == 0)
+ {
+ text = null;
+ }
+ 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)
+ {
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.alignment
+ .getAlignmentAnnotation()[start];
+ if (end == -1)
{
- Dimension d = ap.annotationScroller.getPreferredSize();
- int dif = evt.getY() - oldY;
+ end = ap.av.alignment.getAlignmentAnnotation().length - 1;
+ }
+ AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
- dif /= ap.av.charHeight;
- dif *= ap.av.charHeight;
+ ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
+ ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+ }
- if ( (d.height - dif) > 20)
- {
- 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();
- }
+ resizePanel = false;
+ dragEvent = null;
+ repaint();
+ ap.annotationPanel.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseEntered(MouseEvent evt)
+ {
+ if (evt.getY() < 10)
+ {
+ resizePanel = true;
+ repaint();
+ }
+ }
+
+ /**
+ * 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)
+ {
+ Dimension d = ap.annotationScroller.getPreferredSize();
+ int dif = evt.getY() - oldY;
+
+ dif /= ap.av.charHeight;
+ dif *= ap.av.charHeight;
- ap.addNotify();
+ if ((d.height - dif) > 20)
+ {
+ 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);
}
- else
- repaint();
- }
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseMoved(MouseEvent evt)
+ ap.addNotify();
+ }
+ else
{
- resizePanel = evt.getY()<10;
-
repaint();
}
-
- /**
- * DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
- */
- public void mouseClicked(MouseEvent evt)
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent evt)
+ {
+ resizePanel = evt.getY() < 10;
+
+ getSelectedRow(evt.getY() - scrollOffset);
+
+ if (selectedRow > -1
+ && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
{
- if(!SwingUtilities.isRightMouseButton(evt))
- return;
+ AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
+
+ 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("")<0))
+ {
+ // clean the description ready for embedding in html
+ desc = new StringBuffer(Pattern.compile("<").matcher(desc).replaceAll("<"));
+ desc.insert(0, "");
+ } else {
+ // remove terminating html if any
+ int i=desc.substring(desc.length()-7).toLowerCase().lastIndexOf("");
+ if (i>-1) {
+ desc.setLength(desc.length()-7+i);
+ }
+ }
+ if (aa.hasScore())
+ {
+ desc.append("
");
+ }
+
+
+ } else {
+ // begin the tooltip's html fragment
+ desc.append("");
+ }
+ 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);
+ }
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ if (desc.length() > 6)
+ {
+ desc.append("");
+ this.setToolTipText(desc.toString());
+ }
+ else
+ this.setToolTipText(null);
+ }
- if ((aa == null) || (aa.length == 0))
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
+ */
+ public void mouseClicked(MouseEvent evt)
+ {
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ if (SwingUtilities.isLeftMouseButton(evt))
+ {
+ 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)
+ {
+ 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.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(HIDE);
- item.addActionListener(this);
- pop.add(item);
- item = new JMenuItem(DELETE);
- item.addActionListener(this);
- pop.add(item);
+ JPopupMenu pop = new JPopupMenu("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].label.equals("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.getSequence()));
- sq.setDatasetSequence(dseqs[0]);
}
- Alignment ds=new Alignment(dseqs);
- if (av.hasHiddenColumns)
+ else if (aa[selectedRow].label.indexOf("Consensus") > -1)
{
- omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0, sq.getLength(), seqs);
+ 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()
+ {
+ 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);
+ }
+ 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.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.repaint();
+ // ap.annotationPanel.paint(ap.annotationPanel.getGraphics());
+ }
+ });
+ pop.add(cprof);
+ }
+ 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()));
- String output = new FormatAdapter().formatSequences(
- "Fasta",
- seqs,
- omitHidden);
+ 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);
+ Toolkit.getDefaultToolkit().getSystemClipboard()
+ .setContents(new StringSelection(output), Desktop.instance);
- Vector hiddenColumns = null;
- if(av.hasHiddenColumns)
+ Vector hiddenColumns = null;
+ if (av.hasHiddenColumns)
+ {
+ hiddenColumns = new Vector();
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
{
- hiddenColumns =new Vector();
- for(int i=0; i0 && aa[i].graphHeight>0)
- {
- graphExtras = y;
-
- y += (aa[i].height / 3);
-
- if(aa[i].graphGroup<0)
- graphExtras = y + fontHeight;
- }
-
- 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; gg0)
- {
- /* 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;
- }
- }
+ offset += fm.getHeight() / 2;
+ offset -= fm.getDescent();
}
+ else
+ offset += fm.getDescent();
- if (resizePanel)
+ x = width - fm.stringWidth(aa[i].label) - 3;
+
+ if (aa[i].graphGroup > -1)
{
- g.drawImage(image, 2, 0 - scrollOffset, this);
+ 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, y - graphExtras);
+ if (aa[gg].annotations[0] != null)
+ {
+ g.setColor(aa[gg].annotations[0].colour);
+ }
+
+ g.drawLine(x, y - graphExtras - 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
+
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
+ }
+ }
}
- 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 ((aa == null) || (aa.length < 1))
+ {
+ g.drawString("Right click", 2, 8);
+ g.drawString("to add annotation", 2, 18);
}
+ }
}