X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationLabels.java;h=1577477d78d94a203cfeb18658bd56cb8a78343d;hb=59d682209891099d46b960509907c79e3fb276fe;hp=3f8478a0bdb5d15a44e94cdcb37af57caec9f701;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/gui/AnnotationLabels.java b/src/jalview/gui/AnnotationLabels.java
index 3f8478a..1577477 100755
--- a/src/jalview/gui/AnnotationLabels.java
+++ b/src/jalview/gui/AnnotationLabels.java
@@ -1,28 +1,29 @@
/*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 java.util.*;
+import java.util.regex.Pattern;
import java.awt.*;
import java.awt.datatransfer.*;
import java.awt.event.*;
+import java.awt.geom.AffineTransform;
import java.awt.image.*;
import javax.swing.*;
@@ -31,36 +32,56 @@ import jalview.io.*;
/**
* DOCUMENT ME!
- *
+ *
* @author $author$
* @version $Revision$
*/
-public class AnnotationLabels
- extends JPanel implements MouseListener,
- MouseMotionListener, ActionListener
+public class AnnotationLabels extends JPanel implements MouseListener,
+ MouseMotionListener, ActionListener
{
+ static String TOGGLE_LABELSCALE = "Scale Label to Column";
+
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);
+ private boolean hasHiddenRows;
+
/**
* Creates a new AnnotationLabels object.
- *
- * @param ap DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
*/
public AnnotationLabels(AlignmentPanel ap)
{
@@ -81,14 +102,12 @@ public class AnnotationLabels
MediaTracker mt = new MediaTracker(this);
mt.addImage(temp, 0);
mt.waitForID(0);
- }
- catch (Exception ex)
+ } catch (Exception ex)
{
}
BufferedImage bi = new BufferedImage(temp.getHeight(this),
- temp.getWidth(this),
- BufferedImage.TYPE_INT_RGB);
+ 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);
@@ -96,6 +115,7 @@ public class AnnotationLabels
addMouseListener(this);
addMouseMotionListener(this);
+ addMouseWheelListener(ap.annotationPanel);
}
public AnnotationLabels(AlignViewport av)
@@ -105,8 +125,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param y DOCUMENT ME!
+ *
+ * @param y
+ * DOCUMENT ME!
*/
public void setScrollOffset(int y)
{
@@ -114,15 +135,24 @@ public class AnnotationLabels
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();
-
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ selectedRow = -2;
if (aa != null)
{
for (int i = 0; i < aa.length; i++)
{
+ selectedRow = -1;
if (!aa[i].visible)
{
continue;
@@ -142,31 +172,27 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
- int dif = 0;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
- null,
- new Annotation[ap.av.alignment.getWidth()]);
+ null, new Annotation[ap.av.getAlignment().getWidth()]);
if (!editLabelDescription(newAnnotation))
{
return;
}
- ap.av.alignment.addAnnotation(newAnnotation);
- ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
- if (aa != null)
- {
- dif = aa[aa.length - 1].height;
- }
+ ap.av.getAlignment().addAnnotation(newAnnotation);
+ ap.av.getAlignment().setAnnotationIndex(newAnnotation, 0);
}
else if (evt.getActionCommand().equals(EDITNAME))
{
@@ -176,66 +202,68 @@ public class AnnotationLabels
else if (evt.getActionCommand().equals(HIDE))
{
aa[selectedRow].visible = false;
-
- if (aa[selectedRow].label.equals("Quality"))
- {
- ap.av.quality = null;
- }
-
- dif = aa[selectedRow].height * -1;
}
else if (evt.getActionCommand().equals(DELETE))
{
- ap.av.alignment.deleteAnnotation(aa[selectedRow]);
- dif = aa[selectedRow].height * -1;
+ ap.av.getAlignment().deleteAnnotation(aa[selectedRow]);
}
else if (evt.getActionCommand().equals(SHOWALL))
{
for (int i = 0; i < aa.length; i++)
{
- if (!aa[i].visible)
+ if (!aa[i].visible && aa[i].annotations != null)
{
- dif += aa[i].height;
aa[i].visible = true;
}
}
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
- new AnnotationExporter().exportAnnotations(
- ap,
- new AlignmentAnnotation[]
- {aa[selectedRow]},
- null
- );
+ new AnnotationExporter().exportAnnotations(ap,
+ new AlignmentAnnotation[]
+ { aa[selectedRow] }, null, null);
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- SequenceI cons = av.getConsensusSeq();
+ SequenceI cons = null;
+ if (aa[selectedRow].groupRef != null)
+ {
+ cons = aa[selectedRow].groupRef.getConsensusSeq();
+ }
+ else
+ {
+ cons = av.getConsensusSeq();
+ }
if (cons != null)
{
copy_annotseqtoclipboard(cons);
}
}
+ else if (evt.getActionCommand().equals(TOGGLE_LABELSCALE))
+ {
+ aa[selectedRow].scaleColLabel = !aa[selectedRow].scaleColLabel;
+ }
- ap.annotationPanel.adjustPanelHeight();
- ap.annotationScroller.validate();
+ ap.validateAnnotationDimensions(false);
+ ap.addNotify();
ap.repaint();
+ // validate();
+ // ap.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param e 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");
+ annotation.description, " Annotation Name ",
+ "Annotation Description ", "Edit Annotation Name/Description",
+ ap.alignFrame);
if (!dialog.accept)
{
@@ -245,7 +273,7 @@ public class AnnotationLabels
annotation.label = dialog.getName();
String text = dialog.getDescription();
- if (text.length() == 0)
+ if (text != null && text.length() == 0)
{
text = null;
}
@@ -256,8 +284,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
@@ -267,8 +296,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
@@ -278,13 +308,18 @@ public class AnnotationLabels
if (start != end)
{
- //Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
- start];
- AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[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.alignment.getAlignmentAnnotation()[end] = startAA;
- ap.av.alignment.getAlignmentAnnotation()[start] = endAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[end] = startAA;
+ ap.av.getAlignment().getAlignmentAnnotation()[start] = endAA;
}
resizePanel = false;
@@ -295,8 +330,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
@@ -309,8 +345,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
@@ -323,8 +360,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
@@ -338,14 +376,14 @@ public class AnnotationLabels
dif /= ap.av.charHeight;
dif *= ap.av.charHeight;
- if ( (d.height - dif) > 20)
+ if ((d.height - dif) > 20)
{
ap.annotationScroller.setPreferredSize(new Dimension(d.width,
- d.height - dif));
+ d.height - dif));
d = ap.annotationSpaceFillerHolder.getPreferredSize();
ap.annotationSpaceFillerHolder.setPreferredSize(new Dimension(
- d.width, d.height - dif));
- ap.repaint();
+ d.width, d.height - dif));
+ ap.paintAlignment(true);
}
ap.addNotify();
@@ -358,8 +396,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
@@ -368,43 +407,126 @@ public class AnnotationLabels
getSelectedRow(evt.getY() - scrollOffset);
if (selectedRow > -1
- && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ && ap.av.getAlignment().getAlignmentAnnotation().length > selectedRow)
{
- String desc = ap.av.alignment.
- getAlignmentAnnotation()[selectedRow].description;
+ AlignmentAnnotation aa = ap.av.getAlignment()
+ .getAlignmentAnnotation()[selectedRow];
- if (desc != null && !desc.equals("New description"))
+ StringBuffer desc = new StringBuffer();
+ if (aa.description != null
+ && !aa.description.equals("New description"))
{
- setToolTipText(ap.av.alignment.
- getAlignmentAnnotation()[selectedRow].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);
}
+ if (desc.length() > 6)
+ {
+ desc.append("");
+ this.setToolTipText(desc.toString());
+ }
+ else
+ this.setToolTipText(null);
}
- repaint();
+
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
- if (!SwingUtilities.isRightMouseButton(evt))
+ AlignmentAnnotation[] aa = ap.av.getAlignment()
+ .getAlignmentAnnotation();
+ if (SwingUtilities.isLeftMouseButton(evt))
{
- return;
- }
-
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+ 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.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 ( (aa == null) || (aa.length == 0))
+ }
+ }
+ }
+ if (!SwingUtilities.isRightMouseButton(evt))
{
- JPopupMenu pop = new JPopupMenu("Annotations");
- JMenuItem item = new JMenuItem(ADDNEW);
- item.addActionListener(this);
- pop.add(item);
- pop.show(this, evt.getX(), evt.getY());
-
return;
}
@@ -412,6 +534,17 @@ public class AnnotationLabels
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);
+ }
+ pop.show(this, evt.getX(), evt.getY());
+ return;
+ }
item = new JMenuItem(EDITNAME);
item.addActionListener(this);
pop.add(item);
@@ -421,100 +554,251 @@ public class AnnotationLabels
item = new JMenuItem(DELETE);
item.addActionListener(this);
pop.add(item);
- item = new JMenuItem(SHOWALL);
- 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);
- // annotation object should be typed
- if (aa[selectedRow] == ap.av.consensus)
- {
- pop.addSeparator();
- final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- "Ignore Gaps In Consensus",
- ap.av.getIgnoreGapsConsensus());
- cbmi.addActionListener(new ActionListener()
+ // TODO: annotation object should be typed for autocalculated/derived
+ // property methods
+ if (selectedRow < aa.length)
+ {
+ if (!aa[selectedRow].autoCalculated)
{
- public void actionPerformed(ActionEvent e)
+ if (aa[selectedRow].graph == AlignmentAnnotation.NO_GRAPH)
{
- ap.av.setIgnoreGapsConsensus(cbmi.getState(), ap);
+ // display formatting settings for this row.
+ pop.addSeparator();
+ // av and sequencegroup need to implement same interface for
+ item = new JCheckBoxMenuItem(TOGGLE_LABELSCALE,
+ aa[selectedRow].scaleColLabel);
+ item.addActionListener(this);
+ pop.add(item);
}
- });
- pop.add(cbmi);
- final JMenuItem consclipbrd = new JMenuItem(COPYCONS_SEQ);
- consclipbrd.addActionListener(this);
- pop.add(consclipbrd);
- }
+ }
+ else if (aa[selectedRow].label.indexOf("Consensus") > -1)
+ {
+ 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);
+ final JCheckBoxMenuItem cproflnorm = new JCheckBoxMenuItem(
+ "Normalise Group Logo",
+ aa[selectedRow].groupRef.isNormaliseSequenceLogo());
+ cproflnorm.addActionListener(new ActionListener()
+ {
+ public void actionPerformed(ActionEvent e)
+ {
+ // 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
+ *
+ * @param sq
+ * sequence to be copied to clipboard
*/
protected void copy_annotseqtoclipboard(SequenceI sq)
{
SequenceI[] seqs = new SequenceI[]
- {
- sq};
+ { sq };
String[] omitHidden = null;
SequenceI[] dseqs = new SequenceI[]
- {
- sq.getDatasetSequence()};
+ { sq.getDatasetSequence() };
if (dseqs[0] == null)
{
dseqs[0] = new Sequence(sq);
- dseqs[0].setSequence(
- jalview.analysis.AlignSeq.extractGaps(
- jalview.util.Comparison.GapChars,
- sq.getSequenceAsString()));
+ 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)
+ if (av.hasHiddenColumns())
{
omitHidden = av.getColumnSelection().getVisibleSequenceStrings(0,
- sq.getLength(), seqs);
+ sq.getLength(), seqs);
}
- String output = new FormatAdapter().formatSequences(
- "Fasta",
- seqs,
- omitHidden);
+ String output = new FormatAdapter().formatSequences("Fasta", seqs,
+ omitHidden);
Toolkit.getDefaultToolkit().getSystemClipboard()
- .setContents(new StringSelection(output), Desktop.instance);
+ .setContents(new StringSelection(output), Desktop.instance);
Vector hiddenColumns = null;
- if (av.hasHiddenColumns)
+ if (av.hasHiddenColumns())
{
hiddenColumns = 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);
hiddenColumns.addElement(new int[]
- {region[0],
- region[1]});
+ { region[0], region[1] });
}
}
Desktop.jalviewClipboard = new Object[]
- {
- seqs,
- ds, // what is the dataset of a consensus sequence ? need to flag sequence as special.
- hiddenColumns};
+ { seqs, ds, // what is the dataset of a consensus sequence ? need to flag
+ // sequence as special.
+ hiddenColumns };
}
/**
* DOCUMENT ME!
- *
- * @param g1 DOCUMENT ME!
+ *
+ * @param g1
+ * DOCUMENT ME!
*/
public void paintComponent(Graphics g)
{
@@ -529,7 +813,7 @@ public class AnnotationLabels
if (av.antiAlias)
{
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
drawComponent(g2, width);
@@ -538,8 +822,9 @@ public class AnnotationLabels
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int width)
{
@@ -559,34 +844,43 @@ public class AnnotationLabels
g.translate(0, scrollOffset);
g.setColor(Color.black);
- AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
+ AlignmentAnnotation[] aa = av.getAlignment().getAlignmentAnnotation();
int fontHeight = g.getFont().getSize();
- int y = fontHeight;
+ int y = 0;
int x = 0;
int graphExtras = 0;
-
+ int offset = 0;
+ Font baseFont = g.getFont();
+ FontMetrics baseMetrics = fm;
+ int ofontH = fontHeight;
+ boolean visible = true;
if (aa != null)
{
+ hasHiddenRows = false;
for (int i = 0; i < aa.length; i++)
{
+ visible = true;
+ g.setColor(Color.black);
+
if (!aa[i].visible)
{
+ hasHiddenRows = true;
continue;
}
- x = width - fm.stringWidth(aa[i].label) - 3;
-
- if (aa[i].graph > 0 && aa[i].graphHeight > 0)
- {
- graphExtras = y;
+ y += aa[i].height;
- y += (aa[i].height / 3);
+ offset = -aa[i].height / 2;
- if (aa[i].graphGroup < 0)
- {
- graphExtras = y + fontHeight;
- }
+ 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[i].graphGroup > -1)
{
@@ -598,66 +892,59 @@ public class AnnotationLabels
groupSize++;
}
}
-
if (groupSize * (fontHeight + 8) < aa[i].height)
{
- graphExtras += (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
+ graphExtras = (aa[i].height - (groupSize * (fontHeight + 8))) / 2;
}
-
- for (int gg = 0; gg < aa.length; gg++)
+ else
{
- if (aa[gg].graphGroup == aa[i].graphGroup)
+ // scale font to fit
+ float h = aa[i].height / (float) groupSize, s;
+ if (h < 9)
{
- 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;
+ 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;
}
}
- }
- else
- {
- g.drawString(aa[i].label, x, y);
- }
-
- if (aa[i].graph > 0)
- {
- /* if (aa[i].graphLines != null)
+ if (visible)
+ {
+ for (int gg = 0; gg < aa.length; gg++)
{
- for (int gl = 0; gl < aa[i].graphLines.size(); gl++)
+ if (aa[gg].graphGroup == aa[i].graphGroup)
{
- 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());
+ x = width - fm.stringWidth(aa[gg].label) - 3;
+ g.drawString(aa[gg].label, x, y - graphExtras);
+
+ if (aa[gg]._linecolour != null)
+ {
+
+ g.setColor(aa[gg]._linecolour);
+ g.drawLine(x, y - graphExtras + 3,
+ x + fm.stringWidth(aa[gg].label), y - graphExtras
+ + 3);
+ }
+
+ g.setColor(Color.black);
+ graphExtras += fontHeight + 8;
}
- }*/
- y += ( (2 * aa[i].height) / 3);
+ }
+ }
+ g.setFont(baseFont);
+ fm = baseMetrics;
+ fontHeight = ofontH;
}
else
{
- y += aa[i].height;
+ g.drawString(aa[i].label, x, y + offset);
}
}
}
@@ -670,10 +957,10 @@ public class AnnotationLabels
{
g.setColor(Color.lightGray);
g.drawString(aa[selectedRow].label, dragEvent.getX(),
- dragEvent.getY() - scrollOffset);
+ dragEvent.getY() - scrollOffset);
}
- if ( (aa == null) || (aa.length < 1))
+ if ((aa == null) || (aa.length < 1))
{
g.drawString("Right click", 2, 8);
g.drawString("to add annotation", 2, 18);