/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
+ * Copyright (C) 2008 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
/**
* 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 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!
+ *
+ * @param ap
+ * DOCUMENT ME!
*/
public AnnotationLabels(AlignmentPanel ap)
{
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);
+ 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);
/**
* DOCUMENT ME!
- *
- * @param y DOCUMENT ME!
+ *
+ * @param y
+ * DOCUMENT ME!
*/
public void setScrollOffset(int y)
{
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void actionPerformed(ActionEvent evt)
{
if (evt.getActionCommand().equals(ADDNEW))
{
AlignmentAnnotation newAnnotation = new AlignmentAnnotation(null,
- null,
- new Annotation[ap.av.alignment.getWidth()]);
+ null, new Annotation[ap.av.alignment.getWidth()]);
if (!editLabelDescription(newAnnotation))
{
{
for (int i = 0; i < aa.length; i++)
{
- if (!aa[i].visible && aa[i].annotations!=null)
+ if (!aa[i].visible && aa[i].annotations != null)
{
aa[i].visible = true;
}
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
- new AnnotationExporter().exportAnnotations(
- ap,
- new AlignmentAnnotation[]
- {aa[selectedRow]},
- null, null
- );
+ new AnnotationExporter().exportAnnotations(ap,
+ new AlignmentAnnotation[]
+ { aa[selectedRow] }, null, null);
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
/**
* 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");
if (!dialog.accept)
{
annotation.label = dialog.getName();
String text = dialog.getDescription();
- if (text!=null && text.length() == 0)
+ if (text != null && text.length() == 0)
{
text = null;
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mousePressed(MouseEvent evt)
{
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseReleased(MouseEvent evt)
{
if (start != end)
{
- //Swap these annotations
- AlignmentAnnotation startAA = ap.av.alignment.getAlignmentAnnotation()[
- start];
+ // Swap these annotations
+ AlignmentAnnotation startAA = ap.av.alignment
+ .getAlignmentAnnotation()[start];
AlignmentAnnotation endAA = ap.av.alignment.getAlignmentAnnotation()[end];
ap.av.alignment.getAlignmentAnnotation()[end] = startAA;
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseEntered(MouseEvent evt)
{
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseExited(MouseEvent evt)
{
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseDragged(MouseEvent evt)
{
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));
+ d.width, d.height - dif));
ap.paintAlignment(true);
}
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseMoved(MouseEvent evt)
{
getSelectedRow(evt.getY() - scrollOffset);
-
if (selectedRow > -1
- && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
+ && ap.av.alignment.getAlignmentAnnotation().length > selectedRow)
{
- AlignmentAnnotation aa = ap.av.alignment.
- getAlignmentAnnotation()[selectedRow];
+ AlignmentAnnotation aa = ap.av.alignment.getAlignmentAnnotation()[selectedRow];
StringBuffer desc = new StringBuffer("<html>");
- if (aa.description != null && !aa.description.equals("New description"))
+ if (aa.description != null
+ && !aa.description.equals("New description"))
{
desc.append(aa.getDescription(true));
- if(aa.hasScore)
+ if (aa.hasScore)
desc.append("<br>");
}
- if(aa.hasScore())
+ if (aa.hasScore())
{
- desc.append("Score: "+aa.score);
+ desc.append("Score: " + aa.score);
}
- if(desc.length()!=6)
+ if (desc.length() != 6)
{
desc.append("</html>");
this.setToolTipText(desc.toString());
/**
* DOCUMENT ME!
- *
- * @param evt DOCUMENT ME!
+ *
+ * @param evt
+ * DOCUMENT ME!
*/
public void mouseClicked(MouseEvent evt)
{
JMenuItem item = new JMenuItem(ADDNEW);
item.addActionListener(this);
- if ( (aa == null) || (aa.length == 0))
+ if ((aa == null) || (aa.length == 0))
{
item = new JMenuItem(SHOWALL);
item.addActionListener(this);
item.addActionListener(this);
pop.add(item);
// annotation object should be typed
- if (selectedRow<aa.length && aa[selectedRow] == ap.av.consensus)
+ if (selectedRow < aa.length && aa[selectedRow] == ap.av.consensus)
{
pop.addSeparator();
final JCheckBoxMenuItem cbmi = new JCheckBoxMenuItem(
- "Ignore Gaps In Consensus",
- ap.av.getIgnoreGapsConsensus());
+ "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
cbmi.addActionListener(new ActionListener()
{
public void actionPerformed(ActionEvent e)
/**
* 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]);
}
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);
+ Toolkit.getDefaultToolkit().getSystemClipboard().setContents(
+ new StringSelection(output), Desktop.instance);
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);
+ 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)
{
if (av.antiAlias)
{
g2.setRenderingHint(RenderingHints.KEY_ANTIALIASING,
- RenderingHints.VALUE_ANTIALIAS_ON);
+ RenderingHints.VALUE_ANTIALIAS_ON);
}
drawComponent(g2, width);
/**
* DOCUMENT ME!
- *
- * @param g DOCUMENT ME!
+ *
+ * @param g
+ * DOCUMENT ME!
*/
public void drawComponent(Graphics g, int width)
{
int y = 0;
int x = 0;
int graphExtras = 0;
- int offset =0;
+ int offset = 0;
if (aa != null)
{
continue;
}
-
y += aa[i].height;
- offset = -aa[i].height/2;
+ offset = -aa[i].height / 2;
- if(aa[i].hasText)
+ if (aa[i].hasText)
{
- offset += fm.getHeight()/2;
+ offset += fm.getHeight() / 2;
offset -= fm.getDescent();
}
else
if (aa[gg].graphGroup == aa[i].graphGroup)
{
x = width - fm.stringWidth(aa[gg].label) - 3;
- g.drawString(aa[gg].label, x,y - graphExtras);
+ 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.drawLine(x, y - graphExtras - 3, x
+ + fm.stringWidth(aa[gg].label), y - graphExtras - 3);
g.setColor(Color.black);
graphExtras += fontHeight + 8;
}
else
{
- g.drawString(aa[i].label, x, y +offset);
+ g.drawString(aa[i].label, x, y + offset);
}
}
}
else if (dragEvent != null && aa != null)
{
g.setColor(Color.lightGray);
- g.drawString(aa[selectedRow].label, dragEvent.getX(),
- dragEvent.getY() - scrollOffset);
+ g.drawString(aa[selectedRow].label, dragEvent.getX(), 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);
git://source.jalview.org / jalview.git / blobdiff