/*
- * 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 2.6)
+ * Copyright (C) 2010 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 <http://www.gnu.org/licenses/>.
*/
-
package jalview.appletgui;
+import java.util.*;
+
import java.awt.*;
import java.awt.event.*;
-import java.util.Vector;
import jalview.datamodel.*;
-public class AnnotationLabels
- extends Panel implements ActionListener
+public class AnnotationLabels extends Panel implements ActionListener,
+ MouseListener, MouseMotionListener
{
+ Image image;
+
boolean active = false;
+
AlignmentPanel ap;
+
AlignViewport av;
+
boolean resizing = false;
+
int oldY, mouseX;
- static String ADDNEW = "Add new row";
- static String HIDE = "Hide this row";
- static String DELETE = "Delete this row";
- static String SHOWALL = "Show all hidden rows";
+
+ static String ADDNEW = "Add New Row";
+
+ static String EDITNAME = "Edit Label/Description";
+
+ static String HIDE = "Hide This Row";
+
+ static String SHOWALL = "Show All Hidden Rows";
+
static String OUTPUT_TEXT = "Show Values In Textbox";
+
static String COPYCONS_SEQ = "Copy Consensus Sequence";
-
- int selectedRow = 0;
+
int scrollOffset = 0;
+ int selectedRow = -1;
+
+ Tooltip tooltip;
+
+ private boolean hasHiddenRows;
+
public AnnotationLabels(AlignmentPanel ap)
{
this.ap = ap;
this.av = ap.av;
setLayout(null);
- addMouseListener(new MouseAdapter()
- {
- public void mousePressed(MouseEvent evt)
- {
- doMousePressed(evt);
- }
- });
+ addMouseListener(this);
+ addMouseMotionListener(this);
}
public AnnotationLabels(AlignViewport av)
-{
- this.av = av;
-}
-
+ {
+ this.av = av;
+ }
public void setScrollOffset(int y)
{
repaint();
}
+ /**
+ *
+ * @param y
+ * @return -2 if no rows are visible at all, -1 if no visible rows were selected
+ */
+ int getSelectedRow(int y)
+ {
+ int row = -2;
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ if (aa == null)
+ {
+ return row;
+ }
+ int height = 0;
+ for (int i = 0; i < aa.length; i++)
+ {
+ row = -1;
+ if (!aa[i].visible)
+ {
+ continue;
+ }
+ height += aa[i].height;
+ if (y < height)
+ {
+ row = i;
+ break;
+ }
+ }
+
+ return row;
+ }
+
public void actionPerformed(ActionEvent evt)
{
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- if (evt.getActionCommand().equals(HIDE))
+ if (evt.getActionCommand().equals(ADDNEW))
+ {
+ AlignmentAnnotation newAnnotation = new AlignmentAnnotation("", null,
+ new Annotation[ap.av.alignment.getWidth()]);
+
+ if (!editLabelDescription(newAnnotation))
+ {
+ return;
+ }
+
+ ap.av.alignment.addAnnotation(newAnnotation);
+ ap.av.alignment.setAnnotationIndex(newAnnotation, 0);
+ }
+ else if (evt.getActionCommand().equals(EDITNAME))
+ {
+ editLabelDescription(aa[selectedRow]);
+ }
+ else if (evt.getActionCommand().equals(HIDE))
{
aa[selectedRow].visible = false;
}
{
for (int i = 0; i < aa.length; i++)
{
- aa[i].visible = true;
+ aa[i].visible = (aa[i].annotations == null) ? false : true;
}
}
else if (evt.getActionCommand().equals(OUTPUT_TEXT))
{
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, ap.alignFrame);
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false,
+ ap.alignFrame);
Frame frame = new Frame();
frame.add(cap);
- jalview.bin.JalviewLite.addFrame(frame,
- ap.alignFrame.getTitle() + " - " +
- aa[selectedRow].label, 500, 100);
+ jalview.bin.JalviewLite.addFrame(frame, ap.alignFrame.getTitle()
+ + " - " + aa[selectedRow].label, 500, 100);
cap.setText(aa[selectedRow].toString());
}
else if (evt.getActionCommand().equals(COPYCONS_SEQ))
{
- SequenceI cons=av.getConsensusSeq();
- if (cons!=null)
+ SequenceI cons = av.getConsensusSeq();
+ if (cons != null)
+ {
copy_annotseqtoclipboard(cons);
-
+ }
+
}
ap.annotationPanel.adjustPanelHeight();
setSize(getSize().width, ap.annotationPanel.getSize().height);
ap.validate();
- ap.repaint();
+ ap.paintAlignment(true);
}
- public void doMousePressed(MouseEvent evt)
+ boolean editLabelDescription(AlignmentAnnotation annotation)
{
- int y = evt.getY() - scrollOffset;
- AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
- int height = 0;
- for (int i = 0; i < aa.length; i++)
+ Checkbox padGaps = new Checkbox("Fill Empty Gaps With \""
+ + ap.av.getGapCharacter() + "\"", annotation.padGaps);
+
+ EditNameDialog dialog = new EditNameDialog(annotation.label,
+ annotation.description, " Annotation Label",
+ "Annotation Description", ap.alignFrame,
+ "Edit Annotation Name / Description", 500, 180, false);
+
+ Panel empty = new Panel(new FlowLayout());
+ empty.add(padGaps);
+ dialog.add(empty);
+ dialog.pack();
+
+ dialog.setVisible(true);
+
+ if (dialog.accept)
{
- if (!aa[i].visible)
+ annotation.label = dialog.getName();
+ annotation.description = dialog.getDescription();
+ annotation.setPadGaps(padGaps.getState(), av.getGapCharacter());
+ repaint();
+ return true;
+ }
+ else
+ return false;
+
+ }
+
+ public void mouseMoved(MouseEvent evt)
+ {
+ int row = getSelectedRow(evt.getY() - scrollOffset);
+
+ if (row > -1)
+ {
+ if (tooltip == null)
{
- continue;
+ tooltip = new Tooltip(ap.av.alignment.getAlignmentAnnotation()[row]
+ .getDescription(true), this);
}
-
- height += aa[i].height;
- if (y < height)
+ else
{
- selectedRow = i;
- break;
+ tooltip.setTip(ap.av.alignment.getAlignmentAnnotation()[row]
+ .getDescription(true));
}
}
+ else if (tooltip != null)
+ {
+ tooltip.setTip("");
+ }
+
+ }
+
+ public void mouseDragged(MouseEvent evt)
+ {
+ }
+
+ public void mouseClicked(MouseEvent evt)
+ {
+ }
+
+ public void mouseReleased(MouseEvent evt)
+ {
+ }
+
+ public void mouseEntered(MouseEvent evt)
+ {
+ }
+
+ public void mouseExited(MouseEvent evt)
+ {
+ }
- PopupMenu pop = new PopupMenu("Annotations");
- MenuItem item = new MenuItem(HIDE);
+ public void mousePressed(MouseEvent evt)
+ {
+ selectedRow = getSelectedRow(evt.getY() - scrollOffset);
+
+ AlignmentAnnotation[] aa = ap.av.alignment.getAlignmentAnnotation();
+
+ PopupMenu popup = new PopupMenu("Annotations");
+
+ MenuItem item = new MenuItem(ADDNEW);
+ item.addActionListener(this);
+ popup.add(item);
+ if (selectedRow<0)
+ {
+ // this never happens at moment: - see comment on JAL-563
+ if (hasHiddenRows)
+ {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
+ popup.show(this, evt.getX(), evt.getY());
+ return;
+ }
+ // add the rest if there are actually rows to show
+ item = new MenuItem(EDITNAME);
item.addActionListener(this);
- pop.add(item);
- item = new MenuItem(SHOWALL);
+ popup.add(item);
+ item = new MenuItem(HIDE);
item.addActionListener(this);
- pop.add(item);
- this.add(pop);
+ popup.add(item);
+ if (hasHiddenRows) {
+ item = new MenuItem(SHOWALL);
+ item.addActionListener(this);
+ popup.add(item);
+ }
+ this.add(popup);
item = new MenuItem(OUTPUT_TEXT);
item.addActionListener(this);
- pop.add(item);
+ popup.add(item);
- if (aa[selectedRow].label.equals("Consensus"))
+ if (aa[selectedRow] == ap.av.consensus)
{
- pop.addSeparator();
+ popup.addSeparator();
final CheckboxMenuItem cbmi = new CheckboxMenuItem(
- "Ignore Gaps In Consensus",
- ap.av.getIgnoreGapsConsensus());
+ "Ignore Gaps In Consensus", ap.av.getIgnoreGapsConsensus());
cbmi.addItemListener(new ItemListener()
{
public void itemStateChanged(ItemEvent e)
{
ap.av.setIgnoreGapsConsensus(cbmi.getState());
- ap.repaint();
+ ap.paintAlignment(true);
}
});
- pop.add(cbmi);
- final MenuItem cpcons=new MenuItem(COPYCONS_SEQ);
- cpcons.addActionListener(this);
- pop.add(cpcons);
+ popup.add(cbmi);
+ item = new MenuItem(COPYCONS_SEQ);
+ item.addActionListener(this);
+ popup.add(item);
}
- pop.show(this, evt.getX(), evt.getY());
+ popup.show(this, evt.getX(), evt.getY());
}
-/**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- protected void copy_annotseqtoclipboard(SequenceI sq)
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ protected void copy_annotseqtoclipboard(SequenceI sq)
+ {
+ if (sq == null || sq.getLength() < 1)
{
- if (sq==null || sq.getLength()<1)
- return;
- jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
- jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t" +
- sq.getStart() + "\t" +
- sq.getEnd() + "\t" +
- sq.getSequenceAsString() + "\n");
- if (av.hasHiddenColumns)
+ return;
+ }
+ jalview.appletgui.AlignFrame.copiedSequences = new StringBuffer();
+ jalview.appletgui.AlignFrame.copiedSequences.append(sq.getName() + "\t"
+ + sq.getStart() + "\t" + sq.getEnd() + "\t"
+ + sq.getSequenceAsString() + "\n");
+ if (av.hasHiddenColumns)
+ {
+ jalview.appletgui.AlignFrame.copiedHiddenColumns = new Vector();
+ for (int i = 0; i < av.getColumnSelection().getHiddenColumns().size(); i++)
{
- jalview.appletgui.AlignFrame.copiedHiddenColumns=new Vector();
- for(int i=0; i<av.getColumnSelection().getHiddenColumns().size(); i++)
- {
- int[] region = (int[])
- av.getColumnSelection().getHiddenColumns().elementAt(i);
+ int[] region = (int[]) av.getColumnSelection().getHiddenColumns()
+ .elementAt(i);
- jalview.appletgui.AlignFrame.copiedHiddenColumns.addElement(new int[]{region[0],
- region[1]});
- }
+ jalview.appletgui.AlignFrame.copiedHiddenColumns
+ .addElement(new int[]
+ { region[0], region[1] });
}
}
+ }
+
+ public void update(Graphics g)
+ {
+ paint(g);
+ }
public void paint(Graphics g)
{
- drawComponent(g, getSize().width);
+ int w = getSize().width;
+ if (image == null || w != image.getWidth(this))
+ {
+ image = createImage(w, ap.annotationPanel.getSize().height);
+ }
+
+ drawComponent(image.getGraphics(), w);
+ g.drawImage(image, 0, 0, this);
}
public void drawComponent(Graphics g, int width)
g.setColor(Color.black);
AlignmentAnnotation[] aa = av.alignment.getAlignmentAnnotation();
- int y = g.getFont().getSize();
- int x = 0;
+ int y = 0, fy=g.getFont().getSize();
+ int x = 0, offset;
if (aa != null)
{
+ hasHiddenRows=false;
for (int i = 0; i < aa.length; i++)
{
if (!aa[i].visible)
{
+ hasHiddenRows=true;
continue;
}
x = width - fm.stringWidth(aa[i].label) - 3;
- if (aa[i].graph>0)
- {
- y += (aa[i].height / 3);
- }
-
- g.drawString(aa[i].label, x, y);
+ y += aa[i].height;
+ offset = -(aa[i].height-fy)/2;
- if (aa[i].graph>0)
- {
- y += (2 * aa[i].height / 3);
- }
- else
- {
- y += aa[i].height;
- }
+ g.drawString(aa[i].label, x, y+offset);
}
}
}
git://source.jalview.org / jalview.git / blobdiff