X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=3cc0ed301843ebd32bdd959b18b567e8375c14ba;hb=bd894ca9f2aae448653d7431ab8a170e1105e85c;hp=a781830d18a3f2de3174eed626d52a5b1420a590;hpb=506d60f0e188723ddc91c26824b41ac7034df3fe;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a781830..3cc0ed3 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,47 +1,66 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
*
- * 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 file is part of Jalview.
*
- * 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 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 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.gui;
-import java.awt.*;
-import java.awt.event.*;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.Platform;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
/**
- * DOCUMENT ME!
+ * This panel hosts alignment sequence ids and responds to mouse clicks on them,
+ * as well as highlighting ids matched by a search from the Find menu.
*
* @author $author$
* @version $Revision$
*/
-public class IdPanel extends JPanel implements MouseListener,
- MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel
+ implements MouseListener, MouseMotionListener, MouseWheelListener
{
- protected IdCanvas idCanvas;
+ private IdCanvas idCanvas;
- protected AlignViewport av;
+ protected AlignmentViewport av;
protected AlignmentPanel alignPanel;
ScrollThread scrollThread = null;
+ String linkImageURL;
+
int offy;
// int width;
@@ -49,21 +68,23 @@ public class IdPanel extends JPanel implements MouseListener,
boolean mouseDragging = false;
+ private final SequenceAnnotationReport seqAnnotReport;
+
/**
* Creates a new IdPanel object.
*
* @param av
- * DOCUMENT ME!
* @param parent
- * DOCUMENT ME!
*/
public IdPanel(AlignViewport av, AlignmentPanel parent)
{
this.av = av;
alignPanel = parent;
- idCanvas = new IdCanvas(av);
+ setIdCanvas(new IdCanvas(av));
+ linkImageURL = getClass().getResource("/images/link.gif").toString();
+ seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
setLayout(new BorderLayout());
- add(idCanvas, BorderLayout.CENTER);
+ add(getIdCanvas(), BorderLayout.CENTER);
addMouseListener(this);
addMouseMotionListener(this);
addMouseWheelListener(this);
@@ -71,82 +92,41 @@ public class IdPanel extends JPanel implements MouseListener,
}
/**
- * DOCUMENT ME!
+ * Respond to mouse movement by constructing tooltip text for the sequence id
+ * under the mouse.
*
* @param e
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
+ @Override
public void mouseMoved(MouseEvent e)
{
- int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
- String tmp;
- if (seq > -1 && seq < av.alignment.getHeight())
+ SeqPanel sp = alignPanel.getSeqPanel();
+ int seq = Math.max(0, sp.findSeq(e));
+ if (seq > -1 && seq < av.getAlignment().getHeight())
{
- SequenceI sequence = av.alignment.getSequenceAt(seq);
- StringBuffer tip = new StringBuffer();
- tip.append("");
-
- int maxWidth = 0;
- if (sequence.getDescription() != null)
- {
- tmp = sequence.getDescription();
- tip.append("
" + tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
-
- DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
- if (dbrefs != null)
- {
- for (int i = 0; i < dbrefs.length; i++)
- {
- tip.append("
");
- tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
- tip.append(tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
- }
-
- // ADD NON POSITIONAL SEQUENCE INFO
- SequenceFeature[] features = sequence.getDatasetSequence()
- .getSequenceFeatures();
- if (features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].begin == 0 && features[i].end == 0)
- {
- tmp = features[i].featureGroup + " " + features[i].getType()
- + " " + features[i].description;
- tip.append("
" + tmp);
- maxWidth = Math.max(maxWidth, tmp.length());
- }
- }
- }
-
- if (maxWidth > 60)
- {
- tip.insert(0, "");
- }
-
- tip.append("