X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=4ea35caac9c99ed337c954bbdc3fd8e947fe12b2;hb=be32c14cd8e48fe0a207cd7030cb9cd46f894678;hp=0480ffa6c6314f136df9fc37f5892c7442b32c22;hpb=f52f7b378972cc884b5d3e5cc250f89667f558f7;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 0480ffa..4ea35ca 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,42 +1,58 @@
/*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
- * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
- *
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
+ *
* 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
+ * 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 .
+ *
+ * You should have received a copy of the GNU General Public License
+ * 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 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.UrlLink;
+
+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 java.util.Vector;
-import javax.swing.*;
-
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
+import javax.swing.JOptionPane;
+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
{
- protected IdCanvas idCanvas;
+ private IdCanvas idCanvas;
protected AlignViewport av;
@@ -53,22 +69,23 @@ 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);
@@ -76,88 +93,42 @@ 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!
*/
@Override
public void mouseMoved(MouseEvent e)
{
- SeqPanel sp = alignPanel.seqPanel;
+ SeqPanel sp = alignPanel.getSeqPanel();
int seq = Math.max(0, sp.findSeq(e));
- String tmp;
if (seq > -1 && seq < av.getAlignment().getHeight())
{
SequenceI sequence = av.getAlignment().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 (av.isShowDbRefs() && 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();
- SequenceFeature[] tfeat = new SequenceFeature[1];
- if (av.isShowNpFeats() && features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].begin == 0 && features[i].end == 0)
- {
- int sz = -tip.length();
- tfeat[0] = features[i];
- sp.appendFeatures(tip, linkImageURL, 0, tfeat,
- sp.seqCanvas.fr.minmax);
- sz += tip.length();
- maxWidth = Math.max(maxWidth, sz);
- }
- }
- }
-
- if (maxWidth > 60)
- {
- tip.insert(0, "");
- }
-
- tip.append("