X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b5fd0c17251e002c84c3198bd211958b692a2b76;hb=59d682209891099d46b960509907c79e3fb276fe;hp=a325618e324fc24a90f56fe31756d553a78bcc39;hpb=21f3e784749a8eb93cd716fca379d50732f08827;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index a325618..b5fd0c1 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,30 +1,31 @@
/*
- * 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 2.8)
+ * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 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
+ * You should have received a copy of the GNU General Public License along with Jalview. If not, see .
*/
package jalview.gui;
import java.awt.*;
import java.awt.event.*;
+import java.util.List;
import java.util.Vector;
import javax.swing.*;
import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
import jalview.util.UrlLink;
/**
@@ -44,6 +45,8 @@ public class IdPanel extends JPanel implements MouseListener,
ScrollThread scrollThread = null;
+ String linkImageURL;
+
int offy;
// int width;
@@ -51,19 +54,23 @@ public class IdPanel extends JPanel implements MouseListener,
boolean mouseDragging = false;
+ private final SequenceAnnotationReport seqAnnotReport;
+
/**
* Creates a new IdPanel object.
*
* @param av
- * DOCUMENT ME!
+ * DOCUMENT ME!
* @param parent
- * DOCUMENT ME!
+ * DOCUMENT ME!
*/
public IdPanel(AlignViewport av, AlignmentPanel parent)
{
this.av = av;
alignPanel = parent;
idCanvas = new IdCanvas(av);
+ linkImageURL = getClass().getResource("/images/link.gif").toString();
+ seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
setLayout(new BorderLayout());
add(idCanvas, BorderLayout.CENTER);
addMouseListener(this);
@@ -76,74 +83,23 @@ public class IdPanel extends JPanel implements MouseListener,
* DOCUMENT ME!
*
* @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.seqPanel;
+ int seq = Math.max(0, sp.findSeq(e));
+ if (seq > -1 && seq < av.getAlignment().getHeight())
{
- SequenceI sequence = av.alignment.getSequenceAt(seq);
+ 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();
- if (av.isShowNpFeats() && features != null)
- {
- for (int i = 0; i < features.length; i++)
- {
- if (features[i].begin == 0 && features[i].end == 0)
- {
- tip.append("
");
- int sz = -tip.length();
- boolean nl=false;
- if (features[i].getFeatureGroup()!=null) { tip.append(features[i].getFeatureGroup()); nl=true;};
- if (features[i].getType()!=null) { tip.append(" "); tip.append(features[i].getType()); nl=true;};
- if (features[i].getDescription()!=null) { tip.append(" "); tip.append(features[i].getDescription()); nl=true;};
- if (features[i].getScore()!=Float.NaN && features[i].getScore()!=0f) { tip.append(" Score = "); tip.append(features[i].getScore()); nl=true;};
- if (features[i].getStatus()!=null && features[i].getStatus().length()>0) { tip.append(" ("); tip.append(features[i].getStatus()); tip.append(")");nl=true;};
- if (nl) {
- sz+=tip.length();
- tip.append("
");
- maxWidth = Math.max(maxWidth, sz);
- }
- }
- }
- }
-
- if (maxWidth > 60)
- {
- tip.insert(0, "");
- }
-
- tip.append("