JAL-1503 update version in GPL header

[jalview.git] / src / jalview / gui / IdPanel.java

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 0480ffa..2b87d21 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,19 +1,20 @@
 /*
- * 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 2.8.1)
+ * Copyright (C) 2014 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
+ * 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
+ *  
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.gui;
 
@@ -25,11 +26,12 @@ import java.util.Vector;
 import javax.swing.*;
 
 import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
 import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
- *
+ * 
  * @author $author$
  * @version $Revision$
  */
@@ -53,9 +55,11 @@ 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
@@ -67,6 +71,7 @@ public class IdPanel extends JPanel implements MouseListener,
     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);
@@ -77,7 +82,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -86,69 +91,22 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     SeqPanel sp = alignPanel.seqPanel;
     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("<i>");
-
-      int maxWidth = 0;
-      if (sequence.getDescription() != null)
-      {
-        tmp = sequence.getDescription();
-        tip.append("<br>" + 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("<br>");
-          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, "<table width=350 border=0><tr><td><i>");
-        tip.append("</i></td></tr></table>");
-      }
-
-      tip.append("</html>");
-
+      seqAnnotReport
+              .createSequenceAnnotationReport(tip, sequence,
+                      av.isShowDbRefs(), av.isShowNpFeats(),
+                      sp.seqCanvas.fr.minmax);
       setToolTipText("<html>" + sequence.getDisplayId(true) + " "
-              + tip.toString());
+              + tip.toString() + "</html>");
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -178,17 +136,32 @@ public class IdPanel extends JPanel implements MouseListener,
     e.consume();
     if (e.getWheelRotation() > 0)
     {
-      alignPanel.scrollUp(false);
+      if (e.isShiftDown())
+      {
+        alignPanel.scrollRight(true);
+
+      }
+      else
+      {
+        alignPanel.scrollUp(false);
+      }
     }
     else
     {
-      alignPanel.scrollUp(true);
+      if (e.isShiftDown())
+      {
+        alignPanel.scrollRight(false);
+      }
+      else
+      {
+        alignPanel.scrollUp(true);
+      }
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -261,7 +234,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -276,7 +249,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -302,7 +275,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -322,7 +295,8 @@ public class IdPanel extends JPanel implements MouseListener,
       // build a new links menu based on the current links + any non-positional
       // features
       Vector nlinks = new Vector(Preferences.sequenceURLLinks);
-      SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().getSequenceFeatures();
+      SequenceFeature sf[] = sq == null ? null : sq.getDatasetSequence()
+              .getSequenceFeatures();
       for (int sl = 0; sf != null && sl < sf.length; sl++)
       {
         if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
@@ -366,7 +340,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param seq
    *          DOCUMENT ME!
    */
@@ -380,7 +354,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param start
    *          DOCUMENT ME!
    * @param end
@@ -411,13 +385,13 @@ public class IdPanel extends JPanel implements MouseListener,
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), true);
+              av.getAlignment().getSequenceAt(i), i == end);
     }
   }
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param e
    *          DOCUMENT ME!
    */
@@ -437,7 +411,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
   /**
    * DOCUMENT ME!
-   *
+   * 
    * @param list
    *          DOCUMENT ME!
    */