X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=a42251ef66b59081db3078de9ee8d874f7abbda2;hb=e33b171845992fd21094ba754498f9ab3d29f110;hp=d4e7c773c9f5d77522953322632deb2c8dfcb7e9;hpb=8dd1cd955b1c6f1a89afc2068ab1cdfca3824934;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index d4e7c77..a42251e 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,28 +1,32 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * 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
  *
- * This program is free software; you can redistribute it and/or
+ * 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 2
- * of the License, or (at your option) any later version.
+ * as published by the Free Software Foundation, either version 3 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.
+ * 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 <http://www.gnu.org/licenses/>.
  */
 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;
 
 /**
  * DOCUMENT ME!
@@ -30,30 +34,42 @@ import jalview.datamodel.*;
  * @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;
+
   protected AlignViewport av;
+
   protected AlignmentPanel alignPanel;
+
   ScrollThread scrollThread = null;
+
+  String linkImageURL;
+
   int offy;
+
   // int width;
   int lastid = -1;
+
   boolean mouseDragging = false;
+  private final SequenceAnnotationReport seqAnnotReport;
 
   /**
    * Creates a new IdPanel object.
    *
-   * @param av DOCUMENT ME!
-   * @param parent DOCUMENT ME!
+   * @param av
+   *          DOCUMENT ME!
+   * @param parent
+   *          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);
@@ -61,78 +77,36 @@ public class IdPanel
     addMouseWheelListener(this);
     ToolTipManager.sharedInstance().registerComponent(this);
   }
-
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          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("<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 (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();
-      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("<br>" + tmp);
-            maxWidth = Math.max(maxWidth, tmp.length());
-          }
-        }
-      }
-
-      if(maxWidth > 60)
-      {
-         tip.insert(0, "<table width=350 border=0><tr><td><i>");
-         tip.append("</i></td></tr></table>");
-      }
-
-      tip.append("</html>");
-
-      setToolTipText("<html>"+sequence.getDisplayId(true)+tip.toString());
+      seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+              av.isShowDbRefs(), av.isShowNpFeats(),
+              sp.seqCanvas.fr.minmax);
+      setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+              + tip.toString()+"</html>");
     }
   }
 
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseDragged(MouseEvent e)
   {
     mouseDragging = true;
@@ -152,24 +126,38 @@ public class IdPanel
     alignPanel.paintAlignment(true);
   }
 
+  @Override
   public void mouseWheelMoved(MouseWheelEvent e)
   {
     e.consume();
-      if (e.getWheelRotation() > 0)
+    if (e.getWheelRotation() > 0)
+    {
+      if (e.isShiftDown())
       {
+        alignPanel.scrollRight(true);
+        
+      } else {
         alignPanel.scrollUp(false);
       }
-      else
+    }
+    else
+    {
+      if (e.isShiftDown())
       {
+        alignPanel.scrollRight(false);
+      } else {
         alignPanel.scrollUp(true);
       }
+    }
   }
 
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
@@ -184,42 +172,65 @@ public class IdPanel
     }
 
     int seq = alignPanel.seqPanel.findSeq(e);
-
-    //DEFAULT LINK IS FIRST IN THE LINK LIST
-
+    String url = null;
+    int i = 0;
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    if (id.indexOf("|") > -1)
+    while (url == null && i < links.size())
     {
-      id = id.substring(id.lastIndexOf("|") + 1);
-    }
-
-    String url = links.elementAt(0).toString();
-    url = url.substring(url.indexOf("|") + 1);
-
-    int index = url.indexOf("$SEQUENCE_ID$");
-    url = url.substring(0, index) + id + url.substring(index + 13);
+      // DEFAULT LINK IS FIRST IN THE LINK LIST
+      // BUT IF ITS A REGEX AND DOES NOT MATCH THE NEXT ONE WILL BE TRIED
+      url = links.elementAt(i++).toString();
+      jalview.util.UrlLink urlLink = null;
+      try
+      {
+        urlLink = new UrlLink(url);
+      } catch (Exception foo)
+      {
+        jalview.bin.Cache.log.error("Exception for URLLink '" + url + "'",
+                foo);
+        url = null;
+        continue;
+      }
+      ;
+      if (!urlLink.isValid())
+      {
+        jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+        url = null;
+        continue;
+      }
 
+      String urls[] = urlLink.makeUrls(id, true);
+      if (urls == null || urls[0] == null || urls[0].length() < 4)
+      {
+        url = null;
+        continue;
+      }
+      // just take first URL made from regex
+      url = urls[1];
+    }
     try
     {
       jalview.util.BrowserLauncher.openURL(url);
-    }
-    catch (Exception ex)
+    } catch (Exception ex)
     {
-      JOptionPane.showInternalMessageDialog(Desktop.desktop,
-                                            "Unixers: Couldn't find default web browser."
-                                            +
-          "\nAdd the full path to your browser in Preferences.",
-                                            "Web browser not found",
-                                            JOptionPane.WARNING_MESSAGE);
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "Unixers: Couldn't find default web browser."
+                              + "\nAdd the full path to your browser in Preferences.",
+                      "Web browser not found", JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
+
   }
 
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (scrollThread != null)
@@ -231,8 +242,10 @@ public class IdPanel
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -245,8 +258,8 @@ public class IdPanel
       scrollThread = new ScrollThread(true);
     }
 
-    if (mouseDragging && (e.getY() >= getHeight()) &&
-        (av.alignment.getHeight() > av.getEndSeq()))
+    if (mouseDragging && (e.getY() >= getHeight())
+            && (av.getAlignment().getHeight() > av.getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -255,8 +268,10 @@ public class IdPanel
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
+  @Override
   public void mousePressed(MouseEvent e)
   {
     if (e.getClickCount() == 2)
@@ -268,20 +283,39 @@ public class IdPanel
 
     if (javax.swing.SwingUtilities.isRightMouseButton(e))
     {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          (Sequence) av.getAlignment().getSequenceAt(seq),
-          Preferences.sequenceURLLinks);
+      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+      // 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();
+      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      {
+        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+        {
+          if (sf[sl].links != null && sf[sl].links.size() > 0)
+          {
+            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+            {
+              nlinks.addElement(sf[sl].links.elementAt(l));
+            }
+          }
+        }
+      }
+
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
+              nlinks, new Vector(Preferences.getGroupURLLinks()));
       pop.show(this, e.getX(), e.getY());
 
       return;
     }
 
-    if ( (av.getSelectionGroup() == null) ||
-        ( (!e.isControlDown() && !e.isShiftDown()) && av.getSelectionGroup() != null))
+    if ((av.getSelectionGroup() == null)
+            || ((!e.isControlDown() && !e.isShiftDown()) && av
+                    .getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
-      av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
+      av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1);
     }
 
     if (e.isShiftDown() && (lastid != -1))
@@ -292,14 +326,14 @@ public class IdPanel
     {
       selectSeq(seq);
     }
-
     alignPanel.paintAlignment(true);
   }
 
   /**
    * DOCUMENT ME!
    *
-   * @param seq DOCUMENT ME!
+   * @param seq
+   *          DOCUMENT ME!
    */
   void selectSeq(int seq)
   {
@@ -312,8 +346,10 @@ public class IdPanel
   /**
    * DOCUMENT ME!
    *
-   * @param start DOCUMENT ME!
-   * @param end DOCUMENT ME!
+   * @param start
+   *          DOCUMENT ME!
+   * @param end
+   *          DOCUMENT ME!
    */
   void selectSeqs(int start, int end)
   {
@@ -339,16 +375,18 @@ public class IdPanel
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
-                                         true);
+      av.getSelectionGroup().addSequence(
+              av.getAlignment().getSequenceAt(i), true);
     }
   }
 
   /**
    * DOCUMENT ME!
    *
-   * @param e DOCUMENT ME!
+   * @param e
+   *          DOCUMENT ME!
    */
+  @Override
   public void mouseReleased(MouseEvent e)
   {
     if (scrollThread != null)
@@ -358,36 +396,39 @@ public class IdPanel
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
   }
 
   /**
    * DOCUMENT ME!
    *
-   * @param found DOCUMENT ME!
+   * @param list
+   *          DOCUMENT ME!
    */
-  public void highlightSearchResults(java.util.Vector found)
+  public void highlightSearchResults(List<SequenceI> list)
   {
-    idCanvas.setHighlighted(found);
+    idCanvas.setHighlighted(list);
 
-    if (found == null)
+    if (list == null)
     {
       return;
     }
 
-    int index = av.alignment.findIndex( (SequenceI) found.get(0));
+    int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ( (av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
     {
       alignPanel.setScrollValues(av.getStartRes(), index);
     }
   }
 
   // this class allows scrolling off the bottom of the visible alignment
-  class ScrollThread
-      extends Thread
+  class ScrollThread extends Thread
   {
     boolean running = false;
+
     boolean up = true;
 
     public ScrollThread(boolean up)
@@ -401,6 +442,7 @@ public class IdPanel
       running = false;
     }
 
+    @Override
     public void run()
     {
       running = true;
@@ -438,8 +480,7 @@ public class IdPanel
         try
         {
           Thread.sleep(100);
-        }
-        catch (Exception ex)
+        } catch (Exception ex)
         {
         }
       }