Merge branch 'develop' into features/JAL-250_hideredundantseqs

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

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 59d12d9..3cc0ed3 100755 (executable)
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -27,7 +27,6 @@ import jalview.datamodel.SequenceI;
 import jalview.io.SequenceAnnotationReport;
 import jalview.util.MessageManager;
 import jalview.util.Platform;
-import jalview.util.UrlLink;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
@@ -37,9 +36,7 @@ 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.JOptionPane;
 import javax.swing.JPanel;
 import javax.swing.SwingUtilities;
 import javax.swing.ToolTipManager;
@@ -51,8 +48,8 @@ import javax.swing.ToolTipManager;
  * @author $author$
  * @version $Revision$
  */
-public class IdPanel extends JPanel implements MouseListener,
-        MouseMotionListener, MouseWheelListener
+public class IdPanel extends JPanel
+        implements MouseListener, MouseMotionListener, MouseWheelListener
 {
   private IdCanvas idCanvas;
 
@@ -141,7 +138,7 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     lastid = seq;
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
   /**
@@ -155,22 +152,22 @@ public class IdPanel extends JPanel implements MouseListener,
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(true);
+        av.getRanges().scrollRight(true);
       }
-      else
+      else if (!av.getWrapAlignment())
       {
-        alignPanel.scrollUp(false);
+        av.getRanges().scrollUp(false);
       }
     }
     else
     {
       if (e.isShiftDown())
       {
-        alignPanel.scrollRight(false);
+        av.getRanges().scrollRight(false);
       }
-      else
+      else if (!av.getWrapAlignment())
       {
-        alignPanel.scrollUp(true);
+        av.getRanges().scrollUp(true);
       }
     }
   }
@@ -199,56 +196,10 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    Vector links = Preferences.sequenceURLLinks;
-    if (links == null || links.size() < 1)
-    {
-      return;
-    }
-
     int seq = alignPanel.getSeqPanel().findSeq(e);
-    String url = null;
-    int i = 0;
     String id = av.getAlignment().getSequenceAt(seq).getName();
-    while (url == null && i < links.size())
-    {
-      // 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.usesDBAccession())
-      {
-        // this URL requires an accession id, not the name of a sequence
-        url = null;
-        continue;
-      }
+    String url = Preferences.sequenceUrlLinks.getPrimaryUrl(id);
 
-      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);
@@ -291,13 +242,14 @@ public class IdPanel extends JPanel implements MouseListener,
       return;
     }
 
-    if (mouseDragging && (e.getY() < 0) && (av.getStartSeq() > 0))
+    if (mouseDragging && (e.getY() < 0)
+            && (av.getRanges().getStartSeq() > 0))
     {
       scrollThread = new ScrollThread(true);
     }
 
     if (mouseDragging && (e.getY() >= getHeight())
-            && (av.getAlignment().getHeight() > av.getEndSeq()))
+            && (av.getAlignment().getHeight() > av.getRanges().getEndSeq()))
     {
       scrollThread = new ScrollThread(false);
     }
@@ -341,8 +293,8 @@ public class IdPanel extends JPanel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown() && av
-                    .getSelectionGroup() != null))
+            || (!jalview.util.Platform.isControlDown(e) && !e.isShiftDown()
+                    && av.getSelectionGroup() != null))
     {
       av.setSelectionGroup(new SequenceGroup());
       av.getSelectionGroup().setStartRes(0);
@@ -361,7 +313,7 @@ public class IdPanel extends JPanel implements MouseListener,
 
     av.isSelectionGroupChanged(true);
 
-    alignPanel.paintAlignment(true);
+    alignPanel.paintAlignment(false);
   }
 
   /**
@@ -373,23 +325,19 @@ public class IdPanel extends JPanel implements MouseListener,
   {
     int seq2 = alignPanel.getSeqPanel().findSeq(e);
     Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq2);
-    // build a new links menu based on the current links + any non-positional
-    // features
-    Vector<String> nlinks = new Vector<String>(Preferences.sequenceURLLinks);
-    SequenceFeature sfs[] = sq == null ? null : sq.getSequenceFeatures();
-    if (sfs != null)
+
+    /*
+     *  build a new links menu based on the current links
+     *  and any non-positional features
+     */
+    List<String> nlinks = Preferences.sequenceUrlLinks.getLinksForMenu();
+    for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
     {
-      for (SequenceFeature sf : sfs)
+      if (sf.links != null)
       {
-        if (sf.begin == sf.end && sf.begin == 0)
+        for (String link : sf.links)
         {
-          if (sf.links != null && sf.links.size() > 0)
-          {
-            for (int l = 0, lSize = sf.links.size(); l < lSize; l++)
-            {
-              nlinks.addElement(sf.links.elementAt(l));
-            }
-          }
+          nlinks.add(link);
         }
       }
     }
@@ -443,8 +391,8 @@ public class IdPanel extends JPanel implements MouseListener,
 
     for (int i = start; i <= end; i++)
     {
-      av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), i == end);
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i),
+              i == end);
     }
   }
 
@@ -491,9 +439,10 @@ public class IdPanel extends JPanel implements MouseListener,
     int index = av.getAlignment().findIndex(list.get(0));
 
     // do we need to scroll the panel?
-    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    if ((av.getRanges().getStartSeq() > index)
+            || (av.getRanges().getEndSeq() < index))
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -532,14 +481,14 @@ public class IdPanel extends JPanel implements MouseListener,
 
       while (running)
       {
-        if (alignPanel.scrollUp(up))
+        if (av.getRanges().scrollUp(up))
         {
           // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
+          int seq = av.getRanges().getStartSeq();
 
           if (!up)
           {
-            seq = av.getEndSeq();
+            seq = av.getRanges().getEndSeq();
           }
 
           if (seq < lastid)