X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=a5c2e5ad2c2540179902253e502dd4bbad7e4abd;hb=ffa5c07d90b4a933762a5d9faa0578c11693d63a;hp=ed96b5524fcb2915d452b41938757f7d82ebddbb;hpb=853624fb32058cccc544ae7d13af6ad4b0800b6c;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index ed96b55..a5c2e5a 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -20,11 +20,12 @@
  */
 package jalview.appletgui;
 
-import jalview.datamodel.Sequence;
 import jalview.datamodel.SequenceFeature;
 import jalview.datamodel.SequenceGroup;
 import jalview.datamodel.SequenceI;
-import jalview.util.UrlLink;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
 import jalview.viewmodel.AlignmentViewport;
 
 import java.awt.BorderLayout;
@@ -33,8 +34,9 @@ import java.awt.event.InputEvent;
 import java.awt.event.MouseEvent;
 import java.awt.event.MouseListener;
 import java.awt.event.MouseMotionListener;
+import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
-import java.util.Vector;
 
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
@@ -52,13 +54,13 @@ public class IdPanel extends Panel implements MouseListener,
 
   boolean mouseDragging = false;
 
-  java.util.Vector links = new java.util.Vector();
+  UrlProviderI urlProvider = null;
 
-  public IdPanel(AlignViewport av, AlignmentPanel parent)
+  public IdPanel(AlignViewport viewport, AlignmentPanel parent)
   {
-    this.av = av;
+    this.av = viewport;
     alignPanel = parent;
-    idCanvas = new IdCanvas(av);
+    idCanvas = new IdCanvas(viewport);
     setLayout(new BorderLayout());
     add(idCanvas, BorderLayout.CENTER);
     idCanvas.addMouseListener(this);
@@ -66,36 +68,32 @@ public class IdPanel extends Panel implements MouseListener,
 
     String label, url;
     // TODO: add in group link parameter
-    if (av.applet != null)
+
+    // make a list of label,url pairs
+    HashMap<String, String> urlList = new HashMap<String, String>();
+    if (viewport.applet != null)
     {
       for (int i = 1; i < 10; i++)
       {
-        label = av.applet.getParameter("linkLabel_" + i);
-        url = av.applet.getParameter("linkURL_" + i);
+        label = viewport.applet.getParameter("linkLabel_" + i);
+        url = viewport.applet.getParameter("linkURL_" + i);
 
-        if (label != null && url != null)
+        // only add non-null parameters
+        if (label != null)
         {
-          links.addElement(label + "|" + url);
+          urlList.put(label, url);
         }
-
       }
-    }
-    {
-      // upgrade old SRS link
-      int srsPos = links
-              .indexOf("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
-      if (srsPos > -1)
+
+      if (!urlList.isEmpty())
       {
-        links.setElementAt(
-                "EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$",
-                srsPos);
+        // set default as first entry in list
+        String defaultUrl = viewport.applet.getParameter("linkLabel_1");
+        UrlProviderFactoryI factory = new AppletUrlProviderFactory(
+                defaultUrl, urlList);
+        urlProvider = factory.createUrlProvider();
       }
     }
-    if (links.size() < 1)
-    {
-      links = new java.util.Vector();
-      links.addElement("EMBL-EBI Search|http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$");
-    }
   }
 
   Tooltip tooltip;
@@ -107,64 +105,57 @@ public class IdPanel extends Panel implements MouseListener,
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
 
-    // look for non-pos features
     StringBuffer tooltiptext = new StringBuffer();
-    if (sequence != null)
+    if (sequence == null)
+    {
+      return;
+    }
+    if (sequence.getDescription() != null)
+    {
+      tooltiptext.append(sequence.getDescription());
+      tooltiptext.append("\n");
+    }
+
+    for (SequenceFeature sf : sequence.getFeatures()
+            .getNonPositionalFeatures())
     {
-      if (sequence.getDescription() != null)
+      boolean nl = false;
+      if (sf.getFeatureGroup() != null)
       {
-        tooltiptext.append(sequence.getDescription());
-        tooltiptext.append("\n");
+        tooltiptext.append(sf.getFeatureGroup());
+        nl = true;
       }
-
-      SequenceFeature sf[] = sequence.getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      if (sf.getType() != null)
       {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
-        {
-          boolean nl = false;
-          if (sf[sl].getFeatureGroup() != null)
-          {
-            tooltiptext.append(sf[sl].getFeatureGroup());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getType() != null)
-          {
-            tooltiptext.append(" ");
-            tooltiptext.append(sf[sl].getType());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getDescription() != null)
-          {
-            tooltiptext.append(" ");
-            tooltiptext.append(sf[sl].getDescription());
-            nl = true;
-          }
-          ;
-          if (!Float.isNaN(sf[sl].getScore()) && sf[sl].getScore() != 0f)
-          {
-            tooltiptext.append(" Score = ");
-            tooltiptext.append(sf[sl].getScore());
-            nl = true;
-          }
-          ;
-          if (sf[sl].getStatus() != null && sf[sl].getStatus().length() > 0)
-          {
-            tooltiptext.append(" (");
-            tooltiptext.append(sf[sl].getStatus());
-            tooltiptext.append(")");
-            nl = true;
-          }
-          ;
-          if (nl)
-          {
-            tooltiptext.append("\n");
-          }
-        }
+        tooltiptext.append(" ");
+        tooltiptext.append(sf.getType());
+        nl = true;
+      }
+      if (sf.getDescription() != null)
+      {
+        tooltiptext.append(" ");
+        tooltiptext.append(sf.getDescription());
+        nl = true;
+      }
+      if (!Float.isNaN(sf.getScore()) && sf.getScore() != 0f)
+      {
+        tooltiptext.append(" Score = ");
+        tooltiptext.append(sf.getScore());
+        nl = true;
+      }
+      if (sf.getStatus() != null && sf.getStatus().length() > 0)
+      {
+        tooltiptext.append(" (");
+        tooltiptext.append(sf.getStatus());
+        tooltiptext.append(")");
+        nl = true;
+      }
+      if (nl)
+      {
+        tooltiptext.append("\n");
       }
     }
+
     if (tooltiptext.length() == 0)
     {
       // nothing to display - so clear tooltip if one is visible
@@ -217,7 +208,7 @@ public class IdPanel extends Panel implements MouseListener,
       return;
     }
 
-    // DEFAULT LINK IS FIRST IN THE LINK LIST
+    // get the sequence details
     int seq = alignPanel.seqPanel.findSeq(e);
     SequenceI sq = av.getAlignment().getSequenceAt(seq);
     if (sq == null)
@@ -226,46 +217,15 @@ public class IdPanel extends Panel implements MouseListener,
     }
     String id = sq.getName();
 
-    String target = null;
-    String url = null;
-    int i = 0;
-    while (url == null && i < links.size())
+    // get the default url with the sequence details filled in
+    if (urlProvider == null)
     {
-      // 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);
-        target = urlLink.getTarget();
-      } catch (Exception foo)
-      {
-        System.err.println("Exception for URLLink '" + url + "'");
-        foo.printStackTrace();
-        url = null;
-        continue;
-      }
-      ;
-      if (!urlLink.isValid())
-      {
-        System.err.println(urlLink.getInvalidMessage());
-        url = null;
-        continue;
-      }
-
-      String urls[] = urlLink.makeUrls(id, true);
-      if (urls == null || urls[0] == null || urls[0].length() < 1)
-      {
-        url = null;
-        continue;
-      }
-      // just take first URL made from regex
-      url = urls[1];
+      return;
     }
+    String url = urlProvider.getPrimaryUrl(id);
+    String target = urlProvider.getPrimaryTarget(id);
     try
     {
-
       alignPanel.alignFrame.showURL(url, target);
     } catch (Exception ex)
     {
@@ -290,13 +250,13 @@ public class IdPanel extends Panel 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() >= getSize().height
-            && av.getAlignment().getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
@@ -320,26 +280,29 @@ public class IdPanel extends Panel implements MouseListener,
 
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      Sequence sq = (Sequence) av.getAlignment().getSequenceAt(seq);
+      SequenceI sq = av.getAlignment().getSequenceAt(seq);
 
-      // build a new links menu based on the current links + any non-positional
-      // features
-      Vector nlinks = new Vector();
-      for (int l = 0, lSize = links.size(); l < lSize; l++)
+      /*
+       *  build a new links menu based on the current links
+       *  and any non-positional features
+       */
+      List<String> nlinks;
+      if (urlProvider != null)
       {
-        nlinks.addElement(links.elementAt(l));
+        nlinks = urlProvider.getLinksForMenu();
       }
-      SequenceFeature sf[] = sq == null ? null : sq.getSequenceFeatures();
-      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      else
+      {
+        nlinks = new ArrayList<String>();
+      }
+
+      for (SequenceFeature sf : sq.getFeatures().getNonPositionalFeatures())
       {
-        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+        if (sf.links != null)
         {
-          if (sf[sl].links != null && sf[sl].links.size() > 0)
+          for (String link : sf.links)
           {
-            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
-            {
-              nlinks.addElement(sf[sl].links.elementAt(l));
-            }
+            nlinks.add(link);
           }
         }
       }
@@ -438,9 +401,10 @@ public class IdPanel extends Panel 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);
     }
   }
 
@@ -451,9 +415,9 @@ public class IdPanel extends Panel implements MouseListener,
 
     boolean up = true;
 
-    public ScrollThread(boolean up)
+    public ScrollThread(boolean isUp)
     {
-      this.up = up;
+      this.up = isUp;
       start();
     }
 
@@ -468,13 +432,13 @@ public class IdPanel extends Panel implements MouseListener,
       running = true;
       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)