From 298ac6df4e5542ba4d5aa635831537e8dd887084 Mon Sep 17 00:00:00 2001
From: jprocter <Jim Procter>
Date: Tue, 9 Feb 2010 17:37:02 +0000
Subject: [PATCH] groupURL link prototype

---
 src/jalview/gui/IdPanel.java   |    2 +-
 src/jalview/gui/PopupMenu.java |  137 +++++++++++++++++++++++++++++++++++++++-
 2 files changed, 137 insertions(+), 2 deletions(-)

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index b5c2186..52ac6ad 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -330,7 +330,7 @@ public class IdPanel extends JPanel implements MouseListener,
       
       jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
               sq,
-              nlinks);
+              nlinks, new Vector(Preferences.groupURLLinks));
       pop.show(this, e.getX(), e.getY());
 
       return;
diff --git a/src/jalview/gui/PopupMenu.java b/src/jalview/gui/PopupMenu.java
index 1b0391d..457638a 100755
--- a/src/jalview/gui/PopupMenu.java
+++ b/src/jalview/gui/PopupMenu.java
@@ -30,6 +30,7 @@ import jalview.commands.*;
 import jalview.datamodel.*;
 import jalview.io.*;
 import jalview.schemes.*;
+import jalview.util.GroupUrlLink;
 import jalview.util.UrlLink;
 
 /**
@@ -133,6 +134,8 @@ public class PopupMenu extends JPopupMenu
 
   // JMenuItem annotationMenuItem = new JMenuItem();
 
+  JMenu groupLinksMenu;
+
   /**
    * Creates a new PopupMenu object.
    * 
@@ -141,7 +144,18 @@ public class PopupMenu extends JPopupMenu
    * @param seq
    *                DOCUMENT ME!
    */
-  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links)
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links) 
+  {
+    this(ap, seq, links, null);
+  }
+  /**
+   * 
+   * @param ap
+   * @param seq
+   * @param links
+   * @param groupLinks
+   */
+  public PopupMenu(final AlignmentPanel ap, Sequence seq, Vector links, Vector groupLinks)
   {
     // /////////////////////////////////////////////////////////
     // If this is activated from the sequence panel, the user may want to
@@ -384,6 +398,10 @@ public class PopupMenu extends JPopupMenu
       showText.setSelected(sg.getDisplayText());
       showColourText.setSelected(sg.getColourText());
       showBoxes.setSelected(sg.getDisplayBoxes());
+      // add any groupURLs to the groupURL submenu and make it visible
+      if (groupLinks!=null && groupLinks.size()>0) {
+        buildGroupURLMenu(sg, groupLinks);
+      }
     }
     else
     {
@@ -404,6 +422,7 @@ public class PopupMenu extends JPopupMenu
 
     if (links != null && links.size() > 0)
     {
+      
       JMenu linkMenu = new JMenu("Link");
       Vector linkset = new Vector();
       for (int i = 0; i < links.size(); i++)
@@ -521,6 +540,122 @@ public class PopupMenu extends JPopupMenu
       }
     }
   }
+  
+  private void buildGroupURLMenu(SequenceGroup sg, Vector groupLinks)
+  {
+    
+    // TODO: usability: thread off the generation of group url content so root menu appears asap
+    // sequence only URLs
+    // ID/regex match URLs
+    groupLinksMenu = new JMenu("Group Link");
+    JMenu[] linkMenus = new JMenu[] { null, new JMenu("IDS"), new JMenu("Sequences"), new JMenu("IDS and Sequences")}; // three types of url that might be created.
+    SequenceI[] seqs = ap.av.getSelectionAsNewSequence(); 
+    String[][] idandseqs = GroupUrlLink.formStrings(seqs);
+    Hashtable commonDbrefs = new Hashtable();
+    for (int sq = 0; sq<seqs.length;sq++) {
+
+      int start = seqs[sq].findPosition(sg.getStartRes()),end=seqs[sq].findPosition(sg.getEndRes()); 
+      // just collect ids from dataset sequence
+      // TODO: check if IDs collected from selecton group intersects with the current selection, too
+      SequenceI sqi = seqs[sq];
+      while (sqi.getDatasetSequence()!=null) {
+        sqi = sqi.getDatasetSequence(); }
+      DBRefEntry[] dbr = sqi.getDBRef();
+      if (dbr!=null && dbr.length>0)
+      {
+        for (int d=0;d<dbr.length;d++)
+        {
+          String src =dbr[d].getSource(); // jalview.util.DBRefUtils.getCanonicalName(dbr[d].getSource()).toUpperCase();
+          Object[] sarray = (Object[]) commonDbrefs.get(src);
+          if (sarray==null)
+          {
+            sarray = new Object[2];
+            sarray[0] = new int[] { 0 };
+            sarray[1] = new String[seqs.length];
+            
+            commonDbrefs.put(src,sarray);
+          }
+          
+          if (((String[])sarray[1])[sq]==null) {
+            if (!dbr[d].hasMap() || (dbr[d].getMap().locateMappedRange(start, end)!=null)) {
+              ((String[])sarray[1])[sq] = dbr[d].getAccessionId();
+              ((int[])sarray[0])[0]++;
+            }
+          }
+        }
+      }
+    }
+    // now create group links for all distinct ID/sequence sets.
+    boolean addMenu = false; // indicates if there are any group links to give to user  
+    for (int i = 0; i < groupLinks.size(); i++) {
+        String link = groupLinks.elementAt(i).toString();
+        GroupUrlLink urlLink = null;
+        try
+        {
+          urlLink = new GroupUrlLink(link);
+        } catch (Exception foo)
+        {
+          jalview.bin.Cache.log.error("Exception for GroupURLLink '" + link
+                  + "'", foo);
+          continue;
+        }
+        ;
+        if (!urlLink.isValid())
+        {
+          jalview.bin.Cache.log.error(urlLink.getInvalidMessage());
+          continue;
+        }
+        final String label = urlLink.getLabel();
+        boolean usingNames = false;
+        // Now see which parts of the group apply for this URL
+        String ltarget = urlLink.getTarget(); // jalview.util.DBRefUtils.getCanonicalName(urlLink.getTarget());
+        Object[] idset = (Object[]) commonDbrefs.get(ltarget.toUpperCase());
+        String[] seqstr,ids; // input to makeUrl
+        if (idset!=null)
+        {
+          int numinput = ((int[])idset[0])[0];
+          String[] allids = ((String[])idset[1]);
+          seqstr = new String[numinput];
+          ids = new String[numinput];
+          for (int sq=0,idcount=0;sq<seqs.length;sq++)
+          {
+            if (allids[sq]!=null) {
+              ids[idcount] = allids[sq];
+              seqstr[idcount++] = idandseqs[1][sq];
+            }
+          }
+        } else {
+          // just use the id/seq set
+          seqstr = idandseqs[1];
+          ids = idandseqs[0];
+          usingNames=true;
+        }
+        // and try and make the groupURL!
+        
+        Object[] urlset = urlLink.makeUrls(ids,seqstr, "FromJalview"+System.currentTimeMillis(),false);
+        if (urlset!=null)
+        {
+          System.out.println(urlLink.getGroupURLType() +" "+((String[])urlset[3])[0]);
+          // first two bits ofurlLink type bitfield are sequenceids and sequences
+          // TODO: FUTURE: ensure the groupURL menu structure can be generalised
+          addshowLink(linkMenus[urlLink.getGroupURLType() & 3], label + "("+(usingNames ? "Names" : ltarget)+")", ((String[])urlset[3])[0]);
+          addMenu = true;
+        }
+      }
+    if (addMenu)
+    {
+      groupLinksMenu = new JMenu("Group Links");
+      for (int m=0;m<linkMenus.length; m++)
+      {
+        if (linkMenus[m]!=null && linkMenus[m].getMenuComponentCount()>0)
+        {
+          groupLinksMenu.add(linkMenus[m]);
+        }
+      }
+      
+      groupMenu.add(groupLinksMenu);
+    }
+  }
 
   /**
    * add a show URL menu item to the given linkMenu
-- 
1.7.10.2