X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=a5c2e5ad2c2540179902253e502dd4bbad7e4abd;hb=ffa5c07d90b4a933762a5d9faa0578c11693d63a;hp=b973913802ed7d06bd0c9190d708155de885c4a6;hpb=7d4f1d8e997964bef5c351d04fbdafe4401cf5d7;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b973913..a5c2e5a 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,29 +1,42 @@
 /*
- * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4)
- * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors
  * 
- * This program 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.
+ * This file is part of Jalview.
  * 
- * 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 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 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 
+ * 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
+ * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
  */
 package jalview.appletgui;
 
-import java.awt.*;
-import java.awt.event.*;
-import java.util.Vector;
-
-import jalview.datamodel.*;
-import jalview.util.UrlLink;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.urls.api.UrlProviderFactoryI;
+import jalview.urls.api.UrlProviderI;
+import jalview.urls.applet.AppletUrlProviderFactory;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.Panel;
+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;
 
 public class IdPanel extends Panel implements MouseListener,
         MouseMotionListener
@@ -31,89 +44,119 @@ public class IdPanel extends Panel implements MouseListener,
 
   protected IdCanvas idCanvas;
 
-  protected AlignViewport av;
+  protected AlignmentViewport av;
 
   protected AlignmentPanel alignPanel;
 
   ScrollThread scrollThread = null;
 
-  int offy;
-
-  int width;
-
   int lastid = -1;
 
   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);
     idCanvas.addMouseMotionListener(this);
 
     String label, url;
-    if (av.applet != null)
+    // TODO: add in group link parameter
+
+    // 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);
         }
+      }
 
+      if (!urlList.isEmpty())
+      {
+        // 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("SRS|http://srs.ebi.ac.uk/srsbin/cgi-bin/wgetz?-newId+(([uniprot-all:$SEQUENCE_ID$]))+-view+SwissEntry");
-    }
   }
 
   Tooltip tooltip;
 
+  @Override
   public void mouseMoved(MouseEvent e)
   {
     int seq = alignPanel.seqPanel.findSeq(e);
 
     SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-    
-    // look for non-pos features
-    StringBuffer tooltiptext = new StringBuffer();
-    
 
+    StringBuffer tooltiptext = new StringBuffer();
+    if (sequence == null)
+    {
+      return;
+    }
     if (sequence.getDescription() != null)
     {
       tooltiptext.append(sequence.getDescription());
       tooltiptext.append("\n");
     }
-    
-    SequenceFeature sf[] = sequence.getSequenceFeatures();
-    for (int sl=0;sf!=null && sl<sf.length;sl++)
+
+    for (SequenceFeature sf : sequence.getFeatures()
+            .getNonPositionalFeatures())
     {
-      if (sf[sl].begin==sf[sl].end && sf[sl].begin==0)
+      boolean nl = false;
+      if (sf.getFeatureGroup() != null)
+      {
+        tooltiptext.append(sf.getFeatureGroup());
+        nl = true;
+      }
+      if (sf.getType() != null)
+      {
+        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)
       {
-        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 (sf[sl].getScore()!=Float.NaN && 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("\n");
       }
     }
-    
-    if (tooltiptext.length()==0)
+
+    if (tooltiptext.length() == 0)
     {
       // nothing to display - so clear tooltip if one is visible
       if (tooltip != null)
@@ -134,9 +177,10 @@ public class IdPanel extends Panel implements MouseListener,
       tooltip.setTip(sequence.getDisplayId(true) + "\n"
               + tooltiptext.toString());
     }
-    tooltiptext=null;
+    tooltiptext = null;
   }
 
+  @Override
   public void mouseDragged(MouseEvent e)
   {
     mouseDragging = true;
@@ -156,6 +200,7 @@ public class IdPanel extends Panel implements MouseListener,
     alignPanel.paintAlignment(false);
   }
 
+  @Override
   public void mouseClicked(MouseEvent e)
   {
     if (e.getClickCount() < 2)
@@ -163,50 +208,24 @@ 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);
-    String id = av.getAlignment().getSequenceAt(seq).getName();
-
-    String target = null;
-    String url = null;
-    int i = 0;
-    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);
-        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;
-      }
+    SequenceI sq = av.getAlignment().getSequenceAt(seq);
+    if (sq == null)
+    {
+      return;
+    }
+    String id = sq.getName();
 
-      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];
+    // get the default url with the sequence details filled in
+    if (urlProvider == null)
+    {
+      return;
     }
+    String url = urlProvider.getPrimaryUrl(id);
+    String target = urlProvider.getPrimaryTarget(id);
     try
     {
-
       alignPanel.alignFrame.showURL(url, target);
     } catch (Exception ex)
     {
@@ -214,6 +233,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseEntered(MouseEvent e)
   {
     if (scrollThread != null)
@@ -222,6 +242,7 @@ public class IdPanel extends Panel implements MouseListener,
     }
   }
 
+  @Override
   public void mouseExited(MouseEvent e)
   {
     if (av.getWrapAlignment())
@@ -229,18 +250,19 @@ 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.alignment.getHeight() > av.getEndSeq())
+            && av.getAlignment().getHeight() > av.getRanges().getEndSeq())
     {
       scrollThread = new ScrollThread(false);
     }
   }
 
+  @Override
   public void mousePressed(MouseEvent e)
   {
     if (e.getClickCount() > 1)
@@ -251,36 +273,40 @@ public class IdPanel extends Panel implements MouseListener,
     int y = e.getY();
     if (av.getWrapAlignment())
     {
-      y -= 2 * av.charHeight;
+      y -= 2 * av.getCharHeight();
     }
 
     int seq = alignPanel.seqPanel.findSeq(e);
 
     if ((e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
     {
-      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();
-      for (int l=0,lSize=links.size();l<lSize; l++)
+      SequenceI sq = av.getAlignment().getSequenceAt(seq);
+
+      /*
+       *  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.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);
           }
         }
       }
-      
+
       APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
       this.add(popup);
       popup.show(this, e.getX(), e.getY());
@@ -288,12 +314,12 @@ public class IdPanel extends Panel implements MouseListener,
     }
 
     if ((av.getSelectionGroup() == null)
-            || ((!e.isControlDown() && !e.isShiftDown()) && av
-                    .getSelectionGroup() != null))
+            || ((!jalview.util.Platform.isControlDown(e) && !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)
@@ -312,7 +338,7 @@ public class IdPanel extends Panel implements MouseListener,
   {
     lastid = seq;
     SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, false);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
   }
 
   void selectSeqs(int start, int end)
@@ -332,15 +358,19 @@ public class IdPanel extends Panel implements MouseListener,
       end = tmp;
       lastid = end;
     }
-
+    if (av.getSelectionGroup() == null)
+    {
+      av.setSelectionGroup(new SequenceGroup());
+    }
     for (int i = start; i <= end; i++)
     {
       av.getSelectionGroup().addSequence(
-              av.getAlignment().getSequenceAt(i), false);
+              av.getAlignment().getSequenceAt(i), i == end);
     }
 
   }
 
+  @Override
   public void mouseReleased(MouseEvent e)
   {
     if (scrollThread != null)
@@ -355,23 +385,26 @@ public class IdPanel extends Panel implements MouseListener,
 
     mouseDragging = false;
     PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
   }
 
-  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.elementAt(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.getRanges().getStartSeq() > index
+            || av.getRanges().getEndSeq() < index)
     {
-      alignPanel.setScrollValues(av.getStartRes(), index);
+      av.getRanges().setStartSeq(index);
     }
   }
 
@@ -382,9 +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();
     }
 
@@ -393,25 +426,26 @@ public class IdPanel extends Panel implements MouseListener,
       running = false;
     }
 
+    @Override
     public void run()
     {
       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)
           {
             selectSeqs(lastid - 1, seq);
           }
-          else if (seq > lastid && seq < av.alignment.getHeight())
+          else if (seq > lastid && seq < av.getAlignment().getHeight())
           {
             selectSeqs(lastid + 1, seq);
           }
@@ -433,5 +467,4 @@ public class IdPanel extends Panel implements MouseListener,
       }
     }
   }
-
 }