From: jprocter <Jim Procter>
Date: Tue, 19 Aug 2008 09:37:52 +0000 (+0000)
Subject: regex links for launching URL from single click on sequence ID
X-Git-Tag: Release_2_4~18
X-Git-Url: http://source.jalview.org/gitweb/?a=commitdiff_plain;h=5d01e85b903f9ce67b2b4a32e9e7a02f57d9f2e9;p=jalview.git

regex links for launching URL from single click on sequence ID
---

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index c510803..44a03ec 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,354 +1,380 @@
-/*
- * Jalview - A Sequence Alignment Editor and Viewer
- * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
- *
- * 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 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.
- *
- * 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
- */
-
-package jalview.appletgui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-public class IdPanel
-    extends Panel implements MouseListener, MouseMotionListener
-{
-
-  protected IdCanvas idCanvas;
-  protected AlignViewport 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();
-
-  public IdPanel(AlignViewport av, AlignmentPanel parent)
-  {
-    this.av = av;
-    alignPanel = parent;
-    idCanvas = new IdCanvas(av);
-    setLayout(new BorderLayout());
-    add(idCanvas, BorderLayout.CENTER);
-    idCanvas.addMouseListener(this);
-    idCanvas.addMouseMotionListener(this);
-
-    String label, url;
-    if (av.applet != null)
-    {
-      for (int i = 1; i < 10; i++)
-      {
-        label = av.applet.getParameter("linkLabel_" + i);
-        url = av.applet.getParameter("linkURL_" + i);
-
-        if (label != null && url != null)
-        {
-          links.addElement(label + "|" + url);
-        }
-
-      }
-    }
-    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;
-  public void mouseMoved(MouseEvent e)
-  {
-    int seq = alignPanel.seqPanel.findSeq(e);
-
-    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
-
-    if (sequence.getDescription() == null)
-    {
-      if (tooltip != null)
-      {
-        tooltip.setVisible(false);
-      }
-      tooltip = null;
-      return;
-    }
-
-    if (tooltip == null)
-    {
-      tooltip = new Tooltip(
-          sequence.getDisplayId(true)
-          + "\n" + sequence.getDescription(), idCanvas);
-    }
-    else
-    {
-      tooltip.setTip(sequence.getDisplayId(true)
-                     + "\n" + sequence.getDescription());
-    }
-  }
-
-  public void mouseDragged(MouseEvent e)
-  {
-    mouseDragging = true;
-
-    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
-
-    if (seq < lastid)
-    {
-      selectSeqs(lastid - 1, seq);
-    }
-    else if (seq > lastid)
-    {
-      selectSeqs(lastid + 1, seq);
-    }
-
-    lastid = seq;
-    alignPanel.paintAlignment(false);
-  }
-
-  public void mouseClicked(MouseEvent e)
-  {
-    if (e.getClickCount() < 2)
-    {
-      return;
-    }
-
-    //DEFAULT LINK IS FIRST IN THE LINK LIST
-    int seq = alignPanel.seqPanel.findSeq(e);
-    String id = av.getAlignment().getSequenceAt(seq).getName();
-    if (id.indexOf("|") > -1)
-    {
-      id = id.substring(id.lastIndexOf("|") + 1);
-    }
-
-    String target = links.elementAt(0).toString();
-    target = target.substring(0, target.indexOf("|"));
-    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);
-
-    try
-    {
-
-      alignPanel.alignFrame.showURL(url, target);
-    }
-    catch (Exception ex)
-    {
-      ex.printStackTrace();
-    }
-  }
-
-  public void mouseEntered(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-  }
-
-  public void mouseExited(MouseEvent e)
-  {
-    if (av.getWrapAlignment())
-    {
-      return;
-    }
-
-    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
-    {
-      scrollThread = new ScrollThread(true);
-    }
-
-    if (mouseDragging && e.getY() >= getSize().height &&
-        av.alignment.getHeight() > av.getEndSeq())
-    {
-      scrollThread = new ScrollThread(false);
-    }
-  }
-
-  public void mousePressed(MouseEvent e)
-  {
-    if (e.getClickCount() > 1)
-    {
-      return;
-    }
-
-    int y = e.getY();
-    if (av.getWrapAlignment())
-    {
-      y -= 2 * av.charHeight;
-    }
-
-    int seq = alignPanel.seqPanel.findSeq(e);
-
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
-        InputEvent.BUTTON3_MASK)
-    {
-      APopupMenu popup = new APopupMenu(alignPanel,
-                                        (Sequence) av.getAlignment().
-                                        getSequenceAt(seq), links);
-      this.add(popup);
-      popup.show(this, e.getX(), e.getY());
-      return;
-    }
-
-    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);
-    }
-
-    if (e.isShiftDown() && lastid != -1)
-    {
-      selectSeqs(lastid, seq);
-    }
-    else
-    {
-      selectSeq(seq);
-    }
-
-    alignPanel.paintAlignment(false);
-  }
-
-  void selectSeq(int seq)
-  {
-    lastid = seq;
-    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq, false);
-  }
-
-  void selectSeqs(int start, int end)
-  {
-
-    lastid = start;
-
-    if (end >= av.getAlignment().getHeight())
-    {
-      end = av.getAlignment().getHeight() - 1;
-    }
-
-    if (end < start)
-    {
-      int tmp = start;
-      start = end;
-      end = tmp;
-      lastid = end;
-    }
-
-    for (int i = start; i <= end; i++)
-    {
-      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
-    }
-
-  }
-
-  public void mouseReleased(MouseEvent e)
-  {
-    if (scrollThread != null)
-    {
-      scrollThread.running = false;
-    }
-
-    if (av.getSelectionGroup() != null)
-    {
-      av.getSelectionGroup().recalcConservation();
-    }
-
-    mouseDragging = false;
-    PaintRefresher.Refresh(this, av.getSequenceSetId());
-  }
-
-  public void highlightSearchResults(java.util.Vector found)
-  {
-    idCanvas.setHighlighted(found);
-
-    if (found == null)
-    {
-      return;
-    }
-
-    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
-
-    // do we need to scroll the panel?
-    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
-  {
-    boolean running = false;
-    boolean up = true;
-    public ScrollThread(boolean up)
-    {
-      this.up = up;
-      start();
-    }
-
-    public void stopScrolling()
-    {
-      running = false;
-    }
-
-    public void run()
-    {
-      running = true;
-      while (running)
-      {
-        if (alignPanel.scrollUp(up))
-        {
-          // scroll was ok, so add new sequence to selection
-          int seq = av.getStartSeq();
-          if (!up)
-          {
-            seq = av.getEndSeq();
-          }
-
-          if (seq < lastid)
-          {
-            selectSeqs(lastid - 1, seq);
-          }
-          else if (seq > lastid && seq < av.alignment.getHeight())
-          {
-            selectSeqs(lastid + 1, seq);
-          }
-
-          lastid = seq;
-        }
-        else
-        {
-          running = false;
-        }
-
-        alignPanel.paintAlignment(true);
-        try
-        {
-          Thread.sleep(100);
-        }
-        catch (Exception ex)
-        {}
-      }
-    }
-  }
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
+ *
+ * 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 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.
+ *
+ * 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
+ */
+
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import jalview.datamodel.*;
+import jalview.util.UrlLink;
+
+public class IdPanel
+    extends Panel implements MouseListener, MouseMotionListener
+{
+
+  protected IdCanvas idCanvas;
+  protected AlignViewport 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();
+
+  public IdPanel(AlignViewport av, AlignmentPanel parent)
+  {
+    this.av = av;
+    alignPanel = parent;
+    idCanvas = new IdCanvas(av);
+    setLayout(new BorderLayout());
+    add(idCanvas, BorderLayout.CENTER);
+    idCanvas.addMouseListener(this);
+    idCanvas.addMouseMotionListener(this);
+
+    String label, url;
+    if (av.applet != null)
+    {
+      for (int i = 1; i < 10; i++)
+      {
+        label = av.applet.getParameter("linkLabel_" + i);
+        url = av.applet.getParameter("linkURL_" + i);
+
+        if (label != null && url != null)
+        {
+          links.addElement(label + "|" + url);
+        }
+
+      }
+    }
+    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;
+  public void mouseMoved(MouseEvent e)
+  {
+    int seq = alignPanel.seqPanel.findSeq(e);
+
+    SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+
+    if (sequence.getDescription() == null)
+    {
+      if (tooltip != null)
+      {
+        tooltip.setVisible(false);
+      }
+      tooltip = null;
+      return;
+    }
+
+    if (tooltip == null)
+    {
+      tooltip = new Tooltip(
+          sequence.getDisplayId(true)
+          + "\n" + sequence.getDescription(), idCanvas);
+    }
+    else
+    {
+      tooltip.setTip(sequence.getDisplayId(true)
+                     + "\n" + sequence.getDescription());
+    }
+  }
+
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
+
+    int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+
+    if (seq < lastid)
+    {
+      selectSeqs(lastid - 1, seq);
+    }
+    else if (seq > lastid)
+    {
+      selectSeqs(lastid + 1, seq);
+    }
+
+    lastid = seq;
+    alignPanel.paintAlignment(false);
+  }
+
+  public void mouseClicked(MouseEvent e)
+  {
+    if (e.getClickCount() < 2)
+    {
+      return;
+    }
+
+    //DEFAULT LINK IS FIRST IN THE LINK LIST
+    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;
+      }
+
+      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];
+    }
+    try
+    {
+
+      alignPanel.alignFrame.showURL(url, target);
+    }
+    catch (Exception ex)
+    {
+      ex.printStackTrace();
+    }
+  }
+
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+  }
+
+  public void mouseExited(MouseEvent e)
+  {
+    if (av.getWrapAlignment())
+    {
+      return;
+    }
+
+    if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
+    {
+      scrollThread = new ScrollThread(true);
+    }
+
+    if (mouseDragging && e.getY() >= getSize().height &&
+        av.alignment.getHeight() > av.getEndSeq())
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
+  public void mousePressed(MouseEvent e)
+  {
+    if (e.getClickCount() > 1)
+    {
+      return;
+    }
+
+    int y = e.getY();
+    if (av.getWrapAlignment())
+    {
+      y -= 2 * av.charHeight;
+    }
+
+    int seq = alignPanel.seqPanel.findSeq(e);
+
+    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
+        InputEvent.BUTTON3_MASK)
+    {
+      APopupMenu popup = new APopupMenu(alignPanel,
+                                        (Sequence) av.getAlignment().
+                                        getSequenceAt(seq), links);
+      this.add(popup);
+      popup.show(this, e.getX(), e.getY());
+      return;
+    }
+
+    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);
+    }
+
+    if (e.isShiftDown() && lastid != -1)
+    {
+      selectSeqs(lastid, seq);
+    }
+    else
+    {
+      selectSeq(seq);
+    }
+
+    alignPanel.paintAlignment(false);
+  }
+
+  void selectSeq(int seq)
+  {
+    lastid = seq;
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, false);
+  }
+
+  void selectSeqs(int start, int end)
+  {
+
+    lastid = start;
+
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
+
+    if (end < start)
+    {
+      int tmp = start;
+      start = end;
+      end = tmp;
+      lastid = end;
+    }
+
+    for (int i = start; i <= end; i++)
+    {
+      av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
+    }
+
+  }
+
+  public void mouseReleased(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+
+    if (av.getSelectionGroup() != null)
+    {
+      av.getSelectionGroup().recalcConservation();
+    }
+
+    mouseDragging = false;
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+  }
+
+  public void highlightSearchResults(java.util.Vector found)
+  {
+    idCanvas.setHighlighted(found);
+
+    if (found == null)
+    {
+      return;
+    }
+
+    int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
+
+    // do we need to scroll the panel?
+    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
+  {
+    boolean running = false;
+    boolean up = true;
+    public ScrollThread(boolean up)
+    {
+      this.up = up;
+      start();
+    }
+
+    public void stopScrolling()
+    {
+      running = false;
+    }
+
+    public void run()
+    {
+      running = true;
+      while (running)
+      {
+        if (alignPanel.scrollUp(up))
+        {
+          // scroll was ok, so add new sequence to selection
+          int seq = av.getStartSeq();
+          if (!up)
+          {
+            seq = av.getEndSeq();
+          }
+
+          if (seq < lastid)
+          {
+            selectSeqs(lastid - 1, seq);
+          }
+          else if (seq > lastid && seq < av.alignment.getHeight())
+          {
+            selectSeqs(lastid + 1, seq);
+          }
+
+          lastid = seq;
+        }
+        else
+        {
+          running = false;
+        }
+
+        alignPanel.paintAlignment(true);
+        try
+        {
+          Thread.sleep(100);
+        }
+        catch (Exception ex)
+        {}
+      }
+    }
+  }
+
+}
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index d4e7c77..4741974 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -23,6 +23,7 @@ import java.awt.event.*;
 import javax.swing.*;
 
 import jalview.datamodel.*;
+import jalview.util.UrlLink;
 
 /**
  * DOCUMENT ME!
@@ -184,21 +185,42 @@ 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);
@@ -213,6 +235,7 @@ public class IdPanel
                                             JOptionPane.WARNING_MESSAGE);
       ex.printStackTrace();
     }
+    
   }
 
   /**