X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FIdPanel.java;h=d2832f84f93305d101787cbc5974a6179c36c1fb;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=b6a5b478de71ee7f90b6cada7501699898ba0fec;hpb=ec955aa655d8320258b91eb079bc57f688cd0a07;p=jalview.git

diff --git a/src/jalview/appletgui/IdPanel.java b/src/jalview/appletgui/IdPanel.java
index b6a5b47..d2832f8 100755
--- a/src/jalview/appletgui/IdPanel.java
+++ b/src/jalview/appletgui/IdPanel.java
@@ -1,242 +1,480 @@
-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;
-
-  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);
-  }
-
-  public void mouseMoved(MouseEvent e) {}
-
-
-  public void mouseDragged(MouseEvent e) {
-    mouseDragging = true;
-
-    int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
-    int seq = av.getIndex(y);
-
-    if(seq<0)
-      return;
-
-    if (seq < lastid)
-      selectSeqs(lastid - 1, seq);
-    else if (seq > lastid)
-      selectSeqs(lastid + 1, seq);
-
-    lastid = seq;
-    alignPanel.repaint();
-  }
-
-  public void mouseClicked(MouseEvent e)
-  {
-    if (e.getClickCount() == 2)
-    {
-       int y = e.getY();
-       if(av.getWrapAlignment())
-         y-=2*av.charHeight;
-
-       int seq = av.getIndex(y);
-       String id = av.getAlignment().getSequenceAt(seq).getName();
-
-       try{
-         jalview.bin.JalviewLite.showURL(
-             "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +
-             "]+-vn+2");
-       }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() == 2)
-      return;
-
-    int y = e.getY();
-    if(av.getWrapAlignment())
-      y-=2*av.charHeight;
-
-    int seq = av.getIndex(y);
-    if (seq == -1)
-      return;
-
-    if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) == InputEvent.BUTTON3_MASK)
-    {
-      APopupMenu popup = new APopupMenu(alignPanel, null);
-      this.add(popup);
-      popup.show(this, e.getX(), e.getY());
-      return;
-    }
-
-
-    if(!e.isControlDown() && !e.isShiftDown() && av.alignment.findGroup( av.alignment.getSequenceAt(seq))!=null)
-    {
-
-      SequenceGroup selection = new SequenceGroup();
-      SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
-      selection.setStartRes(0);
-      selection.setEndRes(av.alignment.getWidth()-1);
-      for (int i =0; i< sg.getSize(); i++)
-        selection.addSequence(sg.getSequenceAt(i));
-
-      av.setSelectionGroup(selection);
-      return;
-    }
-
-    if(av.getSelectionGroup()==null || ( !e.isControlDown() && 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.repaint();
-  }
-
-  void selectSeq(int seq)
-  {
-    lastid = seq;
-    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
-    av.getSelectionGroup().addOrRemove(pickedSeq);
-  }
-
-  void selectSeqs(int start, int end) {
-
-    lastid = start;
-    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));
-
-   }
-
-
-  public void mouseReleased(MouseEvent e)
-  {
-    if(scrollThread!=null)
-      scrollThread.running = false;
-
-    mouseDragging = false;
-    PaintRefresher.Refresh(this);
-  }
-
-  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)
-            selectSeqs(lastid + 1, seq);
-
-          lastid = seq;
-        }
-        else
-          running = false;
-
-        alignPanel.repaint();
-        try
-        {
-          Thread.sleep(100);
-        }
-        catch (Exception ex)
-        {}
-      }
-    }
-}
-
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ * 
+ * This file is part of Jalview.
+ * 
+ * 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 Jalview.  If not, see <http://www.gnu.org/licenses/>.
+ */
+package jalview.appletgui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Vector;
+
+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;
+    // TODO: add in group link parameter
+    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);
+
+    // look for non-pos features
+    StringBuffer tooltiptext = new StringBuffer();
+    if (sequence != null)
+    {
+      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++)
+      {
+        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 (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");
+          }
+        }
+      }
+    }
+    if (tooltiptext.length() == 0)
+    {
+      // nothing to display - so clear tooltip if one is visible
+      if (tooltip != null)
+      {
+        tooltip.setVisible(false);
+      }
+      tooltip = null;
+      tooltiptext = null;
+      return;
+    }
+    if (tooltip == null)
+    {
+      tooltip = new Tooltip(sequence.getDisplayId(true) + "\n"
+              + tooltiptext.toString(), idCanvas);
+    }
+    else
+    {
+      tooltip.setTip(sequence.getDisplayId(true) + "\n"
+              + tooltiptext.toString());
+    }
+    tooltiptext = null;
+  }
+
+  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);
+    SequenceI sq = av.getAlignment().getSequenceAt(seq);
+    if (sq==null)
+    {
+      return;
+    }
+    String id = sq.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)
+    {
+      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++)
+      {
+        nlinks.addElement(links.elementAt(l));
+      }
+      SequenceFeature sf[] = sq==null ? null:sq.getSequenceFeatures();
+      for (int sl = 0; sf != null && sl < sf.length; sl++)
+      {
+        if (sf[sl].begin == sf[sl].end && sf[sl].begin == 0)
+        {
+          if (sf[sl].links != null && sf[sl].links.size() > 0)
+          {
+            for (int l = 0, lSize = sf[sl].links.size(); l < lSize; l++)
+            {
+              nlinks.addElement(sf[sl].links.elementAt(l));
+            }
+          }
+        }
+      }
+
+      APopupMenu popup = new APopupMenu(alignPanel, sq, nlinks);
+      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;
+    }
+    if (av.getSelectionGroup() == null)
+    {
+      av.setSelectionGroup(new SequenceGroup());
+    }
+    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());
+    // always send selection message when mouse is released
+    av.sendSelection();
+  }
+
+  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)
+        {
+        }
+      }
+    }
+  }
+
+}