X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=11ef52a6a8d169998b757c807f384e8ac1dda83f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=939a65effad7f8e993120b2b82e37f936137b9dc;hpb=80d695371530259d7530566f0e46a8df10ff2377;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 939a65e..11ef52a 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,150 +1,514 @@
-package jalview.gui;
-
-import java.awt.*;
-import java.awt.event.*;
-
-import jalview.datamodel.*;
-
-import javax.swing.*;
-
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {
-
-  protected IdCanvas       idCanvas;
-  protected AlignViewport  av;
-  protected AlignmentPanel alignPanel;
-
-  protected int            offy;
-  public    int            width;
-  public    int            lastid;
-
-  SequenceGroup selectedSequenceGroup;
-
-  public IdPanel(AlignViewport av, AlignmentPanel parent)
-  {
-    this.av         = av;
-    alignPanel = parent;
-    idCanvas = new IdCanvas(av);
-    setLayout(new BorderLayout());
-    add(idCanvas, BorderLayout.CENTER);
-    addMouseListener(this);
-    addMouseMotionListener(this);
-  }
-
-  public void mouseMoved(MouseEvent e) {}
-
-  public void selectSeqs(int start, int end) {
-     if (end < start)
-     {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-     }
-
-     for (int i = start; i <= end; i++)
-     {
-       SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);
-       if (av.getSelection().contains(pickedSeq))
-       {
-         av.getSelection().removeElement(pickedSeq);
-         selectedSequenceGroup.deleteSequence(pickedSeq);
-       }
-       else
-       {
-         av.getSelection().addElement(pickedSeq);
-         if(selectedSequenceGroup==null)
-         {
-           selectedSequenceGroup = new SequenceGroup();
-           av.setRubberbandGroup( selectedSequenceGroup );
-          // av.alignment.addGroup( selectedSequenceGroup );
-           selectedSequenceGroup.setStartRes(0);
-           selectedSequenceGroup.setEndRes( pickedSeq.getSequence().length());
-         }
-
-         selectedSequenceGroup.addSequence( pickedSeq );
-       }
-
-     }
-
-     alignPanel.seqPanel.seqCanvas.paintFlag=true;
-     alignPanel.repaint();
-     repaint();
-
-   }
-
-  public void mouseDragged(MouseEvent e) {
-    int y = e.getY();
-    int seq = av.getIndex(y);
-
-    if (seq < lastid)
-      selectSeqs(lastid - 1, seq);
-    else if (seq > lastid)
-      selectSeqs(lastid + 1, seq);
-
-    lastid = seq;
-
-    return;
-  }
-
-  public void mouseClicked(MouseEvent e)
-  {
-    if (e.getClickCount() == 2)
-    {
-       int seq = av.getIndex(e.getY());
-       String id = av.getAlignment().getSequenceAt(seq).getName();
-
-       try{
-         jalview.util.BrowserLauncher.openURL(
-             "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) { }
-  public void mouseExited (MouseEvent e) { }
-
-  public void mousePressed(MouseEvent e) {
-    if (e.getClickCount() == 2)
-      return;
-
-    int y = e.getY();
-    int seq = av.getIndex(y);
-
-    if (javax.swing.SwingUtilities.isRightMouseButton(e))
-    {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          av.getAlignment().getSequenceAt(seq));
-      pop.show(this, e.getX(), y);
-      return;
-    }
-
-
-
-    if(av.getRubberbandGroup()!=null && (av.getRubberbandGroup().getSize() == av.getSelection().size()))
-          selectedSequenceGroup = av.getRubberbandGroup();
-
-    if (selectedSequenceGroup == null)
-    {
-      selectedSequenceGroup = new SequenceGroup();
-      av.setRubberbandGroup(selectedSequenceGroup);
-    }
-
-    selectedSequenceGroup.setStartRes(0);
-    selectedSequenceGroup.setEndRes(av.getAlignment().getWidth() - 1);
-
-    if (seq != -1)
-      selectSeqs(seq, seq);
-
-    lastid = seq;
-
-
-    return;
-  }
-
-  public void mouseReleased(MouseEvent e)
-  {
-    lastid = -1;
-    PaintRefresher.Refresh(this);
-    selectedSequenceGroup = null;
-  }
-}
+/*
+ * 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.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.Vector;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.util.UrlLink;
+
+/**
+ * DOCUMENT ME!
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdPanel extends JPanel implements MouseListener,
+        MouseMotionListener, MouseWheelListener
+{
+  protected IdCanvas idCanvas;
+
+  protected AlignViewport av;
+
+  protected AlignmentPanel alignPanel;
+
+  ScrollThread scrollThread = null;
+
+  String linkImageURL;
+
+  int offy;
+
+  // int width;
+  int lastid = -1;
+
+  boolean mouseDragging = false;
+
+  /**
+   * Creates a new IdPanel object.
+   * 
+   * @param av
+   *          DOCUMENT ME!
+   * @param parent
+   *          DOCUMENT ME!
+   */
+  public IdPanel(AlignViewport av, AlignmentPanel parent)
+  {
+    this.av = av;
+    alignPanel = parent;
+    idCanvas = new IdCanvas(av);
+    linkImageURL = getClass().getResource("/images/link.gif").toString();
+    setLayout(new BorderLayout());
+    add(idCanvas, BorderLayout.CENTER);
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    addMouseWheelListener(this);
+    ToolTipManager.sharedInstance().registerComponent(this);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void mouseMoved(MouseEvent e)
+  {
+    SeqPanel sp = alignPanel.seqPanel;
+    int seq = Math.max(0, sp.findSeq(e));
+    String tmp;
+    if (seq > -1 && seq < av.alignment.getHeight())
+    {
+      SequenceI sequence = av.alignment.getSequenceAt(seq);
+      StringBuffer tip = new StringBuffer();
+      tip.append("<i>");
+
+      int maxWidth = 0;
+      if (sequence.getDescription() != null)
+      {
+        tmp = sequence.getDescription();
+        tip.append("<br>" + tmp);
+        maxWidth = Math.max(maxWidth, tmp.length());
+      }
+
+      DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
+      if (av.isShowDbRefs() && dbrefs != null)
+      {
+        for (int i = 0; i < dbrefs.length; i++)
+        {
+          tip.append("<br>");
+          tmp = dbrefs[i].getSource() + " " + dbrefs[i].getAccessionId();
+          tip.append(tmp);
+          maxWidth = Math.max(maxWidth, tmp.length());
+        }
+      }
+
+      // ADD NON POSITIONAL SEQUENCE INFO
+      SequenceFeature[] features = sequence.getDatasetSequence()
+              .getSequenceFeatures();
+      SequenceFeature[] tfeat = new SequenceFeature[1];
+      if (av.isShowNpFeats() && features != null)
+      {
+        for (int i = 0; i < features.length; i++)
+        {
+          if (features[i].begin == 0 && features[i].end == 0)
+          {
+            int sz = -tip.length();
+            tfeat[0] = features[i];
+            sp.appendFeatures(tip, linkImageURL, 0, tfeat,
+                    sp.seqCanvas.fr.minmax);
+            sz += tip.length();
+            maxWidth = Math.max(maxWidth, sz);
+          }
+        }
+      }
+
+      if (maxWidth > 60)
+      {
+        tip.insert(0, "<table width=350 border=0><tr><td><i>");
+        tip.append("</i></td></tr></table>");
+      }
+
+      tip.append("</html>");
+
+      setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+              + tip.toString());
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  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(true);
+  }
+
+  public void mouseWheelMoved(MouseWheelEvent e)
+  {
+    e.consume();
+    if (e.getWheelRotation() > 0)
+    {
+      alignPanel.scrollUp(false);
+    }
+    else
+    {
+      alignPanel.scrollUp(true);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void mouseClicked(MouseEvent e)
+  {
+    if (e.getClickCount() < 2)
+    {
+      return;
+    }
+
+    java.util.Vector links = Preferences.sequenceURLLinks;
+    if (links == null || links.size() < 1)
+    {
+      return;
+    }
+
+    int seq = alignPanel.seqPanel.findSeq(e);
+    String url = null;
+    int i = 0;
+    String id = av.getAlignment().getSequenceAt(seq).getName();
+    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);
+      } 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);
+    } catch (Exception ex)
+    {
+      JOptionPane
+              .showInternalMessageDialog(
+                      Desktop.desktop,
+                      "Unixers: Couldn't find default web browser."
+                              + "\nAdd the full path to your browser in Preferences.",
+                      "Web browser not found", JOptionPane.WARNING_MESSAGE);
+      ex.printStackTrace();
+    }
+
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  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() >= getHeight())
+            && (av.alignment.getHeight() > av.getEndSeq()))
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void mousePressed(MouseEvent e)
+  {
+    if (e.getClickCount() == 2)
+    {
+      return;
+    }
+
+    int seq = alignPanel.seqPanel.findSeq(e);
+
+    if (javax.swing.SwingUtilities.isRightMouseButton(e))
+    {
+      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(Preferences.sequenceURLLinks);
+      SequenceFeature sf[] = sq==null ? null : sq.getDatasetSequence().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));
+            }
+          }
+        }
+      }
+
+      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, sq,
+              nlinks, new Vector(Preferences.getGroupURLLinks()));
+      pop.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(true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param seq
+   *          DOCUMENT ME!
+   */
+  void selectSeq(int seq)
+  {
+    lastid = seq;
+
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param start
+   *          DOCUMENT ME!
+   * @param end
+   *          DOCUMENT ME!
+   */
+  void selectSeqs(int start, int end)
+  {
+    if (av.getSelectionGroup() == null)
+    {
+      return;
+    }
+
+    if (end >= av.getAlignment().getHeight())
+    {
+      end = av.getAlignment().getHeight() - 1;
+    }
+
+    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), true);
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  public void mouseReleased(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+
+    mouseDragging = false;
+    PaintRefresher.Refresh(this, av.getSequenceSetId());
+    // always send selection message when mouse is released
+    av.sendSelection();
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param found
+   *          DOCUMENT ME!
+   */
+  public void highlightSearchResults(java.util.Vector found)
+  {
+    idCanvas.setHighlighted(found);
+
+    if (found == null)
+    {
+      return;
+    }
+
+    int index = av.alignment.findIndex((SequenceI) found.get(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.paintAlignment(false);
+
+        try
+        {
+          Thread.sleep(100);
+        } catch (Exception ex)
+        {
+        }
+      }
+    }
+  }
+}