X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b5569c3ba2c9a7ee430475a29847b2cac81fdc4c;hb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;hp=3444881b52a6d96f01fa2d96171c48813dd05adb;hpb=31a5f9724e7ba5c8f67a6db9a0c0f2356cd81b9d;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 3444881..b5569c3 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,229 +1,535 @@
-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;
-  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);
-    addMouseListener(this);
-    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.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)
-  {
-    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()>=getHeight() && 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 (javax.swing.SwingUtilities.isRightMouseButton(e))
-    {
-      jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
-          (Sequence)av.getAlignment().getSequenceAt(seq));
-      pop.show(this, e.getX(), y);
-      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);
-  }
-
-  // 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 2.9)
+ * Copyright (C) 2015 The Jalview Authors
+ * 
+ * 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/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.io.SequenceAnnotationReport;
+import jalview.util.MessageManager;
+import jalview.util.UrlLink;
+import jalview.viewmodel.AlignmentViewport;
+
+import java.awt.BorderLayout;
+import java.awt.event.MouseEvent;
+import java.awt.event.MouseListener;
+import java.awt.event.MouseMotionListener;
+import java.awt.event.MouseWheelEvent;
+import java.awt.event.MouseWheelListener;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.JOptionPane;
+import javax.swing.JPanel;
+import javax.swing.SwingUtilities;
+import javax.swing.ToolTipManager;
+
+/**
+ * This panel hosts alignment sequence ids and responds to mouse clicks on them,
+ * as well as highlighting ids matched by a search from the Find menu.
+ * 
+ * @author $author$
+ * @version $Revision$
+ */
+public class IdPanel extends JPanel implements MouseListener,
+        MouseMotionListener, MouseWheelListener
+{
+  private IdCanvas idCanvas;
+
+  protected AlignmentViewport av;
+
+  protected AlignmentPanel alignPanel;
+
+  ScrollThread scrollThread = null;
+
+  String linkImageURL;
+
+  int offy;
+
+  // int width;
+  int lastid = -1;
+
+  boolean mouseDragging = false;
+
+  private final SequenceAnnotationReport seqAnnotReport;
+
+  /**
+   * Creates a new IdPanel object.
+   * 
+   * @param av
+   * @param parent
+   */
+  public IdPanel(AlignViewport av, AlignmentPanel parent)
+  {
+    this.av = av;
+    alignPanel = parent;
+    setIdCanvas(new IdCanvas(av));
+    linkImageURL = getClass().getResource("/images/link.gif").toString();
+    seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
+    setLayout(new BorderLayout());
+    add(getIdCanvas(), BorderLayout.CENTER);
+    addMouseListener(this);
+    addMouseMotionListener(this);
+    addMouseWheelListener(this);
+    ToolTipManager.sharedInstance().registerComponent(this);
+  }
+
+  /**
+   * Respond to mouse movement by constructing tooltip text for the sequence id
+   * under the mouse.
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseMoved(MouseEvent e)
+  {
+    SeqPanel sp = alignPanel.getSeqPanel();
+    int seq = Math.max(0, sp.findSeq(e));
+    if (seq > -1 && seq < av.getAlignment().getHeight())
+    {
+      SequenceI sequence = av.getAlignment().getSequenceAt(seq);
+      StringBuffer tip = new StringBuffer(64);
+      seqAnnotReport.createSequenceAnnotationReport(tip, sequence,
+              av.isShowDBRefs(), av.isShowNPFeats(),
+              sp.seqCanvas.fr.getMinMax());
+      setToolTipText("<html>" + sequence.getDisplayId(true) + " "
+              + tip.toString() + "</html>");
+    }
+  }
+
+  /**
+   * Responds to a mouse drag by selecting the sequences under the dragged
+   * region.
+   * 
+   * @param e
+   */
+  @Override
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
+
+    int seq = Math.max(0, alignPanel.getSeqPanel().findSeq(e));
+
+    if (seq < lastid)
+    {
+      selectSeqs(lastid - 1, seq);
+    }
+    else if (seq > lastid)
+    {
+      selectSeqs(lastid + 1, seq);
+    }
+
+    lastid = seq;
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * Response to the mouse wheel by scrolling the alignment panel.
+   */
+  @Override
+  public void mouseWheelMoved(MouseWheelEvent e)
+  {
+    e.consume();
+    if (e.getWheelRotation() > 0)
+    {
+      if (e.isShiftDown())
+      {
+        alignPanel.scrollRight(true);
+      }
+      else
+      {
+        alignPanel.scrollUp(false);
+      }
+    }
+    else
+    {
+      if (e.isShiftDown())
+      {
+        alignPanel.scrollRight(false);
+      }
+      else
+      {
+        alignPanel.scrollUp(true);
+      }
+    }
+  }
+
+  /**
+   * Handle a mouse click event. Currently only responds to a double-click. The
+   * action is to try to open a browser window at a URL that searches for the
+   * selected sequence id. The search URL is configured in Preferences |
+   * Connections | URL link from Sequence ID. For example:
+   * 
+   * http://www.ebi.ac.uk/ebisearch/search.ebi?db=allebi&query=$SEQUENCE_ID$
+   * 
+   * @param e
+   */
+  @Override
+  public void mouseClicked(MouseEvent e)
+  {
+    /*
+     * Ignore single click. Ignore 'left' click followed by 'right' click (user
+     * selects a row then its pop-up menu).
+     */
+    if (e.getClickCount() < 2 || SwingUtilities.isRightMouseButton(e))
+    {
+      return;
+    }
+
+    Vector links = Preferences.sequenceURLLinks;
+    if (links == null || links.size() < 1)
+    {
+      return;
+    }
+
+    int seq = alignPanel.getSeqPanel().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,
+              MessageManager.getString("label.web_browser_not_found_unix"),
+              MessageManager.getString("label.web_browser_not_found"),
+              JOptionPane.WARNING_MESSAGE);
+      ex.printStackTrace();
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+  }
+
+  /**
+   * DOCUMENT ME!
+   * 
+   * @param e
+   *          DOCUMENT ME!
+   */
+  @Override
+  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.getAlignment().getHeight() > av.getEndSeq()))
+    {
+      scrollThread = new ScrollThread(false);
+    }
+  }
+
+  /**
+   * Respond to a mouse press. Does nothing for (left) double-click as this is
+   * handled by mouseClicked().
+   * 
+   * Right mouse down - construct and show context menu.
+   * 
+   * Ctrl-down or Shift-down - add to or expand current selection group if there
+   * is one.
+   * 
+   * Mouse down - select this sequence.
+   * 
+   * @param e
+   */
+  @Override
+  public void mousePressed(MouseEvent e)
+  {
+    if (e.getClickCount() == 2 && SwingUtilities.isLeftMouseButton(e))
+    {
+      return;
+    }
+
+    int seq = alignPanel.getSeqPanel().findSeq(e);
+
+    if (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.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.getAlignment().getWidth() - 1);
+    }
+
+    if (e.isShiftDown() && (lastid != -1))
+    {
+      selectSeqs(lastid, seq);
+    }
+    else
+    {
+      selectSeq(seq);
+    }
+    // TODO is this addition ok here?
+    av.isSelectionGroupChanged(true);
+
+    alignPanel.paintAlignment(true);
+  }
+
+  /**
+   * Toggle whether the sequence is part of the current selection group.
+   * 
+   * @param seq
+   */
+  void selectSeq(int seq)
+  {
+    lastid = seq;
+
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+  }
+
+  /**
+   * Add contiguous rows of the alignment to the current selection group. Does
+   * nothing if there is no selection group.
+   * 
+   * @param start
+   * @param end
+   */
+  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), i == end);
+    }
+  }
+
+  /**
+   * Respond to mouse released. Refreshes the display and triggers broadcast of
+   * the new selection group to any listeners.
+   * 
+   * @param e
+   */
+  @Override
+  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();
+  }
+
+  /**
+   * Highlight sequence ids that match the given list, and if necessary scroll
+   * to the start sequence of the list.
+   * 
+   * @param list
+   */
+  public void highlightSearchResults(List<SequenceI> list)
+  {
+    getIdCanvas().setHighlighted(list);
+
+    if (list == null)
+    {
+      return;
+    }
+
+    int index = av.getAlignment().findIndex(list.get(0));
+
+    // do we need to scroll the panel?
+    if ((av.getStartSeq() > index) || (av.getEndSeq() < index))
+    {
+      alignPanel.setScrollValues(av.getStartRes(), index);
+    }
+  }
+
+  public IdCanvas getIdCanvas()
+  {
+    return idCanvas;
+  }
+
+  public void setIdCanvas(IdCanvas idCanvas)
+  {
+    this.idCanvas = idCanvas;
+  }
+
+  // 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;
+    }
+
+    @Override
+    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)
+        {
+        }
+      }
+    }
+  }
+}