X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=db24821687a8bb83bb2310d6cc44662ee09dfd71;hb=b14411143cbfb4d311f68b3d3b73a645bf8200e8;hp=032992666ef7f19a9139403244ca53f0e9f81382;hpb=dba30c55e191417596da163caeef250c78de132d;p=jalview.git

diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 0329926..db24821 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,30 +1,45 @@
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2005 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.gui;
 
 import java.awt.*;
 import java.awt.event.*;
-
-import jalview.datamodel.*;
-
 import javax.swing.*;
 
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {
+import jalview.datamodel.*;
 
-  protected IdCanvas       idCanvas;
-  protected AlignViewport  av;
+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;
-
-
-
-  boolean mouseDown;
-  boolean mouseUp;
+  ScrollThread scrollThread = null;
+  int offy;
+  int width;
+  int lastid = -1;
+  boolean mouseDragging = false;
 
   public IdPanel(AlignViewport av, AlignmentPanel parent)
   {
-    this.av         = av;
+    this.av = av;
     alignPanel = parent;
     idCanvas = new IdCanvas(av);
     setLayout(new BorderLayout());
@@ -33,109 +48,286 @@ public class IdPanel extends JPanel implements MouseListener, MouseMotionListene
     addMouseMotionListener(this);
   }
 
-  public void mouseMoved(MouseEvent e) {}
+  public void mouseMoved(MouseEvent e)
+  {
+  }
+
+  public void mouseDragged(MouseEvent e)
+  {
+    mouseDragging = true;
 
-  public void selectSeqs(int start, int end) {
-     if (end < start) {
-       int tmp = start;
-       start = end;
-       end   = tmp;
-     }
+    int y = e.getY();
 
-     for (int i = start; i <= end; i++) {
-       SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);
+    if (av.getWrapAlignment())
+    {
+      y -= (2 * av.charHeight);
+    }
 
-       if (av.getSelection().contains(pickedSeq)) {
-         av.getSelection().removeElement(pickedSeq);
-       } else {
-         av.getSelection().addElement(pickedSeq);
-       }
-     }
+    int seq = av.getIndex(y);
 
-     repaint();
+    if (seq < 0)
+    {
+      return;
+    }
 
-   }
+    if (seq < lastid)
+    {
+      selectSeqs(lastid - 1, seq);
+    }
+    else if (seq > lastid)
+    {
+      selectSeqs(lastid + 1, seq);
+    }
 
-  public void mouseDragged(MouseEvent e) {
-    int y = e.getY();
+    lastid = seq;
+    alignPanel.repaint();
+  }
 
-    int seq = av.getIndex(y);
+  public void mouseClicked(MouseEvent e)
+  {
+    if (e.getClickCount() == 2)
+    {
+      int y = e.getY();
 
-    if (mouseDown == true) {
-      if (seq < lastid) {
-        selectSeqs(lastid-1,seq);
-      } else if (seq > lastid) {
-         selectSeqs(lastid+1,seq);
+      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)
+      {
+        // TODO: JBPNote : state dependent error message for real browserLaunch problems rather than unix misconfiguration.
+        System.err.println(ex.getMessage() +
+                           "\nUnixers: Try adding this jalview.browser property line \n" +
+                           "in your jalview.properties file (/usr/local/bin/firefox is an exanmple browser path):\n" +
+                           "jalview.browser=/usr/local/bin/firefox\n");
+
+        //ex.printStackTrace();
       }
-      lastid = seq;
     }
+  }
 
-    return;
+  public void mouseEntered(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
   }
 
-  public void mouseClicked(MouseEvent e)
+  public void mouseExited(MouseEvent e)
   {
-    if (e.getClickCount() == 2)
+    if (av.getWrapAlignment())
     {
-       int seq = av.getIndex(e.getY());
-       String id = av.getAlignment().getSequenceAt(seq).getName();
+      return;
+    }
 
-       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();}
+    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 mouseEntered(MouseEvent e) { }
-  public void mouseExited (MouseEvent e) { }
 
-  public void mousePressed(MouseEvent e) {
+  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);
 
-    mouseDown = true;
+    if (seq == -1)
+    {
+      return;
+    }
 
-      if( javax.swing.SwingUtilities.isRightMouseButton(e))
-      {
-        String id = av.getAlignment().getSequenceAt(seq).getName();
-        String s = (String)JOptionPane.showInternalInputDialog(
-                    this,
-                    "Edit sequence name",
-                    "Edit sequence name",
-                    JOptionPane.PLAIN_MESSAGE,
-                    null,
-                    null,
-                    id);
-
-        if(s!=null)
-        {
-          av.getAlignment().getSequenceAt(seq).setName(s);
-          alignPanel.RefreshPanels();
-        }
+    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);
 
-      }
-      else
-      {
-        if (seq != -1)
-          selectSeqs(seq,seq);
+      return;
+    }
 
-        lastid = seq;
+    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), true);
       }
-    return;
+
+      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();
   }
 
-  public void mouseReleased(MouseEvent e) {
-    lastid = -1;
+  void selectSeq(int seq)
+  {
+    lastid = seq;
 
-    mouseDown = false;
-    mouseUp   = true;
+    SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
+    av.getSelectionGroup().addOrRemove(pickedSeq, true);
+  }
 
-    PaintRefresher.Refresh(this);
+  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), true);
+    }
+  }
+
+  public void mouseReleased(MouseEvent e)
+  {
+    if (scrollThread != null)
+    {
+      scrollThread.running = false;
+    }
+
+    mouseDragging = false;
+    PaintRefresher.Refresh(av.alignment);
+  }
+
+  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.repaint();
+
+        try
+        {
+          Thread.sleep(100);
+        }
+        catch (Exception ex)
+        {
+        }
+      }
+    }
   }
 }