-package jalview.gui;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import javax.swing.*;\r
-\r
-public class IdPanel extends JPanel implements MouseListener, MouseMotionListener {\r
-\r
- protected IdCanvas idCanvas;\r
- protected AlignViewport av;\r
- protected AlignmentPanel alignPanel;\r
-\r
- protected int offy;\r
- public int width;\r
- public int lastid;\r
-\r
-\r
-\r
- boolean mouseDown;\r
- boolean mouseUp;\r
-\r
- public IdPanel(AlignViewport av, AlignmentPanel parent)\r
- {\r
- this.av = av;\r
- alignPanel = parent;\r
- idCanvas = new IdCanvas(av);\r
- setLayout(new BorderLayout());\r
- add(idCanvas, BorderLayout.CENTER);\r
- addMouseListener(this);\r
- addMouseMotionListener(this);\r
- }\r
-\r
- public void mouseMoved(MouseEvent e) {}\r
-\r
- public void selectSeqs(int start, int end) {\r
- if (end < start) {\r
- int tmp = start;\r
- start = end;\r
- end = tmp;\r
- }\r
-\r
- for (int i = start; i <= end; i++) {\r
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);\r
-\r
- if (av.getSelection().contains(pickedSeq)) {\r
- av.getSelection().removeElement(pickedSeq);\r
- } else {\r
- av.getSelection().addElement(pickedSeq);\r
- }\r
- }\r
-\r
- repaint();\r
-\r
- }\r
-\r
- public void mouseDragged(MouseEvent e) {\r
- int y = e.getY();\r
-\r
- int seq = av.getIndex(y);\r
-\r
- if (mouseDown == true) {\r
- if (seq < lastid) {\r
- selectSeqs(lastid-1,seq);\r
- } else if (seq > lastid) {\r
- selectSeqs(lastid+1,seq);\r
- }\r
- lastid = seq;\r
- }\r
-\r
- return;\r
- }\r
-\r
- public void mouseClicked(MouseEvent e)\r
- {\r
- if (e.getClickCount() == 2)\r
- {\r
- int seq = av.getIndex(e.getY());\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
-\r
- try{\r
- jalview.util.BrowserLauncher.openURL(\r
- "http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[swall-id:" + id +\r
- "]+-vn+2");\r
- }catch(Exception ex){ex.printStackTrace();}\r
- }\r
-\r
- }\r
- public void mouseEntered(MouseEvent e) { }\r
- public void mouseExited (MouseEvent e) { }\r
-\r
- public void mousePressed(MouseEvent e) {\r
- if (e.getClickCount() == 2)\r
- return;\r
-\r
- int y = e.getY();\r
- int seq = av.getIndex(y);\r
-\r
- mouseDown = true;\r
-\r
- if( javax.swing.SwingUtilities.isRightMouseButton(e))\r
- {\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
- String s = (String)JOptionPane.showInputDialog(\r
- this,\r
- "Edit sequence name",\r
- "Edit sequence name",\r
- JOptionPane.PLAIN_MESSAGE,\r
- null,\r
- null,\r
- id);\r
-\r
- if(s!=null)\r
- {\r
- av.getAlignment().getSequenceAt(seq).setName(s);\r
- alignPanel.RefreshPanels();\r
- }\r
-\r
- }\r
- else\r
- {\r
- if (seq != -1)\r
- selectSeqs(seq,seq);\r
-\r
- lastid = seq;\r
- }\r
- return;\r
- }\r
-\r
- public void mouseReleased(MouseEvent e) {\r
- lastid = -1;\r
-\r
- mouseDown = false;\r
- mouseUp = true;\r
-\r
- PaintRefresher.Refresh(this);\r
-\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer
+ * Copyright (C) 2006 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 jalview.datamodel.*;
+
+import java.awt.*;
+import java.awt.event.*;
+
+import javax.swing.*;
+
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+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;
+
+ /**
+ * 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);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e DOCUMENT ME!
+ */
+ public void mouseMoved(MouseEvent e)
+ {
+ int seq = Math.max(0, alignPanel.seqPanel.findSeq(e));
+ if(seq>-1 && seq<av.alignment.getHeight())
+ {
+ SequenceI sequence = av.alignment.getSequenceAt(seq);
+ StringBuffer tip = new StringBuffer("<html>");
+ tip.append(sequence.getDisplayId(true));
+ if (av.alignment.getSequenceAt(seq).getDescription() != null)
+ {
+ tip.append("<table width=250 border=0><tr><td><i>");
+ tip.append(av.alignment.getSequenceAt(seq).getDescription());
+
+ //ADD NON POSITIONAL SEQUENCE INFO
+ SequenceFeature [] features = sequence.getDatasetSequence().getSequenceFeatures();
+ if(features!=null)
+ {
+ for(int i=0; i<features.length; i++)
+ {
+ if(features[i].begin == 0 && features[i].end ==0)
+ {
+ tip.append("<br>"+features[i].featureGroup
+ +" "+ features[i].getType()+" "+features[i].description);
+ }
+ }
+ }
+ tip.append("</i></td></tr></table>");
+ }
+
+ DBRefEntry[] dbrefs = sequence.getDatasetSequence().getDBRef();
+ if (dbrefs != null)
+ {
+ tip.append("<i>");
+ for (int i = 0; i < dbrefs.length; i++)
+ {
+ tip.append("<br>");
+ tip.append(dbrefs[i].getSource() + " "
+ + dbrefs[i].getAccessionId());
+ }
+ tip.append("</i>");
+ }
+
+ tip.append("</html>");
+ setToolTipText(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.repaint();
+ }
+
+
+ /**
+ * 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);
+
+ //DEFAULT LINK IS FIRST IN THE LINK LIST
+
+ String id = av.getAlignment().getSequenceAt(seq).getName();
+ if (id.indexOf("|") > -1)
+ 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);
+
+ 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))
+ {
+ jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel,
+ (Sequence) av.getAlignment().getSequenceAt(seq),
+ Preferences.sequenceURLLinks);
+ 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.repaint();
+ }
+
+ /**
+ * 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;
+
+ 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(av.alignment);
+ }
+
+ /**
+ * 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.repaint();
+
+ try
+ {
+ Thread.sleep(100);
+ }
+ catch (Exception ex)
+ {
+ }
+ }
+ }
+ }
+}