-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
- SequenceGroup selectedSequenceGroup;\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
- {\r
- SequenceI pickedSeq = av.getAlignment().getSequenceAt(i);\r
- if (av.getSelection().contains(pickedSeq))\r
- {\r
- av.getSelection().removeElement(pickedSeq);\r
- selectedSequenceGroup.deleteSequence(pickedSeq);\r
- }\r
- else\r
- {\r
- av.getSelection().addElement(pickedSeq);\r
- if(selectedSequenceGroup==null)\r
- {\r
- selectedSequenceGroup = new SequenceGroup();\r
- av.alignment.addGroup( selectedSequenceGroup );\r
- selectedSequenceGroup.setStartRes(0);\r
- selectedSequenceGroup.setEndRes( pickedSeq.getSequence().length());\r
- }\r
-\r
- selectedSequenceGroup.addSequence( pickedSeq );\r
- }\r
-\r
- }\r
-\r
- alignPanel.seqPanel.seqCanvas.paintFlag=true;\r
- alignPanel.repaint();\r
- repaint();\r
-\r
- }\r
-\r
- public void mouseDragged(MouseEvent e) {\r
- int y = e.getY();\r
- int seq = av.getIndex(y);\r
-\r
-\r
-\r
-\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
- 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
-\r
- if( javax.swing.SwingUtilities.isRightMouseButton(e))\r
- {\r
- String id = av.getAlignment().getSequenceAt(seq).getName();\r
- String s = (String)JOptionPane.showInternalInputDialog(\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
- selectedSequenceGroup = av.alignment.findGroup(seq);\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
- {\r
- lastid = -1;\r
- PaintRefresher.Refresh(this);\r
- selectedSequenceGroup = null;\r
- }\r
-}\r
+/*
+ * 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)
+ {
+ }
+ }
+ }
+ }
+}
git://source.jalview.org / jalview.git / blobdiff