X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=97e33668633e43c95bcf89f7f1df6208bddb4213;hb=865a855a4ca87eadb3e5ff284ed32ed307d9c34b;hp=3e8af1774586b0af7b2b76d3ca189b2339bb2820;hpb=22be3f466cd70cb03d5eae619ede8589ae69716a;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 3e8af17..97e3366 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,159 +1,498 @@
-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();
- if(av.getWrapAlignment())
- y-=2*av.charHeight;
- 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 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) { }
- public void mouseExited (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);
-
- 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(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 2.8.0b1)
+ * Copyright (C) 2014 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 .
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.*;
+import java.awt.event.*;
+import java.util.List;
+import java.util.Vector;
+
+import javax.swing.*;
+
+import jalview.datamodel.*;
+import jalview.io.SequenceAnnotationReport;
+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;
+
+ private final SequenceAnnotationReport seqAnnotReport;
+
+ /**
+ * 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();
+ seqAnnotReport = new SequenceAnnotationReport(linkImageURL);
+ setLayout(new BorderLayout());
+ add(idCanvas, BorderLayout.CENTER);
+ addMouseListener(this);
+ addMouseMotionListener(this);
+ addMouseWheelListener(this);
+ ToolTipManager.sharedInstance().registerComponent(this);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void mouseMoved(MouseEvent e)
+ {
+ SeqPanel sp = alignPanel.seqPanel;
+ 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();
+ seqAnnotReport
+ .createSequenceAnnotationReport(tip, sequence,
+ av.isShowDbRefs(), av.isShowNpFeats(),
+ sp.seqCanvas.fr.minmax);
+ setToolTipText("" + sequence.getDisplayId(true) + " "
+ + tip.toString() + "");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ 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);
+ }
+
+ @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);
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ 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!
+ */
+ @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);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ 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.getAlignment().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), i == end);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @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();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param list
+ * DOCUMENT ME!
+ */
+ public void highlightSearchResults(List list)
+ {
+ idCanvas.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);
+ }
+ }
+
+ // 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)
+ {
+ }
+ }
+ }
+ }
+}