X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=11ef52a6a8d169998b757c807f384e8ac1dda83f;hb=797df64fa2a0a30773d0f48f5494d4155e5a8be3;hp=00fe35fa54733efcaece8cf7a83a4ff396b3b6f3;hpb=4ebc6d5b362bc093c39312aa1a69836e3dd6ae84;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 00fe35f..11ef52a 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,333 +1,514 @@
-/*
- * 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 javax.swing.*;
-
-import jalview.datamodel.*;
-
-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)
- {
- // 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();
- }
- }
- }
-
- 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), true);
- }
-
- 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, true);
- }
-
- 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(this);
- }
-
- 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)
- {
- }
- }
- }
- }
-}
+/*
+ * 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 .
+ */
+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("");
+
+ int maxWidth = 0;
+ if (sequence.getDescription() != null)
+ {
+ tmp = sequence.getDescription();
+ tip.append("
" + 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("
");
+ 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, "");
+ }
+
+ tip.append("