X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=ea8b711b02f4679a018a3854606c3dc992d7e050;hb=f60bd625292b277e70cda0125f04756ac7ca05de;hp=0322bdde097374f7579b9211c75a190f8442473c;hpb=af2fbc5499bfc4764ad69e1abaa35eee4dd04817;p=jalview.git
diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java
index 0322bdd..ea8b711 100755
--- a/src/jalview/gui/IdPanel.java
+++ b/src/jalview/gui/IdPanel.java
@@ -1,488 +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 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 y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- final int seq = av.getIndex(y);
- if(seq!=-1)
- {
- SequenceI sequence = av.alignment.getSequenceAt(seq);
- StringBuffer tip = new StringBuffer("");
- tip.append(sequence.getDisplayId(true));
- if (av.alignment.getSequenceAt(seq).getDescription() != null)
- {
- tip.append("
");
- 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[i].featureGroup
- +" "+ features[i].getType()+" "+features[i].description);
- }
- }
- }
-
- tip.append(" |
");
- }
- tip.append("");
- setToolTipText(tip.toString());
- }
-
- if(av.hasHiddenRows)
- {
- if(av.adjustForHiddenSeqs(seq) -
- av.adjustForHiddenSeqs(seq-1)>1)
- {
- JPopupMenu pop = new JPopupMenu();
- JMenuItem item = new JMenuItem("Reveal");
- item.addActionListener(new ActionListener()
- {
- public void actionPerformed(ActionEvent e)
- {
- av.showSequence(seq);
- alignPanel.repaint();
- if(alignPanel.overviewPanel!=null)
- alignPanel.overviewPanel.updateOverviewImage();
- }
- });
- pop.add(item);
- pop.show(this, e.getX(), e.getY());
- }
- }
- }
-
-
- int getWrappedY(int y)
- {
- int hgap = av.charHeight;
- if (av.scaleAboveWrapped)
- hgap += av.charHeight;
-
- return y - hgap;
- }
-
-
- /**
- * DOCUMENT ME!
- *
- * @param e DOCUMENT ME!
- */
- public void mouseDragged(MouseEvent e)
- {
- mouseDragging = true;
-
- int y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- 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();
- }
-
-
- /**
- * 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 y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- //DEFAULT LINK IS FIRST IN THE LINK LIST
- int seq = av.getIndex(y);
- if(seq==-1)
- return;
-
- 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 y = e.getY();
-
- if (av.getWrapAlignment())
- {
- y = getWrappedY(y);
- }
-
- 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),
- Preferences.sequenceURLLinks);
- pop.show(this, e.getX(), y);
-
- return;
- }
-
- /* if (!e.isControlDown() && !e.isShiftDown() &&
- (av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null))
- {
- System.out.println("no modifiers");
- 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() && !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)
- {
- }
- }
- }
- }
-}
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.6)
+ * Copyright (C) 2010 J Procter, AM Waterhouse, 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("