X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=0480ffa6c6314f136df9fc37f5892c7442b32c22;hb=e015538903c8cabb2b90dd030e3e0c419a730db9;hp=222cf8d5d224812e34249200cb6439da3fe204c3;hpb=1576c6118a09c59098483daa16a94e9cca8de260;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 222cf8d..0480ffa 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,25 +1,27 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or + * 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 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 + * 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.List; +import java.util.Vector; + import javax.swing.*; import jalview.datamodel.*; @@ -27,7 +29,7 @@ import jalview.util.UrlLink; /** * DOCUMENT ME! - * + * * @author $author$ * @version $Revision$ */ @@ -42,6 +44,8 @@ public class IdPanel extends JPanel implements MouseListener, ScrollThread scrollThread = null; + String linkImageURL; + int offy; // int width; @@ -51,17 +55,18 @@ public class IdPanel extends JPanel implements MouseListener, /** * Creates a new IdPanel object. - * + * * @param av - * DOCUMENT ME! + * DOCUMENT ME! * @param parent - * DOCUMENT ME! + * 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); @@ -72,17 +77,19 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseMoved(MouseEvent e) { - int seq = Math.max(0, alignPanel.seqPanel.findSeq(e)); + SeqPanel sp = alignPanel.seqPanel; + int seq = Math.max(0, sp.findSeq(e)); String tmp; - if (seq > -1 && seq < av.alignment.getHeight()) + if (seq > -1 && seq < av.getAlignment().getHeight()) { - SequenceI sequence = av.alignment.getSequenceAt(seq); + SequenceI sequence = av.getAlignment().getSequenceAt(seq); StringBuffer tip = new StringBuffer(); tip.append(""); @@ -109,16 +116,19 @@ public class IdPanel extends JPanel implements MouseListener, // 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) { - tmp = features[i].featureGroup + " " + features[i].getType() - + " " + features[i].description; - tip.append("
" + tmp); - maxWidth = Math.max(maxWidth, tmp.length()); + 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); } } } @@ -131,17 +141,18 @@ public class IdPanel extends JPanel implements MouseListener, tip.append(""); - setToolTipText("" + sequence.getDisplayId(true) + setToolTipText("" + sequence.getDisplayId(true) + " " + tip.toString()); } } /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -161,6 +172,7 @@ public class IdPanel extends JPanel implements MouseListener, alignPanel.paintAlignment(true); } + @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); @@ -176,10 +188,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseClicked(MouseEvent e) { if (e.getClickCount() < 2) @@ -248,10 +261,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -262,10 +276,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseExited(MouseEvent e) { if (av.getWrapAlignment()) @@ -279,7 +294,7 @@ public class IdPanel extends JPanel implements MouseListener, } if (mouseDragging && (e.getY() >= getHeight()) - && (av.alignment.getHeight() > av.getEndSeq())) + && (av.getAlignment().getHeight() > av.getEndSeq())) { scrollThread = new ScrollThread(false); } @@ -287,10 +302,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mousePressed(MouseEvent e) { if (e.getClickCount() == 2) @@ -302,9 +318,27 @@ public class IdPanel extends JPanel implements MouseListener, if (javax.swing.SwingUtilities.isRightMouseButton(e)) { - jalview.gui.PopupMenu pop = new jalview.gui.PopupMenu(alignPanel, - (Sequence) av.getAlignment().getSequenceAt(seq), - Preferences.sequenceURLLinks); + 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; @@ -316,7 +350,7 @@ public class IdPanel extends JPanel implements MouseListener, { av.setSelectionGroup(new SequenceGroup()); av.getSelectionGroup().setStartRes(0); - av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1); + av.getSelectionGroup().setEndRes(av.getAlignment().getWidth() - 1); } if (e.isShiftDown() && (lastid != -1)) @@ -327,15 +361,14 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeq(seq); } - alignPanel.paintAlignment(true); } /** * DOCUMENT ME! - * + * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ void selectSeq(int seq) { @@ -347,11 +380,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param start - * DOCUMENT ME! + * DOCUMENT ME! * @param end - * DOCUMENT ME! + * DOCUMENT ME! */ void selectSeqs(int start, int end) { @@ -384,10 +417,11 @@ public class IdPanel extends JPanel implements MouseListener, /** * DOCUMENT ME! - * + * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseReleased(MouseEvent e) { if (scrollThread != null) @@ -397,24 +431,26 @@ public class IdPanel extends JPanel implements MouseListener, mouseDragging = false; PaintRefresher.Refresh(this, av.getSequenceSetId()); + // always send selection message when mouse is released + av.sendSelection(); } /** * DOCUMENT ME! - * - * @param found - * DOCUMENT ME! + * + * @param list + * DOCUMENT ME! */ - public void highlightSearchResults(java.util.Vector found) + public void highlightSearchResults(List list) { - idCanvas.setHighlighted(found); + idCanvas.setHighlighted(list); - if (found == null) + if (list == null) { return; } - int index = av.alignment.findIndex((SequenceI) found.get(0)); + int index = av.getAlignment().findIndex(list.get(0)); // do we need to scroll the panel? if ((av.getStartSeq() > index) || (av.getEndSeq() < index)) @@ -441,6 +477,7 @@ public class IdPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true;