X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FIdPanel.java;h=b5fd0c17251e002c84c3198bd211958b692a2b76;hb=ad20cd92225f2ee8c251d39b00b90555d382a616;hp=222cf8d5d224812e34249200cb6439da3fe204c3;hpb=1576c6118a09c59098483daa16a94e9cca8de260;p=jalview.git diff --git a/src/jalview/gui/IdPanel.java b/src/jalview/gui/IdPanel.java index 222cf8d..b5fd0c1 100755 --- a/src/jalview/gui/IdPanel.java +++ b/src/jalview/gui/IdPanel.java @@ -1,28 +1,31 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.4) - * Copyright (C) 2008 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle + * Jalview - A Sequence Alignment Editor and Viewer (Version 2.8) + * Copyright (C) 2012 J Procter, AM Waterhouse, LM Lui, J Engelhardt, 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 file is part of Jalview. * - * 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. + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * 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.*; +import jalview.io.SequenceAnnotationReport; import jalview.util.UrlLink; /** @@ -42,6 +45,8 @@ public class IdPanel extends JPanel implements MouseListener, ScrollThread scrollThread = null; + String linkImageURL; + int offy; // int width; @@ -49,19 +54,23 @@ public class IdPanel extends JPanel implements MouseListener, boolean mouseDragging = false; + private final SequenceAnnotationReport seqAnnotReport; + /** * 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(); + seqAnnotReport = new SequenceAnnotationReport(linkImageURL); setLayout(new BorderLayout()); add(idCanvas, BorderLayout.CENTER); addMouseListener(this); @@ -74,65 +83,23 @@ 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)); - String tmp; - if (seq > -1 && seq < av.alignment.getHeight()) + SeqPanel sp = alignPanel.seqPanel; + int seq = Math.max(0, sp.findSeq(e)); + 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(""); - - 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(); - 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()); - } - } - } - - if (maxWidth > 60) - { - tip.insert(0, "
"); - tip.append("
"); - } - - tip.append(""); - - setToolTipText("" + sequence.getDisplayId(true) - + tip.toString()); + seqAnnotReport + .createSequenceAnnotationReport(tip, sequence, + av.isShowDbRefs(), av.isShowNpFeats(), + sp.seqCanvas.fr.minmax); + setToolTipText("" + sequence.getDisplayId(true) + " " + + tip.toString() + ""); } } @@ -140,8 +107,9 @@ public class IdPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseDragged(MouseEvent e) { mouseDragging = true; @@ -161,16 +129,32 @@ public class IdPanel extends JPanel implements MouseListener, alignPanel.paintAlignment(true); } + @Override public void mouseWheelMoved(MouseWheelEvent e) { e.consume(); if (e.getWheelRotation() > 0) { - alignPanel.scrollUp(false); + if (e.isShiftDown()) + { + alignPanel.scrollRight(true); + + } + else + { + alignPanel.scrollUp(false); + } } else { - alignPanel.scrollUp(true); + if (e.isShiftDown()) + { + alignPanel.scrollRight(false); + } + else + { + alignPanel.scrollUp(true); + } } } @@ -178,8 +162,9 @@ 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) @@ -250,8 +235,9 @@ public class IdPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param e - * DOCUMENT ME! + * DOCUMENT ME! */ + @Override public void mouseEntered(MouseEvent e) { if (scrollThread != null) @@ -264,8 +250,9 @@ 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 +266,7 @@ 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); } @@ -289,8 +276,9 @@ 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 +290,28 @@ 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 +323,7 @@ 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)) @@ -327,7 +334,6 @@ public class IdPanel extends JPanel implements MouseListener, { selectSeq(seq); } - alignPanel.paintAlignment(true); } @@ -335,7 +341,7 @@ public class IdPanel extends JPanel implements MouseListener, * DOCUMENT ME! * * @param seq - * DOCUMENT ME! + * DOCUMENT ME! */ void selectSeq(int seq) { @@ -349,9 +355,9 @@ 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) { @@ -378,7 +384,7 @@ public class IdPanel extends JPanel implements MouseListener, for (int i = start; i <= end; i++) { av.getSelectionGroup().addSequence( - av.getAlignment().getSequenceAt(i), true); + av.getAlignment().getSequenceAt(i), i == end); } } @@ -386,8 +392,9 @@ 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 +404,26 @@ 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 +450,7 @@ public class IdPanel extends JPanel implements MouseListener, running = false; } + @Override public void run() { running = true;