2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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20 package jalview.appletgui;
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23 import java.awt.event.*;
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25 import jalview.datamodel.*;
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27 public class IdPanel
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28 extends Panel implements MouseListener, MouseMotionListener
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31 protected IdCanvas idCanvas;
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32 protected AlignViewport av;
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33 protected AlignmentPanel alignPanel;
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34 ScrollThread scrollThread = null;
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39 boolean mouseDragging = false;
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40 java.util.Vector links = new java.util.Vector();
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42 public IdPanel(AlignViewport av, AlignmentPanel parent)
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45 alignPanel = parent;
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46 idCanvas = new IdCanvas(av);
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47 setLayout(new BorderLayout());
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48 add(idCanvas, BorderLayout.CENTER);
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49 idCanvas.addMouseListener(this);
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50 idCanvas.addMouseMotionListener(this);
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53 for(int i=1; i<10; i++)
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55 label = parent.alignFrame.applet.getParameter("linkLabel_"+i);
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56 url = parent.alignFrame.applet.getParameter("linkURL_"+i);
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58 if(label!=null && url!=null)
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59 links.addElement(label+"|"+url);
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62 if (links.size() < 1)
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64 links = new java.util.Vector();
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65 links.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
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69 public void mouseMoved(MouseEvent e)
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72 public void mouseDragged(MouseEvent e)
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74 mouseDragging = true;
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77 if (av.getWrapAlignment())
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79 y -= 2 * av.charHeight;
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81 int seq = av.getIndex(y);
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90 selectSeqs(lastid - 1, seq);
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92 else if (seq > lastid)
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94 selectSeqs(lastid + 1, seq);
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98 alignPanel.repaint();
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101 public void mouseClicked(MouseEvent e)
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103 if (e.getClickCount() < 2)
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108 if (av.getWrapAlignment())
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110 y -= (2 * av.charHeight);
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113 //DEFAULT LINK IS FIRST IN THE LINK LIST
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114 int seq = av.getIndex(y);
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115 String id = av.getAlignment().getSequenceAt(seq).getName();
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117 String target = links.elementAt(0).toString();
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118 target = target.substring(0, target.indexOf("|"));
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119 String url = links.elementAt(0).toString();
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120 url = url.substring(url.indexOf("|")+1);
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122 int index = url.indexOf("$SEQUENCE_ID$");
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123 url = url.substring(0, index)+ id + url.substring(index+13);
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127 jalview.bin.JalviewLite.showURL(url, target);
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129 catch (Exception ex)
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131 ex.printStackTrace();
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135 public void mouseEntered(MouseEvent e)
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137 if (scrollThread != null)
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139 scrollThread.running = false;
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143 public void mouseExited(MouseEvent e)
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145 if (av.getWrapAlignment())
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150 if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
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152 scrollThread = new ScrollThread(true);
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155 if (mouseDragging && e.getY() >= getSize().height &&
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156 av.alignment.getHeight() > av.getEndSeq())
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158 scrollThread = new ScrollThread(false);
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162 public void mousePressed(MouseEvent e)
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164 if (e.getClickCount() >1 )
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170 if (av.getWrapAlignment())
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172 y -= 2 * av.charHeight;
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175 int seq = av.getIndex(y);
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181 if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
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182 InputEvent.BUTTON3_MASK)
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184 APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);
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186 popup.show(this, e.getX(), e.getY());
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190 if (!e.isControlDown() && !e.isShiftDown() &&
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191 av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)
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194 SequenceGroup selection = new SequenceGroup();
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195 SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
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196 selection.setStartRes(0);
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197 selection.setEndRes(av.alignment.getWidth() - 1);
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198 for (int i = 0; i < sg.getSize(); i++)
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200 selection.addSequence(sg.getSequenceAt(i), true);
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203 av.setSelectionGroup(selection);
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207 if (av.getSelectionGroup() == null ||
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208 (!e.isControlDown() && av.getSelectionGroup() != null))
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210 av.setSelectionGroup(new SequenceGroup());
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213 av.getSelectionGroup().setStartRes(0);
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214 av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
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216 if (e.isShiftDown() && lastid != -1)
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218 selectSeqs(lastid, seq);
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225 alignPanel.repaint();
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228 void selectSeq(int seq)
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231 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
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232 av.getSelectionGroup().addOrRemove(pickedSeq, false);
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235 void selectSeqs(int start, int end)
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247 for (int i = start; i <= end; i++)
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249 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
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254 public void mouseReleased(MouseEvent e)
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256 if (scrollThread != null)
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258 scrollThread.running = false;
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261 if(av.getSelectionGroup()!=null)
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262 av.getSelectionGroup().recalcConservation();
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264 mouseDragging = false;
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265 PaintRefresher.Refresh(this, av.alignment);
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268 public void highlightSearchResults(java.util.Vector found)
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270 idCanvas.setHighlighted(found);
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277 int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
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279 // do we need to scroll the panel?
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280 if (av.getStartSeq() > index || av.getEndSeq() < index)
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282 alignPanel.setScrollValues(av.getStartRes(), index);
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286 // this class allows scrolling off the bottom of the visible alignment
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290 boolean running = false;
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292 public ScrollThread(boolean up)
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298 public void stopScrolling()
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308 if (alignPanel.scrollUp(up))
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310 // scroll was ok, so add new sequence to selection
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311 int seq = av.getStartSeq();
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314 seq = av.getEndSeq();
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319 selectSeqs(lastid - 1, seq);
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321 else if (seq > lastid)
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323 selectSeqs(lastid + 1, seq);
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333 alignPanel.repaint();
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338 catch (Exception ex)
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