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 if(parent.alignFrame.applet!=null)
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55 for (int i = 1; i < 10; i++)
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57 label = parent.alignFrame.applet.getParameter("linkLabel_" + i);
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58 url = parent.alignFrame.applet.getParameter("linkURL_" + i);
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60 if (label != null && url != null)
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61 links.addElement(label + "|" + url);
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65 if (links.size() < 1)
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67 links = new java.util.Vector();
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68 links.addElement("SRS|http://srs.ebi.ac.uk/srs7bin/cgi-bin/wgetz?-e+[uniprot-all:$SEQUENCE_ID$]+-vn+2");
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72 public void mouseMoved(MouseEvent e)
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75 public void mouseDragged(MouseEvent e)
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77 mouseDragging = true;
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80 if (av.getWrapAlignment())
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82 y -= 2 * av.charHeight;
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84 int seq = av.getIndex(y);
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93 selectSeqs(lastid - 1, seq);
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95 else if (seq > lastid)
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97 selectSeqs(lastid + 1, seq);
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101 alignPanel.repaint();
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104 public void mouseClicked(MouseEvent e)
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106 if (e.getClickCount() < 2)
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111 if (av.getWrapAlignment())
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113 y -= (2 * av.charHeight);
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116 //DEFAULT LINK IS FIRST IN THE LINK LIST
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117 int seq = av.getIndex(y);
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118 String id = av.getAlignment().getSequenceAt(seq).getName();
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119 if (id.indexOf("|") > -1)
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120 id = id.substring(id.lastIndexOf("|") + 1);
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122 String target = links.elementAt(0).toString();
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123 target = target.substring(0, target.indexOf("|"));
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124 String url = links.elementAt(0).toString();
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125 url = url.substring(url.indexOf("|")+1);
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127 int index = url.indexOf("$SEQUENCE_ID$");
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128 url = url.substring(0, index)+ id + url.substring(index+13);
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133 alignPanel.alignFrame.showURL(url, target);
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135 catch (Exception ex)
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137 ex.printStackTrace();
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141 public void mouseEntered(MouseEvent e)
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143 if (scrollThread != null)
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145 scrollThread.running = false;
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149 public void mouseExited(MouseEvent e)
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151 if (av.getWrapAlignment())
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156 if (mouseDragging && e.getY() < 0 && av.getStartSeq() > 0)
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158 scrollThread = new ScrollThread(true);
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161 if (mouseDragging && e.getY() >= getSize().height &&
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162 av.alignment.getHeight() > av.getEndSeq())
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164 scrollThread = new ScrollThread(false);
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168 public void mousePressed(MouseEvent e)
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170 if (e.getClickCount() >1 )
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176 if (av.getWrapAlignment())
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178 y -= 2 * av.charHeight;
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181 int seq = av.getIndex(y);
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187 if ( (e.getModifiers() & InputEvent.BUTTON3_MASK) ==
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188 InputEvent.BUTTON3_MASK)
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190 APopupMenu popup = new APopupMenu(alignPanel, (Sequence) av.getAlignment().getSequenceAt(seq), links);
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192 popup.show(this, e.getX(), e.getY());
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196 if (!e.isControlDown() && !e.isShiftDown() &&
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197 av.alignment.findGroup(av.alignment.getSequenceAt(seq)) != null)
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200 SequenceGroup selection = new SequenceGroup();
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201 SequenceGroup sg = av.alignment.findGroup(av.alignment.getSequenceAt(seq));
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202 selection.setStartRes(0);
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203 selection.setEndRes(av.alignment.getWidth() - 1);
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204 for (int i = 0; i < sg.getSize(); i++)
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206 selection.addSequence(sg.getSequenceAt(i), true);
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209 av.setSelectionGroup(selection);
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213 if (av.getSelectionGroup() == null ||
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214 (!e.isControlDown() && av.getSelectionGroup() != null))
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216 av.setSelectionGroup(new SequenceGroup());
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219 av.getSelectionGroup().setStartRes(0);
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220 av.getSelectionGroup().setEndRes(av.alignment.getWidth() - 1);
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222 if (e.isShiftDown() && lastid != -1)
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224 selectSeqs(lastid, seq);
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231 alignPanel.repaint();
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234 void selectSeq(int seq)
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237 SequenceI pickedSeq = av.getAlignment().getSequenceAt(seq);
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238 av.getSelectionGroup().addOrRemove(pickedSeq, false);
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241 void selectSeqs(int start, int end)
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253 for (int i = start; i <= end; i++)
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255 av.getSelectionGroup().addSequence(av.getAlignment().getSequenceAt(i), false);
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260 public void mouseReleased(MouseEvent e)
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262 if (scrollThread != null)
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264 scrollThread.running = false;
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267 if(av.getSelectionGroup()!=null)
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268 av.getSelectionGroup().recalcConservation();
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270 mouseDragging = false;
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271 PaintRefresher.Refresh(this, av.alignment);
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274 public void highlightSearchResults(java.util.Vector found)
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276 idCanvas.setHighlighted(found);
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283 int index = av.alignment.findIndex( (SequenceI) found.elementAt(0));
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285 // do we need to scroll the panel?
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286 if (av.getStartSeq() > index || av.getEndSeq() < index)
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288 alignPanel.setScrollValues(av.getStartRes(), index);
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292 // this class allows scrolling off the bottom of the visible alignment
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296 boolean running = false;
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298 public ScrollThread(boolean up)
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304 public void stopScrolling()
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314 if (alignPanel.scrollUp(up))
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316 // scroll was ok, so add new sequence to selection
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317 int seq = av.getStartSeq();
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320 seq = av.getEndSeq();
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325 selectSeqs(lastid - 1, seq);
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327 else if (seq > lastid)
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329 selectSeqs(lastid + 1, seq);
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339 alignPanel.repaint();
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344 catch (Exception ex)
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