2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, G Barton, M Clamp, S Searle
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5 * This file is part of Jalview.
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7 * Jalview is free software: you can redistribute it and/or
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8 * modify it under the terms of the GNU General Public License
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9 * as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version.
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11 * Jalview is distributed in the hope that it will be useful, but
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12 * WITHOUT ANY WARRANTY; without even the implied warranty
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13 * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
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14 * PURPOSE. See the GNU General Public License for more details.
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16 * You should have received a copy of the GNU General Public License along with Jalview. If not, see <http://www.gnu.org/licenses/>.
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18 package jalview.bin;
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20 import jalview.api.StructureSelectionManagerProvider;
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21 import jalview.appletgui.AlignFrame;
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22 import jalview.appletgui.AlignViewport;
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23 import jalview.appletgui.EmbmenuFrame;
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24 import jalview.appletgui.FeatureSettings;
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25 import jalview.datamodel.Alignment;
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26 import jalview.datamodel.AlignmentI;
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27 import jalview.datamodel.AlignmentOrder;
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28 import jalview.datamodel.ColumnSelection;
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29 import jalview.datamodel.PDBEntry;
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30 import jalview.datamodel.Sequence;
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31 import jalview.datamodel.SequenceGroup;
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32 import jalview.datamodel.SequenceI;
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33 import jalview.io.AnnotationFile;
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34 import jalview.io.AppletFormatAdapter;
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35 import jalview.io.FileParse;
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36 import jalview.io.IdentifyFile;
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37 import jalview.io.JnetAnnotationMaker;
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38 import jalview.javascript.JSFunctionExec;
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39 import jalview.javascript.JalviewLiteJsApi;
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40 import jalview.javascript.JsCallBack;
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41 import jalview.structure.SelectionListener;
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42 import jalview.structure.StructureSelectionManager;
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44 import java.applet.Applet;
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45 import java.awt.Button;
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46 import java.awt.Color;
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47 import java.awt.Component;
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48 import java.awt.EventQueue;
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49 import java.awt.Font;
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50 import java.awt.Frame;
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51 import java.awt.Graphics;
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52 import java.awt.event.ActionEvent;
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53 import java.awt.event.WindowAdapter;
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54 import java.awt.event.WindowEvent;
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55 import java.io.BufferedReader;
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56 import java.io.InputStreamReader;
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57 import java.net.URL;
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58 import java.util.Hashtable;
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59 import java.util.StringTokenizer;
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60 import java.util.Vector;
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62 import netscape.javascript.JSObject;
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65 * Jalview Applet. Runs in Java 1.18 runtime
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68 * @version $Revision: 1.92 $
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70 public class JalviewLite extends Applet implements
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71 StructureSelectionManagerProvider, JalviewLiteJsApi
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74 public StructureSelectionManager getStructureSelectionManager()
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76 return StructureSelectionManager.getStructureSelectionManager(this);
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79 // /////////////////////////////////////////
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80 // The following public methods maybe called
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81 // externally, eg via javascript in HTML page
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85 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences()
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87 public String getSelectedSequences()
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89 return getSelectedSequencesFrom(getDefaultTargetFrame());
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95 * @see jalview.bin.JalviewLiteJsApi#getSelectedSequences(java.lang.String)
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97 public String getSelectedSequences(String sep)
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99 return getSelectedSequencesFrom(getDefaultTargetFrame(), sep);
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106 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
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109 public String getSelectedSequencesFrom(AlignFrame alf)
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111 return getSelectedSequencesFrom(alf, separator); // ""+0x00AC);
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118 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesFrom(jalview.appletgui
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119 * .AlignFrame, java.lang.String)
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121 public String getSelectedSequencesFrom(AlignFrame alf, String sep)
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123 StringBuffer result = new StringBuffer("");
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124 if (sep == null || sep.length() == 0)
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126 sep = separator; // "+0x00AC;
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128 if (alf.viewport.getSelectionGroup() != null)
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130 SequenceI[] seqs = alf.viewport.getSelectionGroup()
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131 .getSequencesInOrder(alf.viewport.getAlignment());
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133 for (int i = 0; i < seqs.length; i++)
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135 result.append(seqs[i].getName());
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136 result.append(sep);
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140 return result.toString();
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146 * @see jalview.bin.JalviewLiteJsApi#highlight(java.lang.String,
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147 * java.lang.String, java.lang.String)
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149 public void highlight(String sequenceId, String position,
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150 String alignedPosition)
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152 highlightIn(getDefaultTargetFrame(), sequenceId, position,
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159 * @see jalview.bin.JalviewLiteJsApi#highlightIn(jalview.appletgui.AlignFrame,
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160 * java.lang.String, java.lang.String, java.lang.String)
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162 public void highlightIn(final AlignFrame alf, final String sequenceId,
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163 final String position, final String alignedPosition)
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165 // TODO: could try to highlight in all alignments if alf==null
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166 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
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167 alf.viewport.getAlignment().getSequencesArray());
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168 final SequenceI sq = matcher.findIdMatch(sequenceId);
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174 apos = new Integer(position).intValue();
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176 } catch (NumberFormatException ex)
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180 final StructureSelectionManagerProvider me = this;
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181 final int pos = apos;
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182 // use vamsas listener to broadcast to all listeners in scope
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183 if (alignedPosition != null
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184 && (alignedPosition.trim().length() == 0 || alignedPosition
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185 .toLowerCase().indexOf("false") > -1))
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187 java.awt.EventQueue.invokeLater(new Runnable()
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192 StructureSelectionManager.getStructureSelectionManager(me)
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193 .mouseOverVamsasSequence(sq, sq.findIndex(pos), null);
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199 java.awt.EventQueue.invokeLater(new Runnable()
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204 StructureSelectionManager.getStructureSelectionManager(me)
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205 .mouseOverVamsasSequence(sq, pos, null);
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215 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
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216 * java.lang.String)
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218 public void select(String sequenceIds, String columns)
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220 selectIn(getDefaultTargetFrame(), sequenceIds, columns, separator);
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226 * @see jalview.bin.JalviewLiteJsApi#select(java.lang.String,
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227 * java.lang.String, java.lang.String)
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229 public void select(String sequenceIds, String columns, String sep)
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231 selectIn(getDefaultTargetFrame(), sequenceIds, columns, sep);
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237 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
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238 * java.lang.String, java.lang.String)
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240 public void selectIn(AlignFrame alf, String sequenceIds, String columns)
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242 selectIn(alf, sequenceIds, columns, separator);
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248 * @see jalview.bin.JalviewLiteJsApi#selectIn(jalview.appletgui.AlignFrame,
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249 * java.lang.String, java.lang.String, java.lang.String)
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251 public void selectIn(final AlignFrame alf, String sequenceIds,
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252 String columns, String sep)
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254 if (sep == null || sep.length() == 0)
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262 System.err.println("Selecting region using separator string '"
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263 + separator + "'");
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267 String[] ids = separatorListToArray(sequenceIds, sep);
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268 String[] cols = separatorListToArray(columns, sep);
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269 final SequenceGroup sel = new SequenceGroup();
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270 final ColumnSelection csel = new ColumnSelection();
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271 AlignmentI al = alf.viewport.getAlignment();
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272 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
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273 alf.viewport.getAlignment().getSequencesArray());
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274 int start = 0, end = al.getWidth(), alw = al.getWidth();
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275 boolean seqsfound = true;
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276 if (ids != null && ids.length > 0)
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279 for (int i = 0; i < ids.length; i++)
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281 if (ids[i].trim().length() == 0)
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285 SequenceI sq = matcher.findIdMatch(ids[i]);
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289 sel.addSequence(sq, false);
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293 boolean inseqpos = false;
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294 if (cols != null && cols.length > 0)
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296 boolean seset = false;
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297 for (int i = 0; i < cols.length; i++)
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299 String cl = cols[i].trim();
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300 if (cl.length() == 0)
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305 if ((p = cl.indexOf("-")) > -1)
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307 int from = -1, to = -1;
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310 from = new Integer(cl.substring(0, p)).intValue();
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312 } catch (NumberFormatException ex)
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315 .println("ERROR: Couldn't parse first integer in range element column selection string '"
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316 + cl + "' - format is 'from-to'");
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321 to = new Integer(cl.substring(p + 1)).intValue();
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323 } catch (NumberFormatException ex)
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326 .println("ERROR: Couldn't parse second integer in range element column selection string '"
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327 + cl + "' - format is 'from-to'");
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330 if (from >= 0 && to >= 0)
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347 // comment to prevent range extension
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357 for (int r = from; r <= to; r++)
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359 if (r >= 0 && r < alw)
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361 csel.addElement(r);
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366 System.err.println("Range '" + cl + "' deparsed as [" + from
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372 System.err.println("ERROR: Invalid Range '" + cl
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373 + "' deparsed as [" + from + "," + to + "]");
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381 r = new Integer(cl).intValue();
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383 } catch (NumberFormatException ex)
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385 if (cl.toLowerCase().equals("sequence"))
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387 // we are in the dataset sequence's coordinate frame.
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393 .println("ERROR: Couldn't parse integer from point selection element of column selection string '"
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398 if (r >= 0 && r <= alw)
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408 // comment to prevent range extension
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418 csel.addElement(r);
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421 System.err.println("Point selection '" + cl
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422 + "' deparsed as [" + r + "]");
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427 System.err.println("ERROR: Invalid Point selection '" + cl
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428 + "' deparsed as [" + r + "]");
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435 // we only propagate the selection when it was the null selection, or the
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436 // given sequences were found in the alignment.
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437 if (inseqpos && sel.getSize() > 0)
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439 // assume first sequence provides reference frame ?
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440 SequenceI rs = sel.getSequenceAt(0);
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441 start = rs.findIndex(start);
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442 end = rs.findIndex(end);
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445 Vector cs = csel.getSelected();
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447 for (int csi = 0, csiS = cs.size(); csi < csiS; csi++)
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449 csel.addElement(rs.findIndex(((Integer) cs.elementAt(csi))
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454 sel.setStartRes(start);
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455 sel.setEndRes(end);
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456 EventQueue.invokeLater(new Runnable()
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461 alf.select(sel, csel);
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471 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignment(java.lang.
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472 * String, java.lang.String)
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474 public String getSelectedSequencesAsAlignment(String format, String suffix)
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476 return getSelectedSequencesAsAlignmentFrom(getDefaultTargetFrame(),
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484 * jalview.bin.JalviewLiteJsApi#getSelectedSequencesAsAlignmentFrom(jalview
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485 * .appletgui.AlignFrame, java.lang.String, java.lang.String)
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487 public String getSelectedSequencesAsAlignmentFrom(AlignFrame alf,
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488 String format, String suffix)
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492 boolean seqlimits = suffix.equalsIgnoreCase("true");
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493 if (alf.viewport.getSelectionGroup() != null)
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495 String reply = new AppletFormatAdapter().formatSequences(format,
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496 new Alignment(alf.viewport.getSelectionAsNewSequence()),
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500 } catch (Exception ex)
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502 ex.printStackTrace();
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503 return "Error retrieving alignment in " + format + " format. ";
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511 * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
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513 public String getAlignmentOrder()
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515 return getAlignmentOrderFrom(getDefaultTargetFrame());
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522 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
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525 public String getAlignmentOrderFrom(AlignFrame alf)
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527 return getAlignmentOrderFrom(alf, separator);
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534 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
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535 * , java.lang.String)
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537 public String getAlignmentOrderFrom(AlignFrame alf, String sep)
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539 AlignmentI alorder = alf.getAlignViewport().getAlignment();
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540 String[] order = new String[alorder.getHeight()];
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541 for (int i = 0; i < order.length; i++)
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543 order[i] = alorder.getSequenceAt(i).getName();
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545 return arrayToSeparatorList(order);
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551 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
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552 * java.lang.String)
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554 public String orderBy(String order, String undoName)
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556 return orderBy(order, undoName, separator);
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562 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
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563 * java.lang.String, java.lang.String)
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565 public String orderBy(String order, String undoName, String sep)
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567 return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
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574 * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
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575 * java.lang.String, java.lang.String, java.lang.String)
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577 public String orderAlignmentBy(AlignFrame alf, String order,
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578 String undoName, String sep)
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580 String[] ids = separatorListToArray(order, sep);
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581 SequenceI[] sqs = null;
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582 if (ids != null && ids.length > 0)
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584 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
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585 alf.viewport.getAlignment().getSequencesArray());
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587 sqs = new SequenceI[ids.length];
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588 for (int i = 0; i < ids.length; i++)
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590 if (ids[i].trim().length() == 0)
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594 SequenceI sq = matcher.findIdMatch(ids[i]);
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602 SequenceI[] sqq = new SequenceI[s];
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603 System.arraycopy(sqs, 0, sqq, 0, s);
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616 final AlignmentOrder aorder = new AlignmentOrder(sqs);
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618 if (undoName != null && undoName.trim().length() == 0)
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622 final String _undoName = undoName;
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623 // TODO: deal with synchronization here: cannot raise any events until after
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624 // this has returned.
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625 return alf.sortBy(aorder, _undoName) ? "true" : "";
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631 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
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633 public String getAlignment(String format)
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635 return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
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642 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
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643 * java.lang.String)
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645 public String getAlignmentFrom(AlignFrame alf, String format)
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647 return getAlignmentFrom(alf, format, "true");
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653 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
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654 * java.lang.String)
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656 public String getAlignment(String format, String suffix)
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658 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
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665 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
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666 * java.lang.String, java.lang.String)
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668 public String getAlignmentFrom(AlignFrame alf, String format,
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673 boolean seqlimits = suffix.equalsIgnoreCase("true");
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675 String reply = new AppletFormatAdapter().formatSequences(format,
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676 alf.viewport.getAlignment(), seqlimits);
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678 } catch (Exception ex)
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680 ex.printStackTrace();
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681 return "Error retrieving alignment in " + format + " format. ";
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688 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
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690 public void loadAnnotation(String annotation)
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692 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
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699 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
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700 * , java.lang.String)
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702 public void loadAnnotationFrom(AlignFrame alf, String annotation)
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704 if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
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705 .getAlignment(), annotation, AppletFormatAdapter.PASTE))
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707 alf.alignPanel.fontChanged();
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708 alf.alignPanel.setScrollValues(0, 0);
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712 alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
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719 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
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721 public void loadFeatures(String features, boolean autoenabledisplay)
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723 loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
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730 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
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731 * , java.lang.String)
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733 public void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
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735 alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);
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742 * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
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744 public String getFeatures(String format)
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746 return getFeaturesFrom(getDefaultTargetFrame(), format);
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753 * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
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754 * java.lang.String)
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756 public String getFeaturesFrom(AlignFrame alf, String format)
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758 return alf.outputFeatures(false, format);
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764 * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
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766 public String getAnnotation()
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768 return getAnnotationFrom(getDefaultTargetFrame());
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775 * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
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778 public String getAnnotationFrom(AlignFrame alf)
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780 return alf.outputAnnotations(false);
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786 * @see jalview.bin.JalviewLiteJsApi#newView()
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788 public AlignFrame newView()
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790 return newViewFrom(getDefaultTargetFrame());
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796 * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
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798 public AlignFrame newView(String name)
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800 return newViewFrom(getDefaultTargetFrame(), name);
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806 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
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808 public AlignFrame newViewFrom(AlignFrame alf)
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810 return alf.newView(null);
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816 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
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817 * java.lang.String)
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819 public AlignFrame newViewFrom(AlignFrame alf, String name)
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821 return alf.newView(name);
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827 * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
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828 * java.lang.String)
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830 public AlignFrame loadAlignment(String text, String title)
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832 Alignment al = null;
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834 String format = new IdentifyFile().Identify(text,
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835 AppletFormatAdapter.PASTE);
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838 al = new AppletFormatAdapter().readFile(text,
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839 AppletFormatAdapter.PASTE, format);
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840 if (al.getHeight() > 0)
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842 return new AlignFrame(al, this, title, false);
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844 } catch (java.io.IOException ex)
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846 ex.printStackTrace();
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854 * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
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856 public void setMouseoverListener(String listener)
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858 setMouseoverListener(currentAlignFrame, listener);
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861 private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
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867 * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
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868 * , java.lang.String)
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870 public void setMouseoverListener(AlignFrame af, String listener)
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872 if (listener != null)
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874 listener = listener.trim();
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875 if (listener.length() == 0)
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878 .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
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882 jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
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883 this, af, listener);
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884 javascriptListeners.addElement(mol);
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885 StructureSelectionManager.getStructureSelectionManager(this)
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886 .addStructureViewerListener(mol);
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889 System.err.println("Added a mouseover listener for "
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890 + ((af == null) ? "All frames" : "Just views for "
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891 + af.getAlignViewport().getSequenceSetId()));
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892 System.err.println("There are now " + javascriptListeners.size()
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893 + " listeners in total.");
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900 * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
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902 public void setSelectionListener(String listener)
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904 setSelectionListener(null, listener);
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911 * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
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912 * , java.lang.String)
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914 public void setSelectionListener(AlignFrame af, String listener)
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916 if (listener != null)
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918 listener = listener.trim();
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919 if (listener.length() == 0)
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922 .println("jalview Javascript error: Ignoring empty function for selection listener.");
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926 jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
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927 this, af, listener);
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928 javascriptListeners.addElement(mol);
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929 StructureSelectionManager.getStructureSelectionManager(this)
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930 .addSelectionListener(mol);
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933 System.err.println("Added a selection listener for "
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934 + ((af == null) ? "All frames" : "Just views for "
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935 + af.getAlignViewport().getSequenceSetId()));
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936 System.err.println("There are now " + javascriptListeners.size()
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937 + " listeners in total.");
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944 * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
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945 * java.lang.String)
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947 public void setStructureListener(String listener, String modelSet)
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949 if (listener != null)
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951 listener = listener.trim();
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952 if (listener.length() == 0)
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955 .println("jalview Javascript error: Ignoring empty function for selection listener.");
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959 jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
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960 this, listener, separatorListToArray(modelSet));
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961 javascriptListeners.addElement(mol);
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962 StructureSelectionManager.getStructureSelectionManager(this)
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963 .addStructureViewerListener(mol);
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966 System.err.println("Added a javascript structure viewer listener '"
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968 System.err.println("There are now " + javascriptListeners.size()
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969 + " listeners in total.");
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977 * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
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978 * .AlignFrame, java.lang.String)
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980 public void removeJavascriptListener(AlignFrame af, String listener)
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982 if (listener != null)
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984 listener = listener.trim();
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985 if (listener.length() == 0)
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990 boolean rprt = false;
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991 for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
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993 Object lstn = javascriptListeners.elementAt(ms);
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994 JsCallBack lstner = (JsCallBack) lstn;
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995 if ((af == null || lstner.getAlignFrame() == af)
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996 && (listener == null || lstner.getListenerFunction().equals(
\r
999 javascriptListeners.removeElement(lstner);
\r
1001 if (lstner instanceof SelectionListener)
\r
1003 StructureSelectionManager.getStructureSelectionManager(this)
\r
1004 .removeSelectionListener((SelectionListener) lstner);
\r
1008 StructureSelectionManager.getStructureSelectionManager(this)
\r
1009 .removeStructureViewerListener(lstner, null);
\r
1014 System.err.println("Removed listener '" + listener + "'");
\r
1024 System.err.println("There are now " + javascriptListeners.size()
\r
1025 + " listeners in total.");
\r
1029 public void stop()
\r
1031 System.err.println("Applet " + getName() + " stop().");
\r
1035 public void destroy()
\r
1037 System.err.println("Applet " + getName() + " destroy().");
\r
1041 private void tidyUp()
\r
1044 if (currentAlignFrame != null && currentAlignFrame.viewport != null
\r
1045 && currentAlignFrame.viewport.applet != null)
\r
1047 AlignViewport av = currentAlignFrame.viewport;
\r
1048 currentAlignFrame.closeMenuItem_actionPerformed();
\r
1050 currentAlignFrame = null;
\r
1052 if (javascriptListeners != null)
\r
1054 while (javascriptListeners.size() > 0)
\r
1056 jalview.javascript.JSFunctionExec mol = javascriptListeners
\r
1058 javascriptListeners.removeElement(mol);
\r
1059 if (mol instanceof SelectionListener)
\r
1061 StructureSelectionManager.getStructureSelectionManager(this)
\r
1062 .removeSelectionListener((SelectionListener) mol);
\r
1066 StructureSelectionManager.getStructureSelectionManager(this)
\r
1067 .removeStructureViewerListener(mol, null);
\r
1069 mol.jvlite = null;
\r
1072 if (jsFunctionExec != null)
\r
1074 jsFunctionExec.stopQueue();
\r
1075 jsFunctionExec.jvlite = null;
\r
1077 initialAlignFrame = null;
\r
1078 jsFunctionExec = null;
\r
1079 javascriptListeners = null;
\r
1080 StructureSelectionManager.release(this);
\r
1083 private jalview.javascript.JSFunctionExec jsFunctionExec;
\r
1088 * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
\r
1089 * java.lang.String, java.lang.String)
\r
1091 public void mouseOverStructure(final String pdbResNum,
\r
1092 final String chain, final String pdbfile)
\r
1094 final StructureSelectionManagerProvider me = this;
\r
1095 java.awt.EventQueue.invokeLater(new Runnable()
\r
1102 StructureSelectionManager.getStructureSelectionManager(me)
\r
1103 .mouseOverStructure(new Integer(pdbResNum).intValue(),
\r
1107 System.err.println("mouseOver for '" + pdbResNum
\r
1108 + "' in chain '" + chain + "' in structure '" + pdbfile
\r
1111 } catch (NumberFormatException e)
\r
1113 System.err.println("Ignoring invalid residue number string '"
\r
1114 + pdbResNum + "'");
\r
1125 * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
\r
1126 * java.lang.String, java.lang.String)
\r
1128 public void scrollViewToIn(final AlignFrame alf, final String topRow,
\r
1129 final String leftHandColumn)
\r
1131 java.awt.EventQueue.invokeLater(new Runnable()
\r
1138 alf.scrollTo(new Integer(topRow).intValue(), new Integer(
\r
1139 leftHandColumn).intValue());
\r
1141 } catch (Exception ex)
\r
1143 System.err.println("Couldn't parse integer arguments (topRow='"
\r
1144 + topRow + "' and leftHandColumn='" + leftHandColumn
\r
1146 ex.printStackTrace();
\r
1156 * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
\r
1157 * .AlignFrame, java.lang.String)
\r
1160 public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
\r
1163 java.awt.EventQueue.invokeLater(new Runnable()
\r
1170 alf.scrollToRow(new Integer(topRow).intValue());
\r
1172 } catch (Exception ex)
\r
1174 System.err.println("Couldn't parse integer arguments (topRow='"
\r
1176 ex.printStackTrace();
\r
1187 * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
\r
1188 * .AlignFrame, java.lang.String)
\r
1191 public void scrollViewToColumnIn(final AlignFrame alf,
\r
1192 final String leftHandColumn)
\r
1194 java.awt.EventQueue.invokeLater(new Runnable()
\r
1202 alf.scrollToColumn(new Integer(leftHandColumn).intValue());
\r
1204 } catch (Exception ex)
\r
1207 .println("Couldn't parse integer arguments (leftHandColumn='"
\r
1208 + leftHandColumn + "')");
\r
1209 ex.printStackTrace();
\r
1216 // //////////////////////////////////////////////
\r
1217 // //////////////////////////////////////////////
\r
1219 public static int lastFrameX = 200;
\r
1221 public static int lastFrameY = 200;
\r
1223 boolean fileFound = true;
\r
1225 String file = "No file";
\r
1227 Button launcher = new Button("Start Jalview");
\r
1230 * The currentAlignFrame is static, it will change if and when the user
\r
1231 * selects a new window. Note that it will *never* point back to the embedded
\r
1232 * AlignFrame if the applet is started as embedded on the page and then
\r
1233 * afterwards a new view is created.
\r
1235 public AlignFrame currentAlignFrame = null;
\r
1238 * This is the first frame to be displayed, and does not change. API calls
\r
1239 * will default to this instance if currentAlignFrame is null.
\r
1241 AlignFrame initialAlignFrame = null;
\r
1243 boolean embedded = false;
\r
1245 private boolean checkForJmol = true;
\r
1247 private boolean checkedForJmol = false; // ensure we don't check for jmol
\r
1249 // every time the app is re-inited
\r
1251 public boolean jmolAvailable = false;
\r
1253 private boolean alignPdbStructures = false;
\r
1256 * use an external structure viewer exclusively (no jmols or MCViews will be
\r
1257 * opened by JalviewLite itself)
\r
1259 public boolean useXtrnalSviewer = false;
\r
1261 public static boolean debug = false;
\r
1263 static String builddate = null, version = null;
\r
1265 private static void initBuildDetails()
\r
1267 if (builddate == null)
\r
1269 builddate = "unknown";
\r
1271 java.net.URL url = JalviewLite.class
\r
1272 .getResource("/.build_properties");
\r
1277 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1278 url.openStream()));
\r
1280 while ((line = reader.readLine()) != null)
\r
1282 if (line.indexOf("VERSION") > -1)
\r
1284 version = line.substring(line.indexOf("=") + 1);
\r
1286 if (line.indexOf("BUILD_DATE") > -1)
\r
1288 builddate = line.substring(line.indexOf("=") + 1);
\r
1291 } catch (Exception ex)
\r
1293 ex.printStackTrace();
\r
1299 public static String getBuildDate()
\r
1301 initBuildDetails();
\r
1305 public static String getVersion()
\r
1307 initBuildDetails();
\r
1311 // public JSObject scriptObject = null;
\r
1314 * init method for Jalview Applet
\r
1316 public void init()
\r
1318 // remove any handlers that might be hanging around from an earlier instance
\r
1323 System.err.println("Applet context is '"
\r
1324 + getAppletContext().getClass().toString() + "'");
\r
1326 JSObject scriptObject = JSObject.getWindow(this);
\r
1327 if (debug && scriptObject != null)
\r
1329 System.err.println("Applet has Javascript callback support.");
\r
1332 } catch (Exception ex)
\r
1335 .println("Warning: No JalviewLite javascript callbacks available.");
\r
1338 ex.printStackTrace();
\r
1342 * turn on extra applet debugging
\r
1344 String dbg = getParameter("debug");
\r
1347 debug = dbg.toLowerCase().equals("true");
\r
1352 System.err.println("JalviewLite Version " + getVersion());
\r
1353 System.err.println("Build Date : " + getBuildDate());
\r
1356 String externalsviewer = getParameter("externalstructureviewer");
\r
1357 if (externalsviewer != null)
\r
1359 useXtrnalSviewer = externalsviewer.trim().toLowerCase()
\r
1363 * if true disable the check for jmol
\r
1365 String chkforJmol = getParameter("nojmol");
\r
1366 if (chkforJmol != null)
\r
1368 checkForJmol = !chkforJmol.equals("true");
\r
1371 * get the separator parameter if present
\r
1373 String sep = getParameter("separator");
\r
1376 if (sep.length() > 0)
\r
1381 System.err.println("Separator set to '" + separator + "'");
\r
1387 "Invalid separator parameter - must be non-zero length");
\r
1393 String param = getParameter("RGB");
\r
1395 if (param != null)
\r
1399 r = Integer.parseInt(param.substring(0, 2), 16);
\r
1400 g = Integer.parseInt(param.substring(2, 4), 16);
\r
1401 b = Integer.parseInt(param.substring(4, 6), 16);
\r
1402 } catch (Exception ex)
\r
1409 param = getParameter("label");
\r
1410 if (param != null)
\r
1412 launcher.setLabel(param);
\r
1415 setBackground(new Color(r, g, b));
\r
1417 file = getParameter("file");
\r
1421 // Maybe the sequences are added as parameters
\r
1422 StringBuffer data = new StringBuffer("PASTE");
\r
1424 while ((file = getParameter("sequence" + i)) != null)
\r
1426 data.append(file.toString() + "\n");
\r
1429 if (data.length() > 5)
\r
1431 file = data.toString();
\r
1435 final JalviewLite jvapplet = this;
\r
1436 if (getParameter("embedded") != null
\r
1437 && getParameter("embedded").equalsIgnoreCase("true"))
\r
1439 // Launch as embedded applet in page
\r
1441 LoadingThread loader = new LoadingThread(file, jvapplet);
\r
1444 else if (file != null)
\r
1446 if (getParameter("showbutton") == null
\r
1447 || !getParameter("showbutton").equalsIgnoreCase("false"))
\r
1449 // Add the JalviewLite 'Button' to the page
\r
1451 launcher.addActionListener(new java.awt.event.ActionListener()
\r
1453 public void actionPerformed(ActionEvent e)
\r
1455 LoadingThread loader = new LoadingThread(file, jvapplet);
\r
1462 // Open jalviewLite immediately.
\r
1463 LoadingThread loader = new LoadingThread(file, jvapplet);
\r
1469 // jalview initialisation with no alignment. loadAlignment() method can
\r
1470 // still be called to open new alignments.
\r
1472 fileFound = false;
\r
1473 // callInitCallback();
\r
1477 private void callInitCallback()
\r
1479 String initjscallback = getParameter("oninit");
\r
1480 if (initjscallback == null)
\r
1484 initjscallback = initjscallback.trim();
\r
1485 if (initjscallback.length() > 0)
\r
1487 JSObject scriptObject = null;
\r
1490 scriptObject = JSObject.getWindow(this);
\r
1491 } catch (Exception ex)
\r
1495 if (scriptObject != null)
\r
1499 // do onInit with the JS executor thread
\r
1500 new JSFunctionExec(this).executeJavascriptFunction(true,
\r
1501 initjscallback, null, "Calling oninit callback '"
\r
1502 + initjscallback + "'.");
\r
1503 } catch (Exception e)
\r
1505 System.err.println("Exception when executing _oninit callback '"
\r
1506 + initjscallback + "'.");
\r
1507 e.printStackTrace();
\r
1512 System.err.println("Not executing _oninit callback '"
\r
1513 + initjscallback + "' - no scripting allowed.");
\r
1519 * Initialises and displays a new java.awt.Frame
\r
1522 * java.awt.Frame to be displayed
\r
1524 * title of new frame
\r
1526 * width if new frame
\r
1528 * height of new frame
\r
1530 public static void addFrame(final Frame frame, String title, int width,
\r
1533 frame.setLocation(lastFrameX, lastFrameY);
\r
1536 frame.setSize(width, height);
\r
1537 frame.setTitle(title);
\r
1538 frame.addWindowListener(new WindowAdapter()
\r
1540 public void windowClosing(WindowEvent e)
\r
1542 if (frame instanceof AlignFrame)
\r
1544 AlignViewport vp = ((AlignFrame) frame).viewport;
\r
1545 ((AlignFrame) frame).closeMenuItem_actionPerformed();
\r
1546 if (vp.applet.currentAlignFrame == frame)
\r
1548 vp.applet.currentAlignFrame = null;
\r
1556 if (frame instanceof EmbmenuFrame)
\r
1558 ((EmbmenuFrame) frame).destroyMenus();
\r
1560 frame.setMenuBar(null);
\r
1564 public void windowActivated(WindowEvent e)
\r
1566 if (frame instanceof AlignFrame)
\r
1568 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
\r
1571 System.err.println("Activated window " + frame);
\r
1575 super.windowActivated(e);
\r
1578 * Probably not necessary to do this - see TODO above. (non-Javadoc)
\r
1581 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
\r
1584 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
\r
1585 * frame) { currentAlignFrame = null; if (debug) {
\r
1586 * System.err.println("Deactivated window "+frame); } }
\r
1587 * super.windowDeactivated(e); }
\r
1590 frame.setVisible(true);
\r
1594 * This paints the background surrounding the "Launch Jalview button" <br>
\r
1596 * If file given in parameter not found, displays error message
\r
1599 * graphics context
\r
1601 public void paint(Graphics g)
\r
1605 g.setColor(new Color(200, 200, 200));
\r
1606 g.setColor(Color.cyan);
\r
1607 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1608 g.setColor(Color.red);
\r
1609 g.drawString("Jalview can't open file", 5, 15);
\r
1610 g.drawString("\"" + file + "\"", 5, 30);
\r
1612 else if (embedded)
\r
1614 g.setColor(Color.black);
\r
1615 g.setFont(new Font("Arial", Font.BOLD, 24));
\r
1616 g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);
\r
1617 g.drawString("Loading Data...", 50, getSize().height / 2);
\r
1622 * get all components associated with the applet of the given type
\r
1627 public Vector getAppletWindow(Class class1)
\r
1629 Vector wnds = new Vector();
\r
1630 Component[] cmp = getComponents();
\r
1633 for (int i = 0; i < cmp.length; i++)
\r
1635 if (class1.isAssignableFrom(cmp[i].getClass()))
\r
1637 wnds.addElement(cmp);
\r
1644 class LoadJmolThread extends Thread
\r
1646 private boolean running = false;
\r
1650 if (running || checkedForJmol)
\r
1659 if (!System.getProperty("java.version").startsWith("1.1"))
\r
1661 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
\r
1662 jmolAvailable = true;
\r
1664 if (!jmolAvailable)
\r
1667 .println("Jmol not available - Using MCview for structures");
\r
1669 } catch (java.lang.ClassNotFoundException ex)
\r
1675 jmolAvailable = false;
\r
1679 .println("Skipping Jmol check. Will use MCView (probably)");
\r
1682 checkedForJmol = true;
\r
1686 public boolean notFinished()
\r
1688 return running || !checkedForJmol;
\r
1692 class LoadingThread extends Thread
\r
1695 * State variable: File source
\r
1700 * State variable: protocol for access to file source
\r
1705 * State variable: format of file source
\r
1711 JalviewLite applet;
\r
1713 private void dbgMsg(String msg)
\r
1717 System.err.println(msg);
\r
1722 * update the protocol state variable for accessing the datasource located
\r
1726 * @return possibly updated datasource string
\r
1728 public String setProtocolState(String file)
\r
1730 if (file.startsWith("PASTE"))
\r
1732 file = file.substring(5);
\r
1733 protocol = AppletFormatAdapter.PASTE;
\r
1735 else if (inArchive(file))
\r
1737 protocol = AppletFormatAdapter.CLASSLOADER;
\r
1741 file = addProtocol(file);
\r
1742 protocol = AppletFormatAdapter.URL;
\r
1744 dbgMsg("Protocol identified as '" + protocol + "'");
\r
1748 public LoadingThread(String _file, JalviewLite _applet)
\r
1750 this._file = _file;
\r
1756 LoadJmolThread jmolchecker = new LoadJmolThread();
\r
1757 jmolchecker.start();
\r
1758 while (jmolchecker.notFinished())
\r
1760 // wait around until the Jmol check is complete.
\r
1764 } catch (Exception e)
\r
1770 // applet.callInitCallback();
\r
1773 private void startLoading()
\r
1775 AlignFrame newAlignFrame;
\r
1776 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
\r
1777 file = setProtocolState(_file);
\r
1779 format = new jalview.io.IdentifyFile().Identify(file, protocol);
\r
1780 dbgMsg("File identified as '" + format + "'");
\r
1781 dbgMsg("Loading started.");
\r
1782 Alignment al = null;
\r
1785 al = new AppletFormatAdapter().readFile(file, protocol, format);
\r
1786 } catch (java.io.IOException ex)
\r
1788 dbgMsg("File load exception.");
\r
1789 ex.printStackTrace();
\r
1794 FileParse fp = new FileParse(file, protocol);
\r
1796 dbgMsg(">>>Dumping contents of '" + file + "' " + "("
\r
1797 + protocol + ")");
\r
1798 while ((ln = fp.nextLine()) != null)
\r
1802 dbgMsg(">>>Dump finished.");
\r
1803 } catch (Exception e)
\r
1806 .println("Exception when trying to dump the content of the file parameter.");
\r
1807 e.printStackTrace();
\r
1811 if ((al != null) && (al.getHeight() > 0))
\r
1813 dbgMsg("Successfully loaded file.");
\r
1814 newAlignFrame = new AlignFrame(al, applet, file, embedded);
\r
1815 if (initialAlignFrame == null)
\r
1817 initialAlignFrame = newAlignFrame;
\r
1819 // update the focus.
\r
1820 currentAlignFrame = newAlignFrame;
\r
1822 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
\r
1824 newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());
\r
1827 newAlignFrame.statusBar.setText("Successfully loaded file " + file);
\r
1829 String treeFile = applet.getParameter("tree");
\r
1830 if (treeFile == null)
\r
1832 treeFile = applet.getParameter("treeFile");
\r
1835 if (treeFile != null)
\r
1839 treeFile = setProtocolState(treeFile);
\r
1841 * if (inArchive(treeFile)) { protocol =
\r
1842 * AppletFormatAdapter.CLASSLOADER; } else { protocol =
\r
1843 * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
\r
1845 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
\r
1850 if (fin.getTree() != null)
\r
1852 newAlignFrame.loadTree(fin, treeFile);
\r
1853 dbgMsg("Successfuly imported tree.");
\r
1857 dbgMsg("Tree parameter did not resolve to a valid tree.");
\r
1859 } catch (Exception ex)
\r
1861 ex.printStackTrace();
\r
1867 * Try to load T-Coffee score file
\r
1869 String sScoreFile = applet.getParameter("scoreFile");
\r
1870 if( sScoreFile != null && !"".equals(sScoreFile) ) {
\r
1872 URL urlScore = new URL(sScoreFile);
\r
1873 newAlignFrame.loadScoreFile(urlScore);
\r
1874 //TODO check the scores matrix matches the MSA dimensions
\r
1877 catch( Exception e ) {
\r
1878 // TODO error message log (shows a warning dialogbox?)
\r
1879 System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());
\r
1884 // ///////////////////////////
\r
1885 // modify display of features
\r
1886 // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed
\r
1888 // hide specific groups
\r
1890 String param = applet.getParameter("hidefeaturegroups");
\r
1891 if (param != null)
\r
1893 newAlignFrame.setFeatureGroupState(separatorListToArray(param), false);
\r
1894 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
\r
1896 // show specific groups
\r
1897 param = applet.getParameter("showfeaturegroups");
\r
1898 if (param != null)
\r
1900 newAlignFrame.setFeatureGroupState(separatorListToArray(param), true);
\r
1901 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
\r
1903 // and now load features
\r
1904 param = applet.getParameter("features");
\r
1905 if (param != null)
\r
1907 param = setProtocolState(param);
\r
1909 newAlignFrame.parseFeaturesFile(param, protocol);
\r
1912 param = applet.getParameter("showFeatureSettings");
\r
1913 if (param != null && param.equalsIgnoreCase("true"))
\r
1915 newAlignFrame.viewport.showSequenceFeatures(true);
\r
1916 new FeatureSettings(newAlignFrame.alignPanel);
\r
1919 param = applet.getParameter("annotations");
\r
1920 if (param != null)
\r
1922 param = setProtocolState(param);
\r
1924 if (new AnnotationFile().readAnnotationFile(
\r
1925 newAlignFrame.viewport.getAlignment(), param, protocol))
\r
1927 newAlignFrame.alignPanel.fontChanged();
\r
1928 newAlignFrame.alignPanel.setScrollValues(0, 0);
\r
1933 .println("Annotations were not added from annotation file '"
\r
1939 param = applet.getParameter("jnetfile");
\r
1940 if (param != null)
\r
1944 param = setProtocolState(param);
\r
1945 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
\r
1947 JnetAnnotationMaker.add_annotation(predictions,
\r
1948 newAlignFrame.viewport.getAlignment(), 0, false); // false==do
\r
1956 newAlignFrame.alignPanel.fontChanged();
\r
1957 newAlignFrame.alignPanel.setScrollValues(0, 0);
\r
1958 } catch (Exception ex)
\r
1960 ex.printStackTrace();
\r
1964 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
\r
1965 * - related to JAL-434
\r
1967 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
\r
1970 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
\r
1971 * PDB|1GAQ|1GAQ|C">
\r
1973 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
\r
1975 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
\r
1978 int pdbFileCount = 0;
\r
1979 // Accumulate pdbs here if they are heading for the same view (if
\r
1980 // alignPdbStructures is true)
\r
1981 Vector pdbs = new Vector();
\r
1982 // create a lazy matcher if we're asked to
\r
1983 jalview.analysis.SequenceIdMatcher matcher = (applet
\r
1984 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
\r
1985 newAlignFrame.getAlignViewport().getAlignment()
\r
1986 .getSequencesArray()) : null;
\r
1990 if (pdbFileCount > 0)
\r
1992 param = applet.getParameter("PDBFILE" + pdbFileCount);
\r
1996 param = applet.getParameter("PDBFILE");
\r
1999 if (param != null)
\r
2001 PDBEntry pdb = new PDBEntry();
\r
2004 SequenceI[] seqs = null;
\r
2005 String[] chains = null;
\r
2007 StringTokenizer st = new StringTokenizer(param, " ");
\r
2009 if (st.countTokens() < 2)
\r
2011 String sequence = applet.getParameter("PDBSEQ");
\r
2012 if (sequence != null)
\r
2013 seqs = new SequenceI[]
\r
2014 { matcher == null ? (Sequence) newAlignFrame
\r
2015 .getAlignViewport().getAlignment()
\r
2016 .findName(sequence) : matcher.findIdMatch(sequence) };
\r
2021 param = st.nextToken();
\r
2022 Vector tmp = new Vector();
\r
2023 Vector tmp2 = new Vector();
\r
2025 while (st.hasMoreTokens())
\r
2027 seqstring = st.nextToken();
\r
2028 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
\r
2029 if (st2.countTokens() > 1)
\r
2031 // This is the chain
\r
2032 tmp2.addElement(st2.nextToken());
\r
2033 seqstring = st2.nextToken();
\r
2035 tmp.addElement(matcher == null ? (Sequence) newAlignFrame
\r
2036 .getAlignViewport().getAlignment()
\r
2037 .findName(seqstring) : matcher
\r
2038 .findIdMatch(seqstring));
\r
2041 seqs = new SequenceI[tmp.size()];
\r
2042 tmp.copyInto(seqs);
\r
2043 if (tmp2.size() == tmp.size())
\r
2045 chains = new String[tmp2.size()];
\r
2046 tmp2.copyInto(chains);
\r
2049 param = setProtocolState(param);
\r
2051 if (// !jmolAvailable
\r
2053 protocol == AppletFormatAdapter.CLASSLOADER
\r
2054 && !useXtrnalSviewer)
\r
2056 // Re: JAL-357 : the bug isn't a problem if we are using an
\r
2057 // external viewer!
\r
2058 // TODO: verify this Re:
\r
2059 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
\r
2060 // This exception preserves the current behaviour where, even if
\r
2061 // the local pdb file was identified in the class loader
\r
2062 protocol = AppletFormatAdapter.URL; // this is probably NOT
\r
2064 param = addProtocol(param); //
\r
2067 pdb.setFile(param);
\r
2071 for (int i = 0; i < seqs.length; i++)
\r
2073 if (seqs[i] != null)
\r
2075 ((Sequence) seqs[i]).addPDBId(pdb);
\r
2079 if (JalviewLite.debug)
\r
2081 // this may not really be a problem but we give a warning
\r
2084 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
\r
2090 if (!alignPdbStructures)
\r
2092 newAlignFrame.newStructureView(applet, pdb, seqs, chains,
\r
2097 pdbs.addElement(new Object[]
\r
2098 { pdb, seqs, chains, new String(protocol) });
\r
2104 } while (param != null || pdbFileCount < 10);
\r
2105 if (pdbs.size() > 0)
\r
2107 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
\r
2108 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
\r
2109 String[][] chains = new String[pdbs.size()][];
\r
2110 String[] protocols = new String[pdbs.size()];
\r
2111 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
\r
2113 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
\r
2114 pdb[pdbsi] = (PDBEntry) o[0];
\r
2115 seqs[pdbsi] = (SequenceI[]) o[1];
\r
2116 chains[pdbsi] = (String[]) o[2];
\r
2117 protocols[pdbsi] = (String) o[3];
\r
2119 newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
\r
2126 fileFound = false;
\r
2127 applet.remove(launcher);
\r
2130 callInitCallback();
\r
2134 * Discovers whether the given file is in the Applet Archive
\r
2140 boolean inArchive(String file)
\r
2142 // This might throw a security exception in certain browsers
\r
2143 // Netscape Communicator for instance.
\r
2146 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
\r
2149 System.err.println("Resource '" + file + "' was "
\r
2150 + (rtn ? "" : "not") + " located by classloader.");
\r
2153 } catch (Exception ex)
\r
2155 System.out.println("Exception checking resources: " + file + " "
\r
2161 String addProtocol(String file)
\r
2163 if (file.indexOf("://") == -1)
\r
2165 String fl = applet.resolveUrlForLocalOrAbsolute(file,
\r
2166 getDocumentBase());
\r
2169 if (new java.net.URL(fl).openStream() != null)
\r
2173 System.err.println("Prepended document base for resource: '"
\r
2178 } catch (Exception x)
\r
2182 fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
\r
2185 if (new java.net.URL(fl).openStream() != null)
\r
2189 System.err.println("Prepended codebase for resource: '"
\r
2194 } catch (Exception x)
\r
2206 * @return the default alignFrame acted on by the public applet methods. May
\r
2207 * return null with an error message on System.err indicating the
\r
2210 public AlignFrame getDefaultTargetFrame()
\r
2212 if (currentAlignFrame != null)
\r
2214 return currentAlignFrame;
\r
2216 if (initialAlignFrame != null)
\r
2218 return initialAlignFrame;
\r
2221 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
\r
2226 * separator used for separatorList
\r
2228 protected String separator = "" + ((char) 0x00AC); // the default used to be
\r
2229 // '|' but many sequence
\r
2230 // IDS include pipes.
\r
2233 * set to enable the URL based javascript execution mechanism
\r
2235 public boolean jsfallbackEnabled = false;
\r
2238 * parse the string into a list
\r
2241 * @return elements separated by separator
\r
2243 public String[] separatorListToArray(String list)
\r
2245 return separatorListToArray(list, separator);
\r
2249 * parse the string into a list
\r
2252 * @param separator
\r
2253 * @return elements separated by separator
\r
2255 public String[] separatorListToArray(String list, String separator)
\r
2257 // note separator local variable intentionally masks object field
\r
2258 int seplen = separator.length();
\r
2259 if (list == null || list.equals("") || list.equals(separator))
\r
2261 java.util.Vector jv = new Vector();
\r
2263 while ((pos = list.indexOf(separator, cp)) > cp)
\r
2265 jv.addElement(list.substring(cp, pos));
\r
2266 cp = pos + seplen;
\r
2268 if (cp < list.length())
\r
2270 String c = list.substring(cp);
\r
2271 if (!c.equals(separator))
\r
2276 if (jv.size() > 0)
\r
2278 String[] v = new String[jv.size()];
\r
2279 for (int i = 0; i < v.length; i++)
\r
2281 v[i] = (String) jv.elementAt(i);
\r
2283 jv.removeAllElements();
\r
2286 System.err.println("Array from '" + separator
\r
2287 + "' separated List:\n" + v.length);
\r
2288 for (int i = 0; i < v.length; i++)
\r
2290 System.err.println("item " + i + " '" + v[i] + "'");
\r
2297 System.err.println("Empty Array from '" + separator
\r
2298 + "' separated List");
\r
2304 * concatenate the list with separator
\r
2307 * @return concatenated string
\r
2309 public String arrayToSeparatorList(String[] list)
\r
2311 return arrayToSeparatorList(list, separator);
\r
2315 * concatenate the list with separator
\r
2318 * @param separator
\r
2319 * @return concatenated string
\r
2321 public String arrayToSeparatorList(String[] list, String separator)
\r
2323 StringBuffer v = new StringBuffer();
\r
2324 if (list != null && list.length > 0)
\r
2326 for (int i = 0, iSize = list.length; i < iSize; i++)
\r
2328 if (list[i] != null)
\r
2332 v.append(separator);
\r
2334 v.append(list[i]);
\r
2339 System.err.println("Returning '" + separator
\r
2340 + "' separated List:\n");
\r
2341 System.err.println(v);
\r
2343 return v.toString();
\r
2347 System.err.println("Returning empty '" + separator
\r
2348 + "' separated List\n");
\r
2350 return "" + separator;
\r
2356 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
\r
2358 public String getFeatureGroups()
\r
2360 String lst = arrayToSeparatorList(getDefaultTargetFrame()
\r
2361 .getFeatureGroups());
\r
2369 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
\r
2372 public String getFeatureGroupsOn(AlignFrame alf)
\r
2374 String lst = arrayToSeparatorList(alf.getFeatureGroups());
\r
2381 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
\r
2383 public String getFeatureGroupsOfState(boolean visible)
\r
2385 return arrayToSeparatorList(getDefaultTargetFrame()
\r
2386 .getFeatureGroupsOfState(visible));
\r
2393 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
\r
2394 * .AlignFrame, boolean)
\r
2396 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
\r
2398 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
\r
2404 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
\r
2405 * AlignFrame, java.lang.String, boolean)
\r
2407 public void setFeatureGroupStateOn(final AlignFrame alf,
\r
2408 final String groups, boolean state)
\r
2410 final boolean st = state;// !(state==null || state.equals("") ||
\r
2411 // state.toLowerCase().equals("false"));
\r
2412 java.awt.EventQueue.invokeLater(new Runnable()
\r
2417 alf.setFeatureGroupState(separatorListToArray(groups), st);
\r
2425 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
\r
2428 public void setFeatureGroupState(String groups, boolean state)
\r
2430 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
\r
2436 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
\r
2438 public String getSeparator()
\r
2446 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
\r
2448 public void setSeparator(String separator)
\r
2450 if (separator == null || separator.length() < 1)
\r
2452 // reset to default
\r
2453 separator = "" + ((char) 0x00AC);
\r
2455 this.separator = separator;
\r
2458 System.err.println("Default Separator now: '" + separator + "'");
\r
2463 * get boolean value of applet parameter 'name' and return default if
\r
2464 * parameter is not set
\r
2467 * name of paremeter
\r
2469 * the value to return otherwise
\r
2470 * @return true or false
\r
2472 public boolean getDefaultParameter(String name, boolean def)
\r
2475 if ((stn = getParameter(name)) == null)
\r
2479 if (stn.toLowerCase().equals("true"))
\r
2489 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
\r
2490 * java.lang.String, java.lang.String, java.lang.String)
\r
2492 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
\r
2493 String pdbEntryString, String pdbFile)
\r
2495 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
\r
2498 protected void setAlignPdbStructures(boolean alignPdbStructures)
\r
2500 this.alignPdbStructures = alignPdbStructures;
\r
2503 public boolean isAlignPdbStructures()
\r
2505 return alignPdbStructures;
\r
2508 public void start()
\r
2510 // callInitCallback();
\r
2513 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
\r
2515 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
\r
2517 public void setJsMessageSet(String messageclass, String viewId,
\r
2518 String[] colcommands)
\r
2520 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
\r
2521 if (msgset == null)
\r
2523 msgset = new Hashtable<String, String[]>();
\r
2524 jsmessages.put(messageclass, msgset);
\r
2526 msgset.put(viewId, colcommands);
\r
2527 long[] l = new long[colcommands.length];
\r
2528 for (int i = 0; i < colcommands.length; i++)
\r
2530 l[i] = colcommands[i].hashCode();
\r
2532 jshashes.put(messageclass + "|" + viewId, l);
\r
2538 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
\r
2539 * java.lang.String)
\r
2541 public String getJsMessage(String messageclass, String viewId)
\r
2543 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
\r
2544 if (msgset != null)
\r
2546 String[] msgs = msgset.get(viewId);
\r
2549 for (int i = 0; i < msgs.length; i++)
\r
2551 if (msgs[i] != null)
\r
2553 String m = msgs[i];
\r
2563 public boolean isJsMessageSetChanged(String string, String string2,
\r
2564 String[] colcommands)
\r
2566 long[] l = jshashes.get(string + "|" + string2);
\r
2567 if (l == null && colcommands != null)
\r
2571 for (int i = 0; i < colcommands.length; i++)
\r
2573 if (l[i] != colcommands[i].hashCode())
\r
2581 private Vector jsExecQueue = new Vector();
\r
2583 public Vector getJsExecQueue()
\r
2585 return jsExecQueue;
\r
2588 public void setExecutor(JSFunctionExec jsFunctionExec2)
\r
2590 jsFunctionExec = jsFunctionExec2;
\r
2594 * return the given colour value parameter or the given default if parameter
\r
2598 * @param defcolour
\r
2601 public Color getDefaultColourParameter(String colparam, Color defcolour)
\r
2603 String colprop = getParameter(colparam);
\r
2604 if (colprop == null || colprop.trim().length() == 0)
\r
2608 Color col = jalview.schemes.ColourSchemeProperty
\r
2609 .getAWTColorFromName(colprop);
\r
2614 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
\r
2615 } catch (Exception ex)
\r
2617 System.err.println("Couldn't parse '" + colprop
\r
2618 + "' as a colour for " + colparam);
\r
2622 return (col == null) ? defcolour : col;
\r
2626 public void openJalviewHelpUrl()
\r
2628 String helpUrl = getParameter("jalviewhelpurl");
\r
2629 if (helpUrl == null || helpUrl.trim().length() < 5)
\r
2631 helpUrl = "http://www.jalview.org/help.html";
\r
2633 showURL(helpUrl, "HELP");
\r
2637 * form a complete URL given a path to a resource and a reference location on
\r
2641 * - an absolute path on the same server as localref or a document
\r
2642 * located relative to localref
\r
2644 * - a URL on the same server as url
\r
2645 * @return a complete URL for the resource located by url
\r
2647 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
\r
2649 String codebase = localref.toString();
\r
2650 if (url.indexOf("/") == 0)
\r
2652 url = codebase.substring(0, codebase.length()
\r
2653 - localref.getFile().length())
\r
2658 url = localref + url;
\r
2664 * open a URL in the browser - resolving it according to relative refs and
\r
2665 * coping with javascript: protocol if necessary.
\r
2670 public void showURL(String url, String target)
\r
2674 if (url.indexOf(":") == -1)
\r
2676 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
\r
2678 // Should really use docbase, not codebase.
\r
2680 url = resolveUrlForLocalOrAbsolute(
\r
2682 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
\r
2687 .println("Show url (prepended "
\r
2689 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
\r
2697 System.err.println("Show url: " + url);
\r
2700 if (url.indexOf("javascript:") == 0)
\r
2702 // no target for the javascript context
\r
2703 getAppletContext().showDocument(new java.net.URL(url));
\r
2707 getAppletContext().showDocument(new java.net.URL(url), target);
\r
2709 } catch (Exception ex)
\r
2711 ex.printStackTrace();
\r
2716 * bind structures in a viewer to any matching sequences in an alignFrame (use
\r
2717 * sequenceIds to limit scope of search to specific sequences)
\r
2721 * @param sequenceIds
\r
2722 * @return TODO: consider making an exception structure for indicating when
\r
2723 * binding fails public SequenceStructureBinding
\r
2724 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
\r
2727 * if (sequenceIds != null && sequenceIds.length() > 0) { return
\r
2728 * alFrame.addStructureViewInstance(viewer,
\r
2729 * separatorListToArray(sequenceIds)); } else { return
\r
2730 * alFrame.addStructureViewInstance(viewer, null); } // return null; }
\r