2 * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
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3 * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, 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 // JBPNote: getSelectionAsNewSequence behaviour has changed - this method now returns a full copy of sequence data
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496 // TODO consider using getSequenceSelection instead here
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497 String reply = new AppletFormatAdapter().formatSequences(format,
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498 new Alignment(alf.viewport.getSelectionAsNewSequence()),
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502 } catch (Exception ex)
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504 ex.printStackTrace();
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505 return "Error retrieving alignment in " + format + " format. ";
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513 * @see jalview.bin.JalviewLiteJsApi#getAlignmentOrder()
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515 public String getAlignmentOrder()
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517 return getAlignmentOrderFrom(getDefaultTargetFrame());
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524 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
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527 public String getAlignmentOrderFrom(AlignFrame alf)
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529 return getAlignmentOrderFrom(alf, separator);
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536 * jalview.bin.JalviewLiteJsApi#getAlignmentOrderFrom(jalview.appletgui.AlignFrame
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537 * , java.lang.String)
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539 public String getAlignmentOrderFrom(AlignFrame alf, String sep)
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541 AlignmentI alorder = alf.getAlignViewport().getAlignment();
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542 String[] order = new String[alorder.getHeight()];
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543 for (int i = 0; i < order.length; i++)
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545 order[i] = alorder.getSequenceAt(i).getName();
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547 return arrayToSeparatorList(order);
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553 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
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554 * java.lang.String)
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556 public String orderBy(String order, String undoName)
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558 return orderBy(order, undoName, separator);
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564 * @see jalview.bin.JalviewLiteJsApi#orderBy(java.lang.String,
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565 * java.lang.String, java.lang.String)
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567 public String orderBy(String order, String undoName, String sep)
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569 return orderAlignmentBy(getDefaultTargetFrame(), order, undoName, sep);
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576 * jalview.bin.JalviewLiteJsApi#orderAlignmentBy(jalview.appletgui.AlignFrame,
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577 * java.lang.String, java.lang.String, java.lang.String)
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579 public String orderAlignmentBy(AlignFrame alf, String order,
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580 String undoName, String sep)
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582 String[] ids = separatorListToArray(order, sep);
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583 SequenceI[] sqs = null;
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584 if (ids != null && ids.length > 0)
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586 jalview.analysis.SequenceIdMatcher matcher = new jalview.analysis.SequenceIdMatcher(
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587 alf.viewport.getAlignment().getSequencesArray());
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589 sqs = new SequenceI[ids.length];
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590 for (int i = 0; i < ids.length; i++)
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592 if (ids[i].trim().length() == 0)
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596 SequenceI sq = matcher.findIdMatch(ids[i]);
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604 SequenceI[] sqq = new SequenceI[s];
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605 System.arraycopy(sqs, 0, sqq, 0, s);
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618 final AlignmentOrder aorder = new AlignmentOrder(sqs);
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620 if (undoName != null && undoName.trim().length() == 0)
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624 final String _undoName = undoName;
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625 // TODO: deal with synchronization here: cannot raise any events until after
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626 // this has returned.
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627 return alf.sortBy(aorder, _undoName) ? "true" : "";
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633 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String)
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635 public String getAlignment(String format)
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637 return getAlignmentFrom(getDefaultTargetFrame(), format, "true");
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644 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
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645 * java.lang.String)
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647 public String getAlignmentFrom(AlignFrame alf, String format)
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649 return getAlignmentFrom(alf, format, "true");
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655 * @see jalview.bin.JalviewLiteJsApi#getAlignment(java.lang.String,
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656 * java.lang.String)
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658 public String getAlignment(String format, String suffix)
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660 return getAlignmentFrom(getDefaultTargetFrame(), format, suffix);
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667 * jalview.bin.JalviewLiteJsApi#getAlignmentFrom(jalview.appletgui.AlignFrame,
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668 * java.lang.String, java.lang.String)
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670 public String getAlignmentFrom(AlignFrame alf, String format,
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675 boolean seqlimits = suffix.equalsIgnoreCase("true");
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677 String reply = new AppletFormatAdapter().formatSequences(format,
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678 alf.viewport.getAlignment(), seqlimits);
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680 } catch (Exception ex)
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682 ex.printStackTrace();
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683 return "Error retrieving alignment in " + format + " format. ";
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690 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
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692 public void loadAnnotation(String annotation)
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694 loadAnnotationFrom(getDefaultTargetFrame(), annotation);
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701 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
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702 * , java.lang.String)
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704 public void loadAnnotationFrom(AlignFrame alf, String annotation)
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706 if (new AnnotationFile().readAnnotationFile(alf.getAlignViewport()
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707 .getAlignment(), annotation, AppletFormatAdapter.PASTE))
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709 alf.alignPanel.fontChanged();
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710 alf.alignPanel.setScrollValues(0, 0);
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714 alf.parseFeaturesFile(annotation, AppletFormatAdapter.PASTE);
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721 * @see jalview.bin.JalviewLiteJsApi#loadAnnotation(java.lang.String)
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723 public void loadFeatures(String features, boolean autoenabledisplay)
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725 loadFeaturesFrom(getDefaultTargetFrame(), features, autoenabledisplay);
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732 * jalview.bin.JalviewLiteJsApi#loadAnnotationFrom(jalview.appletgui.AlignFrame
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733 * , java.lang.String)
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735 public void loadFeaturesFrom(AlignFrame alf, String features, boolean autoenabledisplay)
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737 alf.parseFeaturesFile(features, AppletFormatAdapter.PASTE, autoenabledisplay);
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744 * @see jalview.bin.JalviewLiteJsApi#getFeatures(java.lang.String)
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746 public String getFeatures(String format)
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748 return getFeaturesFrom(getDefaultTargetFrame(), format);
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755 * jalview.bin.JalviewLiteJsApi#getFeaturesFrom(jalview.appletgui.AlignFrame,
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756 * java.lang.String)
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758 public String getFeaturesFrom(AlignFrame alf, String format)
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760 return alf.outputFeatures(false, format);
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766 * @see jalview.bin.JalviewLiteJsApi#getAnnotation()
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768 public String getAnnotation()
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770 return getAnnotationFrom(getDefaultTargetFrame());
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777 * jalview.bin.JalviewLiteJsApi#getAnnotationFrom(jalview.appletgui.AlignFrame
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780 public String getAnnotationFrom(AlignFrame alf)
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782 return alf.outputAnnotations(false);
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788 * @see jalview.bin.JalviewLiteJsApi#newView()
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790 public AlignFrame newView()
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792 return newViewFrom(getDefaultTargetFrame());
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798 * @see jalview.bin.JalviewLiteJsApi#newView(java.lang.String)
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800 public AlignFrame newView(String name)
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802 return newViewFrom(getDefaultTargetFrame(), name);
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808 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame)
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810 public AlignFrame newViewFrom(AlignFrame alf)
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812 return alf.newView(null);
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818 * @see jalview.bin.JalviewLiteJsApi#newViewFrom(jalview.appletgui.AlignFrame,
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819 * java.lang.String)
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821 public AlignFrame newViewFrom(AlignFrame alf, String name)
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823 return alf.newView(name);
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829 * @see jalview.bin.JalviewLiteJsApi#loadAlignment(java.lang.String,
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830 * java.lang.String)
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832 public AlignFrame loadAlignment(String text, String title)
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834 Alignment al = null;
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836 String format = new IdentifyFile().Identify(text,
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837 AppletFormatAdapter.PASTE);
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840 al = new AppletFormatAdapter().readFile(text,
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841 AppletFormatAdapter.PASTE, format);
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842 if (al.getHeight() > 0)
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844 return new AlignFrame(al, this, title, false);
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846 } catch (java.io.IOException ex)
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848 ex.printStackTrace();
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856 * @see jalview.bin.JalviewLiteJsApi#setMouseoverListener(java.lang.String)
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858 public void setMouseoverListener(String listener)
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860 setMouseoverListener(currentAlignFrame, listener);
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863 private Vector<jalview.javascript.JSFunctionExec> javascriptListeners = new Vector<jalview.javascript.JSFunctionExec>();
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869 * jalview.bin.JalviewLiteJsApi#setMouseoverListener(jalview.appletgui.AlignFrame
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870 * , java.lang.String)
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872 public void setMouseoverListener(AlignFrame af, String listener)
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874 if (listener != null)
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876 listener = listener.trim();
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877 if (listener.length() == 0)
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880 .println("jalview Javascript error: Ignoring empty function for mouseover listener.");
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884 jalview.javascript.MouseOverListener mol = new jalview.javascript.MouseOverListener(
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885 this, af, listener);
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886 javascriptListeners.addElement(mol);
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887 StructureSelectionManager.getStructureSelectionManager(this)
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888 .addStructureViewerListener(mol);
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891 System.err.println("Added a mouseover listener for "
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892 + ((af == null) ? "All frames" : "Just views for "
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893 + af.getAlignViewport().getSequenceSetId()));
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894 System.err.println("There are now " + javascriptListeners.size()
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895 + " listeners in total.");
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902 * @see jalview.bin.JalviewLiteJsApi#setSelectionListener(java.lang.String)
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904 public void setSelectionListener(String listener)
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906 setSelectionListener(null, listener);
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913 * jalview.bin.JalviewLiteJsApi#setSelectionListener(jalview.appletgui.AlignFrame
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914 * , java.lang.String)
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916 public void setSelectionListener(AlignFrame af, String listener)
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918 if (listener != null)
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920 listener = listener.trim();
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921 if (listener.length() == 0)
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924 .println("jalview Javascript error: Ignoring empty function for selection listener.");
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928 jalview.javascript.JsSelectionSender mol = new jalview.javascript.JsSelectionSender(
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929 this, af, listener);
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930 javascriptListeners.addElement(mol);
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931 StructureSelectionManager.getStructureSelectionManager(this)
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932 .addSelectionListener(mol);
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935 System.err.println("Added a selection listener for "
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936 + ((af == null) ? "All frames" : "Just views for "
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937 + af.getAlignViewport().getSequenceSetId()));
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938 System.err.println("There are now " + javascriptListeners.size()
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939 + " listeners in total.");
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946 * @see jalview.bin.JalviewLiteJsApi#setStructureListener(java.lang.String,
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947 * java.lang.String)
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949 public void setStructureListener(String listener, String modelSet)
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951 if (listener != null)
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953 listener = listener.trim();
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954 if (listener.length() == 0)
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957 .println("jalview Javascript error: Ignoring empty function for selection listener.");
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961 jalview.javascript.MouseOverStructureListener mol = new jalview.javascript.MouseOverStructureListener(
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962 this, listener, separatorListToArray(modelSet));
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963 javascriptListeners.addElement(mol);
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964 StructureSelectionManager.getStructureSelectionManager(this)
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965 .addStructureViewerListener(mol);
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968 System.err.println("Added a javascript structure viewer listener '"
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970 System.err.println("There are now " + javascriptListeners.size()
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971 + " listeners in total.");
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979 * jalview.bin.JalviewLiteJsApi#removeJavascriptListener(jalview.appletgui
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980 * .AlignFrame, java.lang.String)
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982 public void removeJavascriptListener(AlignFrame af, String listener)
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984 if (listener != null)
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986 listener = listener.trim();
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987 if (listener.length() == 0)
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992 boolean rprt = false;
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993 for (int ms = 0, msSize = javascriptListeners.size(); ms < msSize;)
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995 Object lstn = javascriptListeners.elementAt(ms);
\r
996 JsCallBack lstner = (JsCallBack) lstn;
\r
997 if ((af == null || lstner.getAlignFrame() == af)
\r
998 && (listener == null || lstner.getListenerFunction().equals(
\r
1001 javascriptListeners.removeElement(lstner);
\r
1003 if (lstner instanceof SelectionListener)
\r
1005 StructureSelectionManager.getStructureSelectionManager(this)
\r
1006 .removeSelectionListener((SelectionListener) lstner);
\r
1010 StructureSelectionManager.getStructureSelectionManager(this)
\r
1011 .removeStructureViewerListener(lstner, null);
\r
1016 System.err.println("Removed listener '" + listener + "'");
\r
1026 System.err.println("There are now " + javascriptListeners.size()
\r
1027 + " listeners in total.");
\r
1031 public void stop()
\r
1033 System.err.println("Applet " + getName() + " stop().");
\r
1037 public void destroy()
\r
1039 System.err.println("Applet " + getName() + " destroy().");
\r
1043 private void tidyUp()
\r
1046 if (currentAlignFrame != null && currentAlignFrame.viewport != null
\r
1047 && currentAlignFrame.viewport.applet != null)
\r
1049 AlignViewport av = currentAlignFrame.viewport;
\r
1050 currentAlignFrame.closeMenuItem_actionPerformed();
\r
1052 currentAlignFrame = null;
\r
1054 if (javascriptListeners != null)
\r
1056 while (javascriptListeners.size() > 0)
\r
1058 jalview.javascript.JSFunctionExec mol = javascriptListeners
\r
1060 javascriptListeners.removeElement(mol);
\r
1061 if (mol instanceof SelectionListener)
\r
1063 StructureSelectionManager.getStructureSelectionManager(this)
\r
1064 .removeSelectionListener((SelectionListener) mol);
\r
1068 StructureSelectionManager.getStructureSelectionManager(this)
\r
1069 .removeStructureViewerListener(mol, null);
\r
1071 mol.jvlite = null;
\r
1074 if (jsFunctionExec != null)
\r
1076 jsFunctionExec.stopQueue();
\r
1077 jsFunctionExec.jvlite = null;
\r
1079 initialAlignFrame = null;
\r
1080 jsFunctionExec = null;
\r
1081 javascriptListeners = null;
\r
1082 StructureSelectionManager.release(this);
\r
1085 private jalview.javascript.JSFunctionExec jsFunctionExec;
\r
1090 * @see jalview.bin.JalviewLiteJsApi#mouseOverStructure(java.lang.String,
\r
1091 * java.lang.String, java.lang.String)
\r
1093 public void mouseOverStructure(final String pdbResNum,
\r
1094 final String chain, final String pdbfile)
\r
1096 final StructureSelectionManagerProvider me = this;
\r
1097 java.awt.EventQueue.invokeLater(new Runnable()
\r
1104 StructureSelectionManager.getStructureSelectionManager(me)
\r
1105 .mouseOverStructure(new Integer(pdbResNum).intValue(),
\r
1109 System.err.println("mouseOver for '" + pdbResNum
\r
1110 + "' in chain '" + chain + "' in structure '" + pdbfile
\r
1113 } catch (NumberFormatException e)
\r
1115 System.err.println("Ignoring invalid residue number string '"
\r
1116 + pdbResNum + "'");
\r
1127 * jalview.bin.JalviewLiteJsApi#scrollViewToIn(jalview.appletgui.AlignFrame,
\r
1128 * java.lang.String, java.lang.String)
\r
1130 public void scrollViewToIn(final AlignFrame alf, final String topRow,
\r
1131 final String leftHandColumn)
\r
1133 java.awt.EventQueue.invokeLater(new Runnable()
\r
1140 alf.scrollTo(new Integer(topRow).intValue(), new Integer(
\r
1141 leftHandColumn).intValue());
\r
1143 } catch (Exception ex)
\r
1145 System.err.println("Couldn't parse integer arguments (topRow='"
\r
1146 + topRow + "' and leftHandColumn='" + leftHandColumn
\r
1148 ex.printStackTrace();
\r
1158 * jalview.javascript.JalviewLiteJsApi#scrollViewToRowIn(jalview.appletgui
\r
1159 * .AlignFrame, java.lang.String)
\r
1162 public void scrollViewToRowIn(final AlignFrame alf, final String topRow)
\r
1165 java.awt.EventQueue.invokeLater(new Runnable()
\r
1172 alf.scrollToRow(new Integer(topRow).intValue());
\r
1174 } catch (Exception ex)
\r
1176 System.err.println("Couldn't parse integer arguments (topRow='"
\r
1178 ex.printStackTrace();
\r
1189 * jalview.javascript.JalviewLiteJsApi#scrollViewToColumnIn(jalview.appletgui
\r
1190 * .AlignFrame, java.lang.String)
\r
1193 public void scrollViewToColumnIn(final AlignFrame alf,
\r
1194 final String leftHandColumn)
\r
1196 java.awt.EventQueue.invokeLater(new Runnable()
\r
1204 alf.scrollToColumn(new Integer(leftHandColumn).intValue());
\r
1206 } catch (Exception ex)
\r
1209 .println("Couldn't parse integer arguments (leftHandColumn='"
\r
1210 + leftHandColumn + "')");
\r
1211 ex.printStackTrace();
\r
1218 // //////////////////////////////////////////////
\r
1219 // //////////////////////////////////////////////
\r
1221 public static int lastFrameX = 200;
\r
1223 public static int lastFrameY = 200;
\r
1225 boolean fileFound = true;
\r
1227 String file = "No file";
\r
1229 Button launcher = new Button("Start Jalview");
\r
1232 * The currentAlignFrame is static, it will change if and when the user
\r
1233 * selects a new window. Note that it will *never* point back to the embedded
\r
1234 * AlignFrame if the applet is started as embedded on the page and then
\r
1235 * afterwards a new view is created.
\r
1237 public AlignFrame currentAlignFrame = null;
\r
1240 * This is the first frame to be displayed, and does not change. API calls
\r
1241 * will default to this instance if currentAlignFrame is null.
\r
1243 AlignFrame initialAlignFrame = null;
\r
1245 boolean embedded = false;
\r
1247 private boolean checkForJmol = true;
\r
1249 private boolean checkedForJmol = false; // ensure we don't check for jmol
\r
1251 // every time the app is re-inited
\r
1253 public boolean jmolAvailable = false;
\r
1255 private boolean alignPdbStructures = false;
\r
1258 * use an external structure viewer exclusively (no jmols or MCViews will be
\r
1259 * opened by JalviewLite itself)
\r
1261 public boolean useXtrnalSviewer = false;
\r
1263 public static boolean debug = false;
\r
1265 static String builddate = null, version = null;
\r
1267 private static void initBuildDetails()
\r
1269 if (builddate == null)
\r
1271 builddate = "unknown";
\r
1273 java.net.URL url = JalviewLite.class
\r
1274 .getResource("/.build_properties");
\r
1279 BufferedReader reader = new BufferedReader(new InputStreamReader(
\r
1280 url.openStream()));
\r
1282 while ((line = reader.readLine()) != null)
\r
1284 if (line.indexOf("VERSION") > -1)
\r
1286 version = line.substring(line.indexOf("=") + 1);
\r
1288 if (line.indexOf("BUILD_DATE") > -1)
\r
1290 builddate = line.substring(line.indexOf("=") + 1);
\r
1293 } catch (Exception ex)
\r
1295 ex.printStackTrace();
\r
1301 public static String getBuildDate()
\r
1303 initBuildDetails();
\r
1307 public static String getVersion()
\r
1309 initBuildDetails();
\r
1313 // public JSObject scriptObject = null;
\r
1316 * init method for Jalview Applet
\r
1318 public void init()
\r
1320 // remove any handlers that might be hanging around from an earlier instance
\r
1325 System.err.println("Applet context is '"
\r
1326 + getAppletContext().getClass().toString() + "'");
\r
1328 JSObject scriptObject = JSObject.getWindow(this);
\r
1329 if (debug && scriptObject != null)
\r
1331 System.err.println("Applet has Javascript callback support.");
\r
1334 } catch (Exception ex)
\r
1337 .println("Warning: No JalviewLite javascript callbacks available.");
\r
1340 ex.printStackTrace();
\r
1344 * turn on extra applet debugging
\r
1346 String dbg = getParameter("debug");
\r
1349 debug = dbg.toLowerCase().equals("true");
\r
1354 System.err.println("JalviewLite Version " + getVersion());
\r
1355 System.err.println("Build Date : " + getBuildDate());
\r
1358 String externalsviewer = getParameter("externalstructureviewer");
\r
1359 if (externalsviewer != null)
\r
1361 useXtrnalSviewer = externalsviewer.trim().toLowerCase()
\r
1365 * if true disable the check for jmol
\r
1367 String chkforJmol = getParameter("nojmol");
\r
1368 if (chkforJmol != null)
\r
1370 checkForJmol = !chkforJmol.equals("true");
\r
1373 * get the separator parameter if present
\r
1375 String sep = getParameter("separator");
\r
1378 if (sep.length() > 0)
\r
1383 System.err.println("Separator set to '" + separator + "'");
\r
1389 "Invalid separator parameter - must be non-zero length");
\r
1395 String param = getParameter("RGB");
\r
1397 if (param != null)
\r
1401 r = Integer.parseInt(param.substring(0, 2), 16);
\r
1402 g = Integer.parseInt(param.substring(2, 4), 16);
\r
1403 b = Integer.parseInt(param.substring(4, 6), 16);
\r
1404 } catch (Exception ex)
\r
1411 param = getParameter("label");
\r
1412 if (param != null)
\r
1414 launcher.setLabel(param);
\r
1417 setBackground(new Color(r, g, b));
\r
1419 file = getParameter("file");
\r
1423 // Maybe the sequences are added as parameters
\r
1424 StringBuffer data = new StringBuffer("PASTE");
\r
1426 while ((file = getParameter("sequence" + i)) != null)
\r
1428 data.append(file.toString() + "\n");
\r
1431 if (data.length() > 5)
\r
1433 file = data.toString();
\r
1437 final JalviewLite jvapplet = this;
\r
1438 if (getParameter("embedded") != null
\r
1439 && getParameter("embedded").equalsIgnoreCase("true"))
\r
1441 // Launch as embedded applet in page
\r
1443 LoadingThread loader = new LoadingThread(file, jvapplet);
\r
1446 else if (file != null)
\r
1448 if (getParameter("showbutton") == null
\r
1449 || !getParameter("showbutton").equalsIgnoreCase("false"))
\r
1451 // Add the JalviewLite 'Button' to the page
\r
1453 launcher.addActionListener(new java.awt.event.ActionListener()
\r
1455 public void actionPerformed(ActionEvent e)
\r
1457 LoadingThread loader = new LoadingThread(file, jvapplet);
\r
1464 // Open jalviewLite immediately.
\r
1465 LoadingThread loader = new LoadingThread(file, jvapplet);
\r
1471 // jalview initialisation with no alignment. loadAlignment() method can
\r
1472 // still be called to open new alignments.
\r
1474 fileFound = false;
\r
1475 // callInitCallback();
\r
1479 private void callInitCallback()
\r
1481 String initjscallback = getParameter("oninit");
\r
1482 if (initjscallback == null)
\r
1486 initjscallback = initjscallback.trim();
\r
1487 if (initjscallback.length() > 0)
\r
1489 JSObject scriptObject = null;
\r
1492 scriptObject = JSObject.getWindow(this);
\r
1493 } catch (Exception ex)
\r
1497 if (scriptObject != null)
\r
1501 // do onInit with the JS executor thread
\r
1502 new JSFunctionExec(this).executeJavascriptFunction(true,
\r
1503 initjscallback, null, "Calling oninit callback '"
\r
1504 + initjscallback + "'.");
\r
1505 } catch (Exception e)
\r
1507 System.err.println("Exception when executing _oninit callback '"
\r
1508 + initjscallback + "'.");
\r
1509 e.printStackTrace();
\r
1514 System.err.println("Not executing _oninit callback '"
\r
1515 + initjscallback + "' - no scripting allowed.");
\r
1521 * Initialises and displays a new java.awt.Frame
\r
1524 * java.awt.Frame to be displayed
\r
1526 * title of new frame
\r
1528 * width if new frame
\r
1530 * height of new frame
\r
1532 public static void addFrame(final Frame frame, String title, int width,
\r
1535 frame.setLocation(lastFrameX, lastFrameY);
\r
1538 frame.setSize(width, height);
\r
1539 frame.setTitle(title);
\r
1540 frame.addWindowListener(new WindowAdapter()
\r
1542 public void windowClosing(WindowEvent e)
\r
1544 if (frame instanceof AlignFrame)
\r
1546 AlignViewport vp = ((AlignFrame) frame).viewport;
\r
1547 ((AlignFrame) frame).closeMenuItem_actionPerformed();
\r
1548 if (vp.applet.currentAlignFrame == frame)
\r
1550 vp.applet.currentAlignFrame = null;
\r
1558 if (frame instanceof EmbmenuFrame)
\r
1560 ((EmbmenuFrame) frame).destroyMenus();
\r
1562 frame.setMenuBar(null);
\r
1566 public void windowActivated(WindowEvent e)
\r
1568 if (frame instanceof AlignFrame)
\r
1570 ((AlignFrame) frame).viewport.applet.currentAlignFrame = (AlignFrame) frame;
\r
1573 System.err.println("Activated window " + frame);
\r
1577 super.windowActivated(e);
\r
1580 * Probably not necessary to do this - see TODO above. (non-Javadoc)
\r
1583 * java.awt.event.WindowAdapter#windowDeactivated(java.awt.event.WindowEvent
\r
1586 * public void windowDeactivated(WindowEvent e) { if (currentAlignFrame ==
\r
1587 * frame) { currentAlignFrame = null; if (debug) {
\r
1588 * System.err.println("Deactivated window "+frame); } }
\r
1589 * super.windowDeactivated(e); }
\r
1592 frame.setVisible(true);
\r
1596 * This paints the background surrounding the "Launch Jalview button" <br>
\r
1598 * If file given in parameter not found, displays error message
\r
1601 * graphics context
\r
1603 public void paint(Graphics g)
\r
1607 g.setColor(new Color(200, 200, 200));
\r
1608 g.setColor(Color.cyan);
\r
1609 g.fillRect(0, 0, getSize().width, getSize().height);
\r
1610 g.setColor(Color.red);
\r
1611 g.drawString("Jalview can't open file", 5, 15);
\r
1612 g.drawString("\"" + file + "\"", 5, 30);
\r
1614 else if (embedded)
\r
1616 g.setColor(Color.black);
\r
1617 g.setFont(new Font("Arial", Font.BOLD, 24));
\r
1618 g.drawString("Jalview Applet", 50, getSize().height / 2 - 30);
\r
1619 g.drawString("Loading Data...", 50, getSize().height / 2);
\r
1624 * get all components associated with the applet of the given type
\r
1629 public Vector getAppletWindow(Class class1)
\r
1631 Vector wnds = new Vector();
\r
1632 Component[] cmp = getComponents();
\r
1635 for (int i = 0; i < cmp.length; i++)
\r
1637 if (class1.isAssignableFrom(cmp[i].getClass()))
\r
1639 wnds.addElement(cmp);
\r
1646 class LoadJmolThread extends Thread
\r
1648 private boolean running = false;
\r
1652 if (running || checkedForJmol)
\r
1661 if (!System.getProperty("java.version").startsWith("1.1"))
\r
1663 Class.forName("org.jmol.adapter.smarter.SmarterJmolAdapter");
\r
1664 jmolAvailable = true;
\r
1666 if (!jmolAvailable)
\r
1669 .println("Jmol not available - Using MCview for structures");
\r
1671 } catch (java.lang.ClassNotFoundException ex)
\r
1677 jmolAvailable = false;
\r
1681 .println("Skipping Jmol check. Will use MCView (probably)");
\r
1684 checkedForJmol = true;
\r
1688 public boolean notFinished()
\r
1690 return running || !checkedForJmol;
\r
1694 class LoadingThread extends Thread
\r
1697 * State variable: File source
\r
1702 * State variable: protocol for access to file source
\r
1707 * State variable: format of file source
\r
1713 JalviewLite applet;
\r
1715 private void dbgMsg(String msg)
\r
1719 System.err.println(msg);
\r
1724 * update the protocol state variable for accessing the datasource located
\r
1728 * @return possibly updated datasource string
\r
1730 public String setProtocolState(String file)
\r
1732 if (file.startsWith("PASTE"))
\r
1734 file = file.substring(5);
\r
1735 protocol = AppletFormatAdapter.PASTE;
\r
1737 else if (inArchive(file))
\r
1739 protocol = AppletFormatAdapter.CLASSLOADER;
\r
1743 file = addProtocol(file);
\r
1744 protocol = AppletFormatAdapter.URL;
\r
1746 dbgMsg("Protocol identified as '" + protocol + "'");
\r
1750 public LoadingThread(String _file, JalviewLite _applet)
\r
1752 this._file = _file;
\r
1758 LoadJmolThread jmolchecker = new LoadJmolThread();
\r
1759 jmolchecker.start();
\r
1760 while (jmolchecker.notFinished())
\r
1762 // wait around until the Jmol check is complete.
\r
1766 } catch (Exception e)
\r
1772 // applet.callInitCallback();
\r
1775 private void startLoading()
\r
1777 AlignFrame newAlignFrame;
\r
1778 dbgMsg("Loading thread started with:\n>>file\n" + _file + ">>endfile");
\r
1779 file = setProtocolState(_file);
\r
1781 format = new jalview.io.IdentifyFile().Identify(file, protocol);
\r
1782 dbgMsg("File identified as '" + format + "'");
\r
1783 dbgMsg("Loading started.");
\r
1784 Alignment al = null;
\r
1787 al = new AppletFormatAdapter().readFile(file, protocol, format);
\r
1788 } catch (java.io.IOException ex)
\r
1790 dbgMsg("File load exception.");
\r
1791 ex.printStackTrace();
\r
1796 FileParse fp = new FileParse(file, protocol);
\r
1798 dbgMsg(">>>Dumping contents of '" + file + "' " + "("
\r
1799 + protocol + ")");
\r
1800 while ((ln = fp.nextLine()) != null)
\r
1804 dbgMsg(">>>Dump finished.");
\r
1805 } catch (Exception e)
\r
1808 .println("Exception when trying to dump the content of the file parameter.");
\r
1809 e.printStackTrace();
\r
1813 if ((al != null) && (al.getHeight() > 0))
\r
1815 dbgMsg("Successfully loaded file.");
\r
1816 newAlignFrame = new AlignFrame(al, applet, file, embedded);
\r
1817 if (initialAlignFrame == null)
\r
1819 initialAlignFrame = newAlignFrame;
\r
1821 // update the focus.
\r
1822 currentAlignFrame = newAlignFrame;
\r
1824 if (protocol == jalview.io.AppletFormatAdapter.PASTE)
\r
1826 newAlignFrame.setTitle("Sequences from " + applet.getDocumentBase());
\r
1829 newAlignFrame.statusBar.setText("Successfully loaded file " + file);
\r
1831 String treeFile = applet.getParameter("tree");
\r
1832 if (treeFile == null)
\r
1834 treeFile = applet.getParameter("treeFile");
\r
1837 if (treeFile != null)
\r
1841 treeFile = setProtocolState(treeFile);
\r
1843 * if (inArchive(treeFile)) { protocol =
\r
1844 * AppletFormatAdapter.CLASSLOADER; } else { protocol =
\r
1845 * AppletFormatAdapter.URL; treeFile = addProtocol(treeFile); }
\r
1847 jalview.io.NewickFile fin = new jalview.io.NewickFile(treeFile,
\r
1852 if (fin.getTree() != null)
\r
1854 newAlignFrame.loadTree(fin, treeFile);
\r
1855 dbgMsg("Successfuly imported tree.");
\r
1859 dbgMsg("Tree parameter did not resolve to a valid tree.");
\r
1861 } catch (Exception ex)
\r
1863 ex.printStackTrace();
\r
1869 * Try to load T-Coffee score file
\r
1871 String sScoreFile = applet.getParameter("scoreFile");
\r
1872 if( sScoreFile != null && !"".equals(sScoreFile) ) {
\r
1874 URL urlScore = new URL(sScoreFile);
\r
1875 newAlignFrame.loadScoreFile(urlScore);
\r
1878 catch( Exception e ) {
\r
1879 // TODO error message log (shows a warning dialogbox?)
\r
1880 System.err.printf("Cannot read score file: '%s'. Cause: %s \n", sScoreFile, e.getMessage());
\r
1885 // ///////////////////////////
\r
1886 // modify display of features
\r
1887 // we do this before any features have been loaded, ensuring any hidden groups are hidden when features first displayed
\r
1889 // hide specific groups
\r
1891 String param = applet.getParameter("hidefeaturegroups");
\r
1892 if (param != null)
\r
1894 newAlignFrame.setFeatureGroupState(separatorListToArray(param), false);
\r
1895 // applet.setFeatureGroupStateOn(newAlignFrame, param, false);
\r
1897 // show specific groups
\r
1898 param = applet.getParameter("showfeaturegroups");
\r
1899 if (param != null)
\r
1901 newAlignFrame.setFeatureGroupState(separatorListToArray(param), true);
\r
1902 // applet.setFeatureGroupStateOn(newAlignFrame, param, true);
\r
1904 // and now load features
\r
1905 param = applet.getParameter("features");
\r
1906 if (param != null)
\r
1908 param = setProtocolState(param);
\r
1910 newAlignFrame.parseFeaturesFile(param, protocol);
\r
1913 param = applet.getParameter("showFeatureSettings");
\r
1914 if (param != null && param.equalsIgnoreCase("true"))
\r
1916 newAlignFrame.viewport.showSequenceFeatures(true);
\r
1917 new FeatureSettings(newAlignFrame.alignPanel);
\r
1920 param = applet.getParameter("annotations");
\r
1921 if (param != null)
\r
1923 param = setProtocolState(param);
\r
1925 if (new AnnotationFile().readAnnotationFile(
\r
1926 newAlignFrame.viewport.getAlignment(), param, protocol))
\r
1928 newAlignFrame.alignPanel.fontChanged();
\r
1929 newAlignFrame.alignPanel.setScrollValues(0, 0);
\r
1934 .println("Annotations were not added from annotation file '"
\r
1940 param = applet.getParameter("jnetfile");
\r
1941 if (param != null)
\r
1945 param = setProtocolState(param);
\r
1946 jalview.io.JPredFile predictions = new jalview.io.JPredFile(
\r
1948 JnetAnnotationMaker.add_annotation(predictions,
\r
1949 newAlignFrame.viewport.getAlignment(), 0, false); // false==do
\r
1957 newAlignFrame.alignPanel.fontChanged();
\r
1958 newAlignFrame.alignPanel.setScrollValues(0, 0);
\r
1959 } catch (Exception ex)
\r
1961 ex.printStackTrace();
\r
1965 * <param name="alignpdbfiles" value="false/true"/> Undocumented for 2.6
\r
1966 * - related to JAL-434
\r
1968 applet.setAlignPdbStructures(getDefaultParameter("alignpdbfiles",
\r
1971 * <param name="PDBfile" value="1gaq.txt PDB|1GAQ|1GAQ|A PDB|1GAQ|1GAQ|B
\r
1972 * PDB|1GAQ|1GAQ|C">
\r
1974 * <param name="PDBfile2" value="1gaq.txt A=SEQA B=SEQB C=SEQB">
\r
1976 * <param name="PDBfile3" value="1q0o Q45135_9MICO">
\r
1979 int pdbFileCount = 0;
\r
1980 // Accumulate pdbs here if they are heading for the same view (if
\r
1981 // alignPdbStructures is true)
\r
1982 Vector pdbs = new Vector();
\r
1983 // create a lazy matcher if we're asked to
\r
1984 jalview.analysis.SequenceIdMatcher matcher = (applet
\r
1985 .getDefaultParameter("relaxedidmatch", false)) ? new jalview.analysis.SequenceIdMatcher(
\r
1986 newAlignFrame.getAlignViewport().getAlignment()
\r
1987 .getSequencesArray()) : null;
\r
1991 if (pdbFileCount > 0)
\r
1993 param = applet.getParameter("PDBFILE" + pdbFileCount);
\r
1997 param = applet.getParameter("PDBFILE");
\r
2000 if (param != null)
\r
2002 PDBEntry pdb = new PDBEntry();
\r
2005 SequenceI[] seqs = null;
\r
2006 String[] chains = null;
\r
2008 StringTokenizer st = new StringTokenizer(param, " ");
\r
2010 if (st.countTokens() < 2)
\r
2012 String sequence = applet.getParameter("PDBSEQ");
\r
2013 if (sequence != null)
\r
2014 seqs = new SequenceI[]
\r
2015 { matcher == null ? (Sequence) newAlignFrame
\r
2016 .getAlignViewport().getAlignment()
\r
2017 .findName(sequence) : matcher.findIdMatch(sequence) };
\r
2022 param = st.nextToken();
\r
2023 Vector tmp = new Vector();
\r
2024 Vector tmp2 = new Vector();
\r
2026 while (st.hasMoreTokens())
\r
2028 seqstring = st.nextToken();
\r
2029 StringTokenizer st2 = new StringTokenizer(seqstring, "=");
\r
2030 if (st2.countTokens() > 1)
\r
2032 // This is the chain
\r
2033 tmp2.addElement(st2.nextToken());
\r
2034 seqstring = st2.nextToken();
\r
2036 tmp.addElement(matcher == null ? (Sequence) newAlignFrame
\r
2037 .getAlignViewport().getAlignment()
\r
2038 .findName(seqstring) : matcher
\r
2039 .findIdMatch(seqstring));
\r
2042 seqs = new SequenceI[tmp.size()];
\r
2043 tmp.copyInto(seqs);
\r
2044 if (tmp2.size() == tmp.size())
\r
2046 chains = new String[tmp2.size()];
\r
2047 tmp2.copyInto(chains);
\r
2050 param = setProtocolState(param);
\r
2052 if (// !jmolAvailable
\r
2054 protocol == AppletFormatAdapter.CLASSLOADER
\r
2055 && !useXtrnalSviewer)
\r
2057 // Re: JAL-357 : the bug isn't a problem if we are using an
\r
2058 // external viewer!
\r
2059 // TODO: verify this Re:
\r
2060 // https://mantis.lifesci.dundee.ac.uk/view.php?id=36605
\r
2061 // This exception preserves the current behaviour where, even if
\r
2062 // the local pdb file was identified in the class loader
\r
2063 protocol = AppletFormatAdapter.URL; // this is probably NOT
\r
2065 param = addProtocol(param); //
\r
2068 pdb.setFile(param);
\r
2072 for (int i = 0; i < seqs.length; i++)
\r
2074 if (seqs[i] != null)
\r
2076 ((Sequence) seqs[i]).addPDBId(pdb);
\r
2080 if (JalviewLite.debug)
\r
2082 // this may not really be a problem but we give a warning
\r
2085 .println("Warning: Possible input parsing error: Null sequence for attachment of PDB (sequence "
\r
2091 if (!alignPdbStructures)
\r
2093 newAlignFrame.newStructureView(applet, pdb, seqs, chains,
\r
2098 pdbs.addElement(new Object[]
\r
2099 { pdb, seqs, chains, new String(protocol) });
\r
2105 } while (param != null || pdbFileCount < 10);
\r
2106 if (pdbs.size() > 0)
\r
2108 SequenceI[][] seqs = new SequenceI[pdbs.size()][];
\r
2109 PDBEntry[] pdb = new PDBEntry[pdbs.size()];
\r
2110 String[][] chains = new String[pdbs.size()][];
\r
2111 String[] protocols = new String[pdbs.size()];
\r
2112 for (int pdbsi = 0, pdbsiSize = pdbs.size(); pdbsi < pdbsiSize; pdbsi++)
\r
2114 Object[] o = (Object[]) pdbs.elementAt(pdbsi);
\r
2115 pdb[pdbsi] = (PDBEntry) o[0];
\r
2116 seqs[pdbsi] = (SequenceI[]) o[1];
\r
2117 chains[pdbsi] = (String[]) o[2];
\r
2118 protocols[pdbsi] = (String) o[3];
\r
2120 newAlignFrame.alignedStructureView(applet, pdb, seqs, chains,
\r
2127 fileFound = false;
\r
2128 applet.remove(launcher);
\r
2131 callInitCallback();
\r
2135 * Discovers whether the given file is in the Applet Archive
\r
2141 boolean inArchive(String file)
\r
2143 // This might throw a security exception in certain browsers
\r
2144 // Netscape Communicator for instance.
\r
2147 boolean rtn = (getClass().getResourceAsStream("/" + file) != null);
\r
2150 System.err.println("Resource '" + file + "' was "
\r
2151 + (rtn ? "" : "not") + " located by classloader.");
\r
2154 } catch (Exception ex)
\r
2156 System.out.println("Exception checking resources: " + file + " "
\r
2162 String addProtocol(String file)
\r
2164 if (file.indexOf("://") == -1)
\r
2166 String fl = applet.resolveUrlForLocalOrAbsolute(file,
\r
2167 getDocumentBase());
\r
2170 if (new java.net.URL(fl).openStream() != null)
\r
2174 System.err.println("Prepended document base for resource: '"
\r
2179 } catch (Exception x)
\r
2183 fl = applet.resolveUrlForLocalOrAbsolute(file, getCodeBase());
\r
2186 if (new java.net.URL(fl).openStream() != null)
\r
2190 System.err.println("Prepended codebase for resource: '"
\r
2195 } catch (Exception x)
\r
2207 * @return the default alignFrame acted on by the public applet methods. May
\r
2208 * return null with an error message on System.err indicating the
\r
2211 public AlignFrame getDefaultTargetFrame()
\r
2213 if (currentAlignFrame != null)
\r
2215 return currentAlignFrame;
\r
2217 if (initialAlignFrame != null)
\r
2219 return initialAlignFrame;
\r
2222 .println("Implementation error: Jalview Applet API cannot work out which AlignFrame to use.");
\r
2227 * separator used for separatorList
\r
2229 protected String separator = "" + ((char) 0x00AC); // the default used to be
\r
2230 // '|' but many sequence
\r
2231 // IDS include pipes.
\r
2234 * set to enable the URL based javascript execution mechanism
\r
2236 public boolean jsfallbackEnabled = false;
\r
2239 * parse the string into a list
\r
2242 * @return elements separated by separator
\r
2244 public String[] separatorListToArray(String list)
\r
2246 return separatorListToArray(list, separator);
\r
2250 * parse the string into a list
\r
2253 * @param separator
\r
2254 * @return elements separated by separator
\r
2256 public String[] separatorListToArray(String list, String separator)
\r
2258 // note separator local variable intentionally masks object field
\r
2259 int seplen = separator.length();
\r
2260 if (list == null || list.equals("") || list.equals(separator))
\r
2262 java.util.Vector jv = new Vector();
\r
2264 while ((pos = list.indexOf(separator, cp)) > cp)
\r
2266 jv.addElement(list.substring(cp, pos));
\r
2267 cp = pos + seplen;
\r
2269 if (cp < list.length())
\r
2271 String c = list.substring(cp);
\r
2272 if (!c.equals(separator))
\r
2277 if (jv.size() > 0)
\r
2279 String[] v = new String[jv.size()];
\r
2280 for (int i = 0; i < v.length; i++)
\r
2282 v[i] = (String) jv.elementAt(i);
\r
2284 jv.removeAllElements();
\r
2287 System.err.println("Array from '" + separator
\r
2288 + "' separated List:\n" + v.length);
\r
2289 for (int i = 0; i < v.length; i++)
\r
2291 System.err.println("item " + i + " '" + v[i] + "'");
\r
2298 System.err.println("Empty Array from '" + separator
\r
2299 + "' separated List");
\r
2305 * concatenate the list with separator
\r
2308 * @return concatenated string
\r
2310 public String arrayToSeparatorList(String[] list)
\r
2312 return arrayToSeparatorList(list, separator);
\r
2316 * concatenate the list with separator
\r
2319 * @param separator
\r
2320 * @return concatenated string
\r
2322 public String arrayToSeparatorList(String[] list, String separator)
\r
2324 StringBuffer v = new StringBuffer();
\r
2325 if (list != null && list.length > 0)
\r
2327 for (int i = 0, iSize = list.length; i < iSize; i++)
\r
2329 if (list[i] != null)
\r
2333 v.append(separator);
\r
2335 v.append(list[i]);
\r
2340 System.err.println("Returning '" + separator
\r
2341 + "' separated List:\n");
\r
2342 System.err.println(v);
\r
2344 return v.toString();
\r
2348 System.err.println("Returning empty '" + separator
\r
2349 + "' separated List\n");
\r
2351 return "" + separator;
\r
2357 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroups()
\r
2359 public String getFeatureGroups()
\r
2361 String lst = arrayToSeparatorList(getDefaultTargetFrame()
\r
2362 .getFeatureGroups());
\r
2370 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOn(jalview.appletgui.AlignFrame
\r
2373 public String getFeatureGroupsOn(AlignFrame alf)
\r
2375 String lst = arrayToSeparatorList(alf.getFeatureGroups());
\r
2382 * @see jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfState(boolean)
\r
2384 public String getFeatureGroupsOfState(boolean visible)
\r
2386 return arrayToSeparatorList(getDefaultTargetFrame()
\r
2387 .getFeatureGroupsOfState(visible));
\r
2394 * jalview.bin.JalviewLiteJsApi#getFeatureGroupsOfStateOn(jalview.appletgui
\r
2395 * .AlignFrame, boolean)
\r
2397 public String getFeatureGroupsOfStateOn(AlignFrame alf, boolean visible)
\r
2399 return arrayToSeparatorList(alf.getFeatureGroupsOfState(visible));
\r
2405 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupStateOn(jalview.appletgui.
\r
2406 * AlignFrame, java.lang.String, boolean)
\r
2408 public void setFeatureGroupStateOn(final AlignFrame alf,
\r
2409 final String groups, boolean state)
\r
2411 final boolean st = state;// !(state==null || state.equals("") ||
\r
2412 // state.toLowerCase().equals("false"));
\r
2413 java.awt.EventQueue.invokeLater(new Runnable()
\r
2418 alf.setFeatureGroupState(separatorListToArray(groups), st);
\r
2426 * @see jalview.bin.JalviewLiteJsApi#setFeatureGroupState(java.lang.String,
\r
2429 public void setFeatureGroupState(String groups, boolean state)
\r
2431 setFeatureGroupStateOn(getDefaultTargetFrame(), groups, state);
\r
2437 * @see jalview.bin.JalviewLiteJsApi#getSeparator()
\r
2439 public String getSeparator()
\r
2447 * @see jalview.bin.JalviewLiteJsApi#setSeparator(java.lang.String)
\r
2449 public void setSeparator(String separator)
\r
2451 if (separator == null || separator.length() < 1)
\r
2453 // reset to default
\r
2454 separator = "" + ((char) 0x00AC);
\r
2456 this.separator = separator;
\r
2459 System.err.println("Default Separator now: '" + separator + "'");
\r
2464 * get boolean value of applet parameter 'name' and return default if
\r
2465 * parameter is not set
\r
2468 * name of paremeter
\r
2470 * the value to return otherwise
\r
2471 * @return true or false
\r
2473 public boolean getDefaultParameter(String name, boolean def)
\r
2476 if ((stn = getParameter(name)) == null)
\r
2480 if (stn.toLowerCase().equals("true"))
\r
2490 * @see jalview.bin.JalviewLiteJsApi#addPdbFile(jalview.appletgui.AlignFrame,
\r
2491 * java.lang.String, java.lang.String, java.lang.String)
\r
2493 public boolean addPdbFile(AlignFrame alFrame, String sequenceId,
\r
2494 String pdbEntryString, String pdbFile)
\r
2496 return alFrame.addPdbFile(sequenceId, pdbEntryString, pdbFile);
\r
2499 protected void setAlignPdbStructures(boolean alignPdbStructures)
\r
2501 this.alignPdbStructures = alignPdbStructures;
\r
2504 public boolean isAlignPdbStructures()
\r
2506 return alignPdbStructures;
\r
2509 public void start()
\r
2511 // callInitCallback();
\r
2514 private Hashtable<String, long[]> jshashes = new Hashtable<String, long[]>();
\r
2516 private Hashtable<String, Hashtable<String, String[]>> jsmessages = new Hashtable<String, Hashtable<String, String[]>>();
\r
2518 public void setJsMessageSet(String messageclass, String viewId,
\r
2519 String[] colcommands)
\r
2521 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
\r
2522 if (msgset == null)
\r
2524 msgset = new Hashtable<String, String[]>();
\r
2525 jsmessages.put(messageclass, msgset);
\r
2527 msgset.put(viewId, colcommands);
\r
2528 long[] l = new long[colcommands.length];
\r
2529 for (int i = 0; i < colcommands.length; i++)
\r
2531 l[i] = colcommands[i].hashCode();
\r
2533 jshashes.put(messageclass + "|" + viewId, l);
\r
2539 * @see jalview.bin.JalviewLiteJsApi#getJsMessage(java.lang.String,
\r
2540 * java.lang.String)
\r
2542 public String getJsMessage(String messageclass, String viewId)
\r
2544 Hashtable<String, String[]> msgset = jsmessages.get(messageclass);
\r
2545 if (msgset != null)
\r
2547 String[] msgs = msgset.get(viewId);
\r
2550 for (int i = 0; i < msgs.length; i++)
\r
2552 if (msgs[i] != null)
\r
2554 String m = msgs[i];
\r
2564 public boolean isJsMessageSetChanged(String string, String string2,
\r
2565 String[] colcommands)
\r
2567 long[] l = jshashes.get(string + "|" + string2);
\r
2568 if (l == null && colcommands != null)
\r
2572 for (int i = 0; i < colcommands.length; i++)
\r
2574 if (l[i] != colcommands[i].hashCode())
\r
2582 private Vector jsExecQueue = new Vector();
\r
2584 public Vector getJsExecQueue()
\r
2586 return jsExecQueue;
\r
2589 public void setExecutor(JSFunctionExec jsFunctionExec2)
\r
2591 jsFunctionExec = jsFunctionExec2;
\r
2595 * return the given colour value parameter or the given default if parameter
\r
2599 * @param defcolour
\r
2602 public Color getDefaultColourParameter(String colparam, Color defcolour)
\r
2604 String colprop = getParameter(colparam);
\r
2605 if (colprop == null || colprop.trim().length() == 0)
\r
2609 Color col = jalview.schemes.ColourSchemeProperty
\r
2610 .getAWTColorFromName(colprop);
\r
2615 col = new jalview.schemes.UserColourScheme(colprop).findColour('A');
\r
2616 } catch (Exception ex)
\r
2618 System.err.println("Couldn't parse '" + colprop
\r
2619 + "' as a colour for " + colparam);
\r
2623 return (col == null) ? defcolour : col;
\r
2627 public void openJalviewHelpUrl()
\r
2629 String helpUrl = getParameter("jalviewhelpurl");
\r
2630 if (helpUrl == null || helpUrl.trim().length() < 5)
\r
2632 helpUrl = "http://www.jalview.org/help.html";
\r
2634 showURL(helpUrl, "HELP");
\r
2638 * form a complete URL given a path to a resource and a reference location on
\r
2642 * - an absolute path on the same server as localref or a document
\r
2643 * located relative to localref
\r
2645 * - a URL on the same server as url
\r
2646 * @return a complete URL for the resource located by url
\r
2648 private String resolveUrlForLocalOrAbsolute(String url, URL localref)
\r
2650 String codebase = localref.toString();
\r
2651 if (url.indexOf("/") == 0)
\r
2653 url = codebase.substring(0, codebase.length()
\r
2654 - localref.getFile().length())
\r
2659 url = localref + url;
\r
2665 * open a URL in the browser - resolving it according to relative refs and
\r
2666 * coping with javascript: protocol if necessary.
\r
2671 public void showURL(String url, String target)
\r
2675 if (url.indexOf(":") == -1)
\r
2677 // TODO: verify (Bas Vroling bug) prepend codebase or server URL to
\r
2679 // Should really use docbase, not codebase.
\r
2681 url = resolveUrlForLocalOrAbsolute(
\r
2683 prepend = getDefaultParameter("resolvetocodebase", false) ? getDocumentBase()
\r
2688 .println("Show url (prepended "
\r
2690 + " - toggle resolvetocodebase if code/docbase resolution is wrong): "
\r
2698 System.err.println("Show url: " + url);
\r
2701 if (url.indexOf("javascript:") == 0)
\r
2703 // no target for the javascript context
\r
2704 getAppletContext().showDocument(new java.net.URL(url));
\r
2708 getAppletContext().showDocument(new java.net.URL(url), target);
\r
2710 } catch (Exception ex)
\r
2712 ex.printStackTrace();
\r
2717 * bind structures in a viewer to any matching sequences in an alignFrame (use
\r
2718 * sequenceIds to limit scope of search to specific sequences)
\r
2722 * @param sequenceIds
\r
2723 * @return TODO: consider making an exception structure for indicating when
\r
2724 * binding fails public SequenceStructureBinding
\r
2725 * addStructureViewInstance( AlignFrame alFrame, Object viewer, String
\r
2728 * if (sequenceIds != null && sequenceIds.length() > 0) { return
\r
2729 * alFrame.addStructureViewInstance(viewer,
\r
2730 * separatorListToArray(sequenceIds)); } else { return
\r
2731 * alFrame.addStructureViewInstance(viewer, null); } // return null; }
\r