2 * Jalview - A Sequence Alignment Editor and Viewer
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3 * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
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5 * This program is free software; you can redistribute it and/or
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6 * modify it under the terms of the GNU General Public License
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7 * as published by the Free Software Foundation; either version 2
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8 * of the License, or (at your option) any later version.
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10 * This program is distributed in the hope that it will be useful,
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11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
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12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
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13 * GNU General Public License for more details.
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15 * You should have received a copy of the GNU General Public License
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16 * along with this program; if not, write to the Free Software
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17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
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19 package jalview.datamodel;
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21 import jalview.analysis.*;
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23 import jalview.schemes.*;
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34 * @version $Revision$
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36 public class SequenceGroup
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40 Conservation conserve;
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42 boolean displayBoxes = true;
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43 boolean displayText = true;
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44 boolean colourText = true;
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45 private Vector sequences = new Vector();
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48 /** DOCUMENT ME!! */
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49 public ColourSchemeI cs;
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52 Color outlineColour = Color.black;
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53 public int thresholdTextColour = 0;
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54 public Color textColour = Color.black;
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55 public Color textColour2 = Color.white;
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59 * Creates a new SequenceGroup object.
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61 public SequenceGroup()
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63 groupName = "JGroup:"+this.hashCode();
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67 * Creates a new SequenceGroup object.
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69 * @param sequences DOCUMENT ME!
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70 * @param groupName DOCUMENT ME!
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71 * @param scheme DOCUMENT ME!
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72 * @param displayBoxes DOCUMENT ME!
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73 * @param displayText DOCUMENT ME!
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74 * @param colourText DOCUMENT ME!
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75 * @param start DOCUMENT ME!
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76 * @param end DOCUMENT ME!
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78 public SequenceGroup(Vector sequences, String groupName,
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79 ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
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80 boolean colourText, int start, int end)
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82 this.sequences = sequences;
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83 this.groupName = groupName;
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84 this.displayBoxes = displayBoxes;
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85 this.displayText = displayText;
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86 this.colourText = colourText;
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90 recalcConservation();
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93 public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
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95 int iSize = sequences.size();
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96 SequenceI [] seqs = new SequenceI[iSize];
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97 SequenceI [] inorder = getSequencesInOrder(align);
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100 for (int i = 0; i < iSize; i++)
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102 SequenceI seq = inorder[i];
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104 seqs[i] = new Sequence(seq.getName(),
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105 seq.getSequence(startRes, endRes + 1),
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106 seq.findPosition(startRes),
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109 seqs[i].setDescription(seq.getDescription());
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110 seqs[i].setDBRef(seq.getDBRef());
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111 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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112 if (seq.getDatasetSequence() != null)
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113 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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115 if(seq.getAnnotation()!=null)
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117 for(int a=0; a<seq.getAnnotation().length; a++)
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118 seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
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127 * If sequence ends in gaps, the end residue can
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128 * be correctly calculated here
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129 * @param seq SequenceI
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132 public int findEndRes(SequenceI seq)
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137 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
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139 ch = seq.getCharAt(j);
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140 if (!jalview.util.Comparison.isGap( (ch)))
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148 eres += seq.getStart() - 1;
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154 public Vector getSequences(Hashtable hiddenReps)
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156 if(hiddenReps == null)
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160 Vector allSequences = new Vector();
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161 SequenceI seq, seq2;
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162 for (int i = 0; i < sequences.size(); i++)
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164 seq = (SequenceI) sequences.elementAt(i);
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165 allSequences.addElement(seq);
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166 if (hiddenReps.containsKey(seq) )
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168 SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);
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169 for (int h = 0; h < hsg.getSize(); h++)
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171 seq2 = hsg.getSequenceAt(h);
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173 && !allSequences.contains(seq2))
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174 allSequences.addElement(seq2);
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179 return allSequences;
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183 public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
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185 Vector tmp = getSequences(hiddenReps);
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188 SequenceI [] result = new SequenceI[tmp.size()];
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189 for(int i=0; i<result.length; i++)
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190 result[i] = (SequenceI)tmp.elementAt(i);
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198 * @param col DOCUMENT ME!
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200 * @return DOCUMENT ME!
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202 public boolean adjustForRemoveLeft(int col)
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204 // return value is true if the group still exists
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205 if (startRes >= col)
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207 startRes = startRes - col;
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212 endRes = endRes - col;
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214 if (startRes > endRes)
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221 // must delete this group!!
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231 * @param col DOCUMENT ME!
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233 * @return DOCUMENT ME!
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235 public boolean adjustForRemoveRight(int col)
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237 if (startRes > col)
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239 // delete this group
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254 * @return DOCUMENT ME!
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256 public String getName()
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261 public String getDescription()
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263 return description;
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269 * @param name DOCUMENT ME!
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271 public void setName(String name)
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276 public void setDescription(String desc)
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278 description = desc;
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284 * @return DOCUMENT ME!
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286 public Conservation getConservation()
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294 * @param c DOCUMENT ME!
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296 public void setConservation(Conservation c)
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304 * @param s DOCUMENT ME!
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305 * @param recalc DOCUMENT ME!
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307 public void addSequence(SequenceI s, boolean recalc)
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309 if (s!=null && !sequences.contains(s))
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311 sequences.addElement(s);
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316 recalcConservation();
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323 public void recalcConservation()
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330 cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
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332 if (cs instanceof ClustalxColourScheme)
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334 ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
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337 if (cs.conservationApplied())
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339 Conservation c = new Conservation(groupName,
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340 ResidueProperties.propHash, 3, sequences,
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341 startRes, endRes+1);
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343 c.verdict(false, 25);
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345 cs.setConservation(c);
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347 if (cs instanceof ClustalxColourScheme)
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349 ( (ClustalxColourScheme) cs).resetClustalX(sequences,
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354 catch (java.lang.OutOfMemoryError err)
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356 System.out.println("Out of memory loading groups: " + err);
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364 * @param s DOCUMENT ME!
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365 * @param recalc DOCUMENT ME!
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367 public void addOrRemove(SequenceI s, boolean recalc)
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369 if (sequences.contains(s))
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371 deleteSequence(s, recalc);
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375 addSequence(s, recalc);
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382 * @param s DOCUMENT ME!
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383 * @param recalc DOCUMENT ME!
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385 public void deleteSequence(SequenceI s, boolean recalc)
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387 sequences.removeElement(s);
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391 recalcConservation();
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398 * @return DOCUMENT ME!
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400 public int getStartRes()
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408 * @return DOCUMENT ME!
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410 public int getEndRes()
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418 * @param i DOCUMENT ME!
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420 public void setStartRes(int i)
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428 * @param i DOCUMENT ME!
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430 public void setEndRes(int i)
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438 * @return DOCUMENT ME!
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440 public int getSize()
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442 return sequences.size();
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448 * @param i DOCUMENT ME!
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450 * @return DOCUMENT ME!
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452 public SequenceI getSequenceAt(int i)
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454 return (SequenceI) sequences.elementAt(i);
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460 * @param state DOCUMENT ME!
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462 public void setColourText(boolean state)
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464 colourText = state;
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470 * @return DOCUMENT ME!
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472 public boolean getColourText()
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480 * @param state DOCUMENT ME!
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482 public void setDisplayText(boolean state)
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484 displayText = state;
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490 * @return DOCUMENT ME!
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492 public boolean getDisplayText()
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494 return displayText;
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500 * @param state DOCUMENT ME!
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502 public void setDisplayBoxes(boolean state)
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504 displayBoxes = state;
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510 * @return DOCUMENT ME!
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512 public boolean getDisplayBoxes()
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514 return displayBoxes;
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520 * @return DOCUMENT ME!
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522 public int getWidth()
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524 // MC This needs to get reset when characters are inserted and deleted
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525 if (sequences.size() > 0)
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527 width = ((SequenceI) sequences.elementAt(0)).getLength();
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530 for (int i = 1; i < sequences.size(); i++)
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532 SequenceI seq = (SequenceI) sequences.elementAt(i);
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534 if (seq.getLength() > width)
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536 width = seq.getLength();
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546 * @param c DOCUMENT ME!
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548 public void setOutlineColour(Color c)
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556 * @return DOCUMENT ME!
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558 public Color getOutlineColour()
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560 return outlineColour;
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565 * returns the sequences in the group ordered by the ordering given by al
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567 * @param al Alignment
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568 * @return SequenceI[]
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570 public SequenceI[] getSequencesInOrder(AlignmentI al)
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572 int sSize = sequences.size();
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573 int alHeight = al.getHeight();
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575 SequenceI[] seqs = new SequenceI[sSize];
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578 for (int i = 0; i < alHeight && index<sSize; i++)
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580 if(sequences.contains( al.getSequenceAt(i) ) )
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581 seqs[index++] = al.getSequenceAt(i);
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