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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39 Conservation conserve;
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41 boolean displayBoxes;
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42 boolean displayText;
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44 private Vector sequences = new Vector();
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47 /** DOCUMENT ME!! */
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48 public ColourSchemeI cs;
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51 Color outlineColour = Color.black;
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52 public int thresholdTextColour = 0;
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53 public Color textColour = Color.black;
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54 public Color textColour2 = Color.white;
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58 * Creates a new SequenceGroup object.
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60 public SequenceGroup()
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62 groupName = "Group";
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63 this.displayBoxes = true;
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64 this.displayText = true;
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65 this.colourText = false;
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70 * Creates a new SequenceGroup object.
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72 * @param sequences DOCUMENT ME!
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73 * @param groupName DOCUMENT ME!
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74 * @param scheme DOCUMENT ME!
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75 * @param displayBoxes DOCUMENT ME!
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76 * @param displayText DOCUMENT ME!
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77 * @param colourText DOCUMENT ME!
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78 * @param start DOCUMENT ME!
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79 * @param end DOCUMENT ME!
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81 public SequenceGroup(Vector sequences, String groupName,
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82 ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
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83 boolean colourText, int start, int end)
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85 this.sequences = sequences;
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86 this.groupName = groupName;
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87 this.displayBoxes = displayBoxes;
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88 this.displayText = displayText;
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89 this.colourText = colourText;
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93 recalcConservation();
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97 * Creates a new SequenceGroup object.
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99 * @param groupName DOCUMENT ME!
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100 * @param scheme DOCUMENT ME!
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101 * @param displayBoxes DOCUMENT ME!
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102 * @param displayText DOCUMENT ME!
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103 * @param colourText DOCUMENT ME!
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104 * @param start DOCUMENT ME!
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105 * @param end DOCUMENT ME!
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107 public SequenceGroup(String groupName, ColourSchemeI scheme,
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108 boolean displayBoxes, boolean displayText, boolean colourText,
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109 int start, int end)
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111 this.groupName = groupName;
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112 this.displayBoxes = displayBoxes;
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113 this.displayText = displayText;
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114 this.colourText = colourText;
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120 public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
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122 int iSize = sequences.size();
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123 SequenceI [] seqs = new SequenceI[iSize];
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124 SequenceI [] inorder = getSequencesInOrder(align);
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127 for (int i = 0; i < iSize; i++)
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129 SequenceI seq = inorder[i];
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131 seqs[i] = new Sequence(seq.getName(),
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132 seq.getSequence(startRes, endRes + 1),
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133 seq.findPosition(startRes),
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136 seqs[i].setDescription(seq.getDescription());
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137 seqs[i].setDBRef(seq.getDBRef());
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138 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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139 if (seq.getDatasetSequence() != null)
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140 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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142 if(seq.getAnnotation()!=null)
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144 for(int a=0; a<seq.getAnnotation().length; a++)
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145 seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
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154 * If sequence ends in gaps, the end residue can
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155 * be correctly calculated here
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156 * @param seq SequenceI
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159 public int findEndRes(SequenceI seq)
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164 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
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166 ch = seq.getCharAt(j);
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167 if (!jalview.util.Comparison.isGap( (ch)))
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175 eres += seq.getStart() - 1;
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181 public Vector getSequences(Hashtable hiddenReps)
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183 if(hiddenReps == null)
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187 Vector allSequences = new Vector();
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188 SequenceI seq, seq2;
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189 for (int i = 0; i < sequences.size(); i++)
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191 seq = (SequenceI) sequences.elementAt(i);
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192 allSequences.addElement(seq);
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193 if (hiddenReps.containsKey(seq) )
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195 SequenceGroup hsg = (SequenceGroup)hiddenReps.get(seq);
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196 for (int h = 0; h < hsg.getSize(); h++)
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198 seq2 = hsg.getSequenceAt(h);
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200 && !allSequences.contains(seq2))
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201 allSequences.addElement(seq2);
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206 return allSequences;
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210 public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
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212 Vector tmp = getSequences(hiddenReps);
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215 SequenceI [] result = new SequenceI[tmp.size()];
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216 for(int i=0; i<result.length; i++)
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217 result[i] = (SequenceI)tmp.elementAt(i);
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225 * @param col DOCUMENT ME!
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227 * @return DOCUMENT ME!
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229 public boolean adjustForRemoveLeft(int col)
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231 // return value is true if the group still exists
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232 if (startRes >= col)
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234 startRes = startRes - col;
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239 endRes = endRes - col;
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241 if (startRes > endRes)
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248 // must delete this group!!
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258 * @param col DOCUMENT ME!
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260 * @return DOCUMENT ME!
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262 public boolean adjustForRemoveRight(int col)
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264 if (startRes > col)
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266 // delete this group
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281 * @return DOCUMENT ME!
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283 public String getName()
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291 * @param name DOCUMENT ME!
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293 public void setName(String name)
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301 * @return DOCUMENT ME!
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303 public Conservation getConservation()
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311 * @param c DOCUMENT ME!
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313 public void setConservation(Conservation c)
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321 * @param s DOCUMENT ME!
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322 * @param recalc DOCUMENT ME!
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324 public void addSequence(SequenceI s, boolean recalc)
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326 if (s!=null && !sequences.contains(s))
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328 sequences.addElement(s);
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333 recalcConservation();
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340 public void recalcConservation()
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347 cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
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349 if (cs instanceof ClustalxColourScheme)
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351 ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
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354 if (cs.conservationApplied())
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356 Conservation c = new Conservation(groupName,
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357 ResidueProperties.propHash, 3, sequences,
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358 startRes, endRes+1);
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360 c.verdict(false, 25);
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362 cs.setConservation(c);
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364 if (cs instanceof ClustalxColourScheme)
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366 ( (ClustalxColourScheme) cs).resetClustalX(sequences,
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371 catch (java.lang.OutOfMemoryError err)
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373 System.out.println("Out of memory loading groups: " + err);
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381 * @param s DOCUMENT ME!
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382 * @param recalc DOCUMENT ME!
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384 public void addOrRemove(SequenceI s, boolean recalc)
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386 if (sequences.contains(s))
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388 deleteSequence(s, recalc);
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392 addSequence(s, recalc);
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399 * @param s DOCUMENT ME!
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400 * @param recalc DOCUMENT ME!
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402 public void deleteSequence(SequenceI s, boolean recalc)
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404 sequences.removeElement(s);
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408 recalcConservation();
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415 * @return DOCUMENT ME!
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417 public int getStartRes()
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425 * @return DOCUMENT ME!
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427 public int getEndRes()
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435 * @param i DOCUMENT ME!
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437 public void setStartRes(int i)
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445 * @param i DOCUMENT ME!
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447 public void setEndRes(int i)
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455 * @return DOCUMENT ME!
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457 public int getSize()
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459 return sequences.size();
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465 * @param i DOCUMENT ME!
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467 * @return DOCUMENT ME!
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469 public SequenceI getSequenceAt(int i)
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471 return (SequenceI) sequences.elementAt(i);
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477 * @param state DOCUMENT ME!
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479 public void setColourText(boolean state)
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481 colourText = state;
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487 * @return DOCUMENT ME!
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489 public boolean getColourText()
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497 * @param state DOCUMENT ME!
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499 public void setDisplayText(boolean state)
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501 displayText = state;
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507 * @return DOCUMENT ME!
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509 public boolean getDisplayText()
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511 return displayText;
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517 * @param state DOCUMENT ME!
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519 public void setDisplayBoxes(boolean state)
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521 displayBoxes = state;
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527 * @return DOCUMENT ME!
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529 public boolean getDisplayBoxes()
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531 return displayBoxes;
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537 * @return DOCUMENT ME!
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539 public int getWidth()
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541 // MC This needs to get reset when characters are inserted and deleted
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542 if (sequences.size() > 0)
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544 width = ((SequenceI) sequences.elementAt(0)).getLength();
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547 for (int i = 1; i < sequences.size(); i++)
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549 SequenceI seq = (SequenceI) sequences.elementAt(i);
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551 if (seq.getLength() > width)
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553 width = seq.getLength();
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563 * @param c DOCUMENT ME!
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565 public void setOutlineColour(Color c)
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573 * @return DOCUMENT ME!
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575 public Color getOutlineColour()
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577 return outlineColour;
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582 * returns the sequences in the group ordered by the ordering given by al
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584 * @param al Alignment
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585 * @return SequenceI[]
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587 public SequenceI[] getSequencesInOrder(AlignmentI al)
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589 int sSize = sequences.size();
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590 int alHeight = al.getHeight();
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592 SequenceI[] seqs = new SequenceI[sSize];
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595 for (int i = 0; i < alHeight && index<sSize; i++)
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597 if(sequences.contains( al.getSequenceAt(i) ) )
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598 seqs[index++] = al.getSequenceAt(i);
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