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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54 * Creates a new SequenceGroup object.
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56 public SequenceGroup()
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58 groupName = "Group";
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59 this.displayBoxes = true;
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60 this.displayText = true;
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61 this.colourText = false;
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66 * Creates a new SequenceGroup object.
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68 * @param sequences DOCUMENT ME!
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69 * @param groupName DOCUMENT ME!
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70 * @param scheme DOCUMENT ME!
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71 * @param displayBoxes DOCUMENT ME!
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72 * @param displayText DOCUMENT ME!
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73 * @param colourText DOCUMENT ME!
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74 * @param start DOCUMENT ME!
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75 * @param end DOCUMENT ME!
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77 public SequenceGroup(Vector sequences, String groupName,
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78 ColourSchemeI scheme, boolean displayBoxes, boolean displayText,
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79 boolean colourText, int start, int end)
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81 this.sequences = sequences;
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82 this.groupName = groupName;
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83 this.displayBoxes = displayBoxes;
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84 this.displayText = displayText;
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85 this.colourText = colourText;
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89 recalcConservation();
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93 * Creates a new SequenceGroup object.
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95 * @param groupName DOCUMENT ME!
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96 * @param scheme DOCUMENT ME!
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97 * @param displayBoxes DOCUMENT ME!
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98 * @param displayText DOCUMENT ME!
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99 * @param colourText DOCUMENT ME!
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100 * @param start DOCUMENT ME!
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101 * @param end DOCUMENT ME!
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103 public SequenceGroup(String groupName, ColourSchemeI scheme,
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104 boolean displayBoxes, boolean displayText, boolean colourText,
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105 int start, int end)
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107 this.groupName = groupName;
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108 this.displayBoxes = displayBoxes;
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109 this.displayText = displayText;
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110 this.colourText = colourText;
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116 public SequenceI [] getSelectionAsNewSequences(AlignmentI align)
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118 int iSize = sequences.size();
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119 SequenceI [] seqs = new SequenceI[iSize];
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120 SequenceI [] inorder = getSequencesInOrder(align);
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123 for (int i = 0; i < iSize; i++)
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125 SequenceI seq = inorder[i];
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127 seqs[i] = new Sequence(seq.getName(),
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128 seq.getSequence(startRes, endRes + 1),
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129 seq.findPosition(startRes),
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132 seqs[i].setDescription(seq.getDescription());
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133 seqs[i].setDBRef(seq.getDBRef());
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134 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
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135 if (seq.getDatasetSequence() != null)
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136 seqs[i].setDatasetSequence(seq.getDatasetSequence());
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138 if(seq.getAnnotation()!=null)
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140 for(int a=0; a<seq.getAnnotation().length; a++)
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141 seqs[i].addAlignmentAnnotation(seq.getAnnotation()[a]);
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150 * If sequence ends in gaps, the end residue can
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151 * be correctly calculated here
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152 * @param seq SequenceI
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155 public int findEndRes(SequenceI seq)
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160 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
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162 ch = seq.getCharAt(j);
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163 if (!jalview.util.Comparison.isGap( (ch)))
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171 eres += seq.getStart() - 1;
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177 public Vector getSequences(boolean includeHidden)
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183 Vector allSequences = new Vector();
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185 for (int i = 0; i < sequences.size(); i++)
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187 seq = (SequenceI) sequences.elementAt(i);
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188 allSequences.addElement(seq);
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189 if (seq.getHiddenSequences() != null)
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191 for (int h = 0; h < seq.getHiddenSequences().getSize(false); h++)
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193 allSequences.addElement(
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194 seq.getHiddenSequences().getSequenceAt(h)
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200 return allSequences;
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204 public SequenceI[] getSequencesAsArray(boolean includeHidden)
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206 Vector tmp = getSequences(includeHidden);
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209 SequenceI [] result = new SequenceI[tmp.size()];
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210 for(int i=0; i<result.length; i++)
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211 result[i] = (SequenceI)tmp.elementAt(i);
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219 * @param col DOCUMENT ME!
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221 * @return DOCUMENT ME!
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223 public boolean adjustForRemoveLeft(int col)
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225 // return value is true if the group still exists
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226 if (startRes >= col)
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228 startRes = startRes - col;
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233 endRes = endRes - col;
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235 if (startRes > endRes)
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242 // must delete this group!!
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252 * @param col DOCUMENT ME!
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254 * @return DOCUMENT ME!
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256 public boolean adjustForRemoveRight(int col)
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258 if (startRes > col)
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260 // delete this group
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275 * @return DOCUMENT ME!
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277 public String getName()
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285 * @param name DOCUMENT ME!
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287 public void setName(String name)
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295 * @return DOCUMENT ME!
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297 public Conservation getConservation()
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305 * @param c DOCUMENT ME!
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307 public void setConservation(Conservation c)
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315 * @param s DOCUMENT ME!
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316 * @param recalc DOCUMENT ME!
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318 public void addSequence(SequenceI s, boolean recalc)
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320 if (s!=null && !sequences.contains(s))
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322 sequences.addElement(s);
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327 recalcConservation();
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334 public void recalcConservation()
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341 cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes+1));
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343 if (cs instanceof ClustalxColourScheme)
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345 ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
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348 if (cs.conservationApplied())
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350 Conservation c = new Conservation(groupName,
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351 ResidueProperties.propHash, 3, sequences,
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352 startRes, endRes+1);
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354 c.verdict(false, 25);
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356 cs.setConservation(c);
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358 if (cs instanceof ClustalxColourScheme)
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360 ( (ClustalxColourScheme) cs).resetClustalX(sequences,
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365 catch (java.lang.OutOfMemoryError err)
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367 System.out.println("Out of memory loading groups: " + err);
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375 * @param s DOCUMENT ME!
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376 * @param recalc DOCUMENT ME!
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378 public void addOrRemove(SequenceI s, boolean recalc)
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380 if (sequences.contains(s))
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382 deleteSequence(s, recalc);
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386 addSequence(s, recalc);
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393 * @param s DOCUMENT ME!
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394 * @param recalc DOCUMENT ME!
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396 public void deleteSequence(SequenceI s, boolean recalc)
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398 sequences.removeElement(s);
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402 recalcConservation();
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409 * @return DOCUMENT ME!
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411 public int getStartRes()
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419 * @return DOCUMENT ME!
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421 public int getEndRes()
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429 * @param i DOCUMENT ME!
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431 public void setStartRes(int i)
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439 * @param i DOCUMENT ME!
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441 public void setEndRes(int i)
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449 * @return DOCUMENT ME!
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451 public int getSize(boolean includeHidden)
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454 return sequences.size();
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457 int total = sequences.size();
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459 for (int i = 0; i < sequences.size(); i++)
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461 seq = (SequenceI) sequences.elementAt(i);
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462 if (seq.getHiddenSequences() != null)
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464 total += seq.getHiddenSequences().getSize(false);
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474 * @param i DOCUMENT ME!
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476 * @return DOCUMENT ME!
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478 public SequenceI getSequenceAt(int i)
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480 return (SequenceI) sequences.elementAt(i);
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486 * @param state DOCUMENT ME!
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488 public void setColourText(boolean state)
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490 colourText = state;
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496 * @return DOCUMENT ME!
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498 public boolean getColourText()
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506 * @param state DOCUMENT ME!
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508 public void setDisplayText(boolean state)
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510 displayText = state;
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516 * @return DOCUMENT ME!
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518 public boolean getDisplayText()
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520 return displayText;
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526 * @param state DOCUMENT ME!
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528 public void setDisplayBoxes(boolean state)
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530 displayBoxes = state;
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536 * @return DOCUMENT ME!
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538 public boolean getDisplayBoxes()
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540 return displayBoxes;
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546 * @return DOCUMENT ME!
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548 public int getWidth()
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550 // MC This needs to get reset when characters are inserted and deleted
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551 if (sequences.size() > 0)
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553 width = ((SequenceI) sequences.elementAt(0)).getLength();
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556 for (int i = 1; i < sequences.size(); i++)
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558 SequenceI seq = (SequenceI) sequences.elementAt(i);
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560 if (seq.getLength() > width)
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562 width = seq.getLength();
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572 * @param c DOCUMENT ME!
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574 public void setOutlineColour(Color c)
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582 * @return DOCUMENT ME!
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584 public Color getOutlineColour()
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586 return outlineColour;
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591 * returns the sequences in the group ordered by the ordering given by al
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593 * @param al Alignment
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594 * @return SequenceI[]
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596 public SequenceI[] getSequencesInOrder(AlignmentI al)
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598 int sSize = sequences.size();
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599 int alHeight = al.getHeight();
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601 SequenceI[] seqs = new SequenceI[sSize];
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604 for (int i = 0; i < alHeight && index<sSize; i++)
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606 if(sequences.contains( al.getSequenceAt(i) ) )
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607 seqs[index++] = al.getSequenceAt(i);
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