2 * Jalview - A Sequence Alignment Editor and Viewer
3 * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle
5 * This program is free software; you can redistribute it and/or
6 * modify it under the terms of the GNU General Public License
7 * as published by the Free Software Foundation; either version 2
8 * of the License, or (at your option) any later version.
10 * This program is distributed in the hope that it will be useful,
11 * but WITHOUT ANY WARRANTY; without even the implied warranty of
12 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
13 * GNU General Public License for more details.
15 * You should have received a copy of the GNU General Public License
16 * along with this program; if not, write to the Free Software
17 * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
19 package jalview.datamodel;
25 import jalview.analysis.*;
26 import jalview.schemes.*;
34 public class SequenceGroup
38 Conservation conserve;
40 boolean displayBoxes = true;
41 boolean displayText = true;
42 boolean colourText = false;
43 private Vector sequences = new Vector();
47 public ColourSchemeI cs;
50 Color outlineColour = Color.black;
51 public int thresholdTextColour = 0;
52 public Color textColour = Color.black;
53 public Color textColour2 = Color.white;
56 * Creates a new SequenceGroup object.
58 public SequenceGroup()
60 groupName = "JGroup:" + this.hashCode();
64 * Creates a new SequenceGroup object.
66 * @param sequences DOCUMENT ME!
67 * @param groupName DOCUMENT ME!
68 * @param scheme DOCUMENT ME!
69 * @param displayBoxes DOCUMENT ME!
70 * @param displayText DOCUMENT ME!
71 * @param colourText DOCUMENT ME!
72 * @param start DOCUMENT ME!
73 * @param end DOCUMENT ME!
75 public SequenceGroup(Vector sequences, String groupName,
76 ColourSchemeI scheme, boolean displayBoxes,
78 boolean colourText, int start, int end)
80 this.sequences = sequences;
81 this.groupName = groupName;
82 this.displayBoxes = displayBoxes;
83 this.displayText = displayText;
84 this.colourText = colourText;
91 public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
93 int iSize = sequences.size();
94 SequenceI[] seqs = new SequenceI[iSize];
95 SequenceI[] inorder = getSequencesInOrder(align);
97 for (int i = 0,ipos=0; i < inorder.length; i++)
99 SequenceI seq = inorder[i];
101 seqs[ipos] = seq.getSubSequence(startRes, endRes+1);
102 if (seqs[ipos]!=null)
104 seqs[ipos].setDescription(seq.getDescription());
105 seqs[ipos].setDBRef(seq.getDBRef());
106 seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
107 if (seq.getDatasetSequence() != null)
109 seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
112 if (seq.getAnnotation() != null)
114 for (int a = 0; a < seq.getAnnotation().length; a++)
116 AlignmentAnnotation newannot = new AlignmentAnnotation(seq
117 .getAnnotation()[a]);
118 newannot.restrict(startRes, endRes);
119 newannot.setSequenceRef(seqs[ipos]);
120 newannot.adjustForAlignment();
121 seqs[ipos].addAlignmentAnnotation(newannot);
129 if (iSize!=inorder.length)
131 SequenceI[] nseqs = new SequenceI[iSize];
132 System.arraycopy(seqs, 0, nseqs, 0, iSize);
140 * If sequence ends in gaps, the end residue can
141 * be correctly calculated here
142 * @param seq SequenceI
145 public int findEndRes(SequenceI seq)
150 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
152 ch = seq.getCharAt(j);
153 if (!jalview.util.Comparison.isGap( (ch)))
161 eres += seq.getStart() - 1;
167 public Vector getSequences(Hashtable hiddenReps)
169 if (hiddenReps == null)
175 Vector allSequences = new Vector();
177 for (int i = 0; i < sequences.size(); i++)
179 seq = (SequenceI) sequences.elementAt(i);
180 allSequences.addElement(seq);
181 if (hiddenReps.containsKey(seq))
183 SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
184 for (int h = 0; h < hsg.getSize(); h++)
186 seq2 = hsg.getSequenceAt(h);
188 && !allSequences.contains(seq2))
190 allSequences.addElement(seq2);
200 public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
202 Vector tmp = getSequences(hiddenReps);
207 SequenceI[] result = new SequenceI[tmp.size()];
208 for (int i = 0; i < result.length; i++)
210 result[i] = (SequenceI) tmp.elementAt(i);
219 * @param col DOCUMENT ME!
221 * @return DOCUMENT ME!
223 public boolean adjustForRemoveLeft(int col)
225 // return value is true if the group still exists
228 startRes = startRes - col;
233 endRes = endRes - col;
235 if (startRes > endRes)
242 // must delete this group!!
252 * @param col DOCUMENT ME!
254 * @return DOCUMENT ME!
256 public boolean adjustForRemoveRight(int col)
275 * @return DOCUMENT ME!
277 public String getName()
282 public String getDescription()
290 * @param name DOCUMENT ME!
292 public void setName(String name)
297 public void setDescription(String desc)
305 * @return DOCUMENT ME!
307 public Conservation getConservation()
315 * @param c DOCUMENT ME!
317 public void setConservation(Conservation c)
325 * @param s DOCUMENT ME!
326 * @param recalc DOCUMENT ME!
328 public void addSequence(SequenceI s, boolean recalc)
330 if (s != null && !sequences.contains(s))
332 sequences.addElement(s);
337 recalcConservation();
344 public void recalcConservation()
353 cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
355 if (cs instanceof ClustalxColourScheme)
357 ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
360 if (cs.conservationApplied())
362 Conservation c = new Conservation(groupName,
363 ResidueProperties.propHash, 3,
365 startRes, endRes + 1);
367 c.verdict(false, 25);
369 cs.setConservation(c);
371 if (cs instanceof ClustalxColourScheme)
373 ( (ClustalxColourScheme) cs).resetClustalX(sequences,
378 catch (java.lang.OutOfMemoryError err)
380 System.out.println("Out of memory loading groups: " + err);
388 * @param s DOCUMENT ME!
389 * @param recalc DOCUMENT ME!
391 public void addOrRemove(SequenceI s, boolean recalc)
393 if (sequences.contains(s))
395 deleteSequence(s, recalc);
399 addSequence(s, recalc);
406 * @param s DOCUMENT ME!
407 * @param recalc DOCUMENT ME!
409 public void deleteSequence(SequenceI s, boolean recalc)
411 sequences.removeElement(s);
415 recalcConservation();
422 * @return DOCUMENT ME!
424 public int getStartRes()
432 * @return DOCUMENT ME!
434 public int getEndRes()
442 * @param i DOCUMENT ME!
444 public void setStartRes(int i)
452 * @param i DOCUMENT ME!
454 public void setEndRes(int i)
462 * @return DOCUMENT ME!
466 return sequences.size();
472 * @param i DOCUMENT ME!
474 * @return DOCUMENT ME!
476 public SequenceI getSequenceAt(int i)
478 return (SequenceI) sequences.elementAt(i);
484 * @param state DOCUMENT ME!
486 public void setColourText(boolean state)
494 * @return DOCUMENT ME!
496 public boolean getColourText()
504 * @param state DOCUMENT ME!
506 public void setDisplayText(boolean state)
514 * @return DOCUMENT ME!
516 public boolean getDisplayText()
524 * @param state DOCUMENT ME!
526 public void setDisplayBoxes(boolean state)
528 displayBoxes = state;
534 * @return DOCUMENT ME!
536 public boolean getDisplayBoxes()
544 * @return DOCUMENT ME!
546 public int getWidth()
548 // MC This needs to get reset when characters are inserted and deleted
549 if (sequences.size() > 0)
551 width = ( (SequenceI) sequences.elementAt(0)).getLength();
554 for (int i = 1; i < sequences.size(); i++)
556 SequenceI seq = (SequenceI) sequences.elementAt(i);
558 if (seq.getLength() > width)
560 width = seq.getLength();
570 * @param c DOCUMENT ME!
572 public void setOutlineColour(Color c)
580 * @return DOCUMENT ME!
582 public Color getOutlineColour()
584 return outlineColour;
589 * returns the sequences in the group ordered by the ordering given by al
591 * @param al Alignment
592 * @return SequenceI[]
594 public SequenceI[] getSequencesInOrder(AlignmentI al)
596 int sSize = sequences.size();
597 int alHeight = al.getHeight();
599 SequenceI[] seqs = new SequenceI[sSize];
602 for (int i = 0; i < alHeight && index < sSize; i++)
604 if (sequences.contains(al.getSequenceAt(i)))
606 seqs[index++] = al.getSequenceAt(i);