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; i < iSize; i++)
99 SequenceI seq = inorder[i];
101 seqs[i] = seq.getSubSequence(startRes, endRes+1);
103 seqs[i].setDescription(seq.getDescription());
104 seqs[i].setDBRef(seq.getDBRef());
105 seqs[i].setSequenceFeatures(seq.getSequenceFeatures());
106 if (seq.getDatasetSequence() != null)
108 seqs[i].setDatasetSequence(seq.getDatasetSequence());
111 if (seq.getAnnotation() != null)
113 for (int a = 0; a < seq.getAnnotation().length; a++)
115 AlignmentAnnotation newannot = new AlignmentAnnotation(seq.getAnnotation()[a]);
116 newannot.restrict(startRes, endRes);
117 newannot.setSequenceRef(seqs[i]);
118 newannot.adjustForAlignment();
119 seqs[i].addAlignmentAnnotation(newannot);
129 * If sequence ends in gaps, the end residue can
130 * be correctly calculated here
131 * @param seq SequenceI
134 public int findEndRes(SequenceI seq)
139 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
141 ch = seq.getCharAt(j);
142 if (!jalview.util.Comparison.isGap( (ch)))
150 eres += seq.getStart() - 1;
156 public Vector getSequences(Hashtable hiddenReps)
158 if (hiddenReps == null)
164 Vector allSequences = new Vector();
166 for (int i = 0; i < sequences.size(); i++)
168 seq = (SequenceI) sequences.elementAt(i);
169 allSequences.addElement(seq);
170 if (hiddenReps.containsKey(seq))
172 SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
173 for (int h = 0; h < hsg.getSize(); h++)
175 seq2 = hsg.getSequenceAt(h);
177 && !allSequences.contains(seq2))
179 allSequences.addElement(seq2);
189 public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
191 Vector tmp = getSequences(hiddenReps);
196 SequenceI[] result = new SequenceI[tmp.size()];
197 for (int i = 0; i < result.length; i++)
199 result[i] = (SequenceI) tmp.elementAt(i);
208 * @param col DOCUMENT ME!
210 * @return DOCUMENT ME!
212 public boolean adjustForRemoveLeft(int col)
214 // return value is true if the group still exists
217 startRes = startRes - col;
222 endRes = endRes - col;
224 if (startRes > endRes)
231 // must delete this group!!
241 * @param col DOCUMENT ME!
243 * @return DOCUMENT ME!
245 public boolean adjustForRemoveRight(int col)
264 * @return DOCUMENT ME!
266 public String getName()
271 public String getDescription()
279 * @param name DOCUMENT ME!
281 public void setName(String name)
286 public void setDescription(String desc)
294 * @return DOCUMENT ME!
296 public Conservation getConservation()
304 * @param c DOCUMENT ME!
306 public void setConservation(Conservation c)
314 * @param s DOCUMENT ME!
315 * @param recalc DOCUMENT ME!
317 public void addSequence(SequenceI s, boolean recalc)
319 if (s != null && !sequences.contains(s))
321 sequences.addElement(s);
326 recalcConservation();
333 public void recalcConservation()
342 cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
344 if (cs instanceof ClustalxColourScheme)
346 ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
349 if (cs.conservationApplied())
351 Conservation c = new Conservation(groupName,
352 ResidueProperties.propHash, 3,
354 startRes, endRes + 1);
356 c.verdict(false, 25);
358 cs.setConservation(c);
360 if (cs instanceof ClustalxColourScheme)
362 ( (ClustalxColourScheme) cs).resetClustalX(sequences,
367 catch (java.lang.OutOfMemoryError err)
369 System.out.println("Out of memory loading groups: " + err);
377 * @param s DOCUMENT ME!
378 * @param recalc DOCUMENT ME!
380 public void addOrRemove(SequenceI s, boolean recalc)
382 if (sequences.contains(s))
384 deleteSequence(s, recalc);
388 addSequence(s, recalc);
395 * @param s DOCUMENT ME!
396 * @param recalc DOCUMENT ME!
398 public void deleteSequence(SequenceI s, boolean recalc)
400 sequences.removeElement(s);
404 recalcConservation();
411 * @return DOCUMENT ME!
413 public int getStartRes()
421 * @return DOCUMENT ME!
423 public int getEndRes()
431 * @param i DOCUMENT ME!
433 public void setStartRes(int i)
441 * @param i DOCUMENT ME!
443 public void setEndRes(int i)
451 * @return DOCUMENT ME!
455 return sequences.size();
461 * @param i DOCUMENT ME!
463 * @return DOCUMENT ME!
465 public SequenceI getSequenceAt(int i)
467 return (SequenceI) sequences.elementAt(i);
473 * @param state DOCUMENT ME!
475 public void setColourText(boolean state)
483 * @return DOCUMENT ME!
485 public boolean getColourText()
493 * @param state DOCUMENT ME!
495 public void setDisplayText(boolean state)
503 * @return DOCUMENT ME!
505 public boolean getDisplayText()
513 * @param state DOCUMENT ME!
515 public void setDisplayBoxes(boolean state)
517 displayBoxes = state;
523 * @return DOCUMENT ME!
525 public boolean getDisplayBoxes()
533 * @return DOCUMENT ME!
535 public int getWidth()
537 // MC This needs to get reset when characters are inserted and deleted
538 if (sequences.size() > 0)
540 width = ( (SequenceI) sequences.elementAt(0)).getLength();
543 for (int i = 1; i < sequences.size(); i++)
545 SequenceI seq = (SequenceI) sequences.elementAt(i);
547 if (seq.getLength() > width)
549 width = seq.getLength();
559 * @param c DOCUMENT ME!
561 public void setOutlineColour(Color c)
569 * @return DOCUMENT ME!
571 public Color getOutlineColour()
573 return outlineColour;
578 * returns the sequences in the group ordered by the ordering given by al
580 * @param al Alignment
581 * @return SequenceI[]
583 public SequenceI[] getSequencesInOrder(AlignmentI al)
585 int sSize = sequences.size();
586 int alHeight = al.getHeight();
588 SequenceI[] seqs = new SequenceI[sSize];
591 for (int i = 0; i < alHeight && index < sSize; i++)
593 if (sequences.contains(al.getSequenceAt(i)))
595 seqs[index++] = al.getSequenceAt(i);