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.*;
29 * Collects a set contiguous ranges on a set of sequences
33 public class SequenceGroup
37 Conservation conserve;
39 boolean displayBoxes = true;
40 boolean displayText = true;
41 boolean colourText = false;
42 private Vector sequences = new Vector();
46 public ColourSchemeI cs;
49 Color outlineColour = Color.black;
50 public int thresholdTextColour = 0;
51 public Color textColour = Color.black;
52 public Color textColour2 = Color.white;
55 * Creates a new SequenceGroup object.
57 public SequenceGroup()
59 groupName = "JGroup:" + this.hashCode();
63 * Creates a new SequenceGroup object.
71 * @param start first column of group
72 * @param end last column of group
74 public SequenceGroup(Vector sequences, String groupName,
75 ColourSchemeI scheme, boolean displayBoxes,
77 boolean colourText, int start, int end)
79 this.sequences = sequences;
80 this.groupName = groupName;
81 this.displayBoxes = displayBoxes;
82 this.displayText = displayText;
83 this.colourText = colourText;
90 public SequenceI[] getSelectionAsNewSequences(AlignmentI align)
92 int iSize = sequences.size();
93 SequenceI[] seqs = new SequenceI[iSize];
94 SequenceI[] inorder = getSequencesInOrder(align);
96 for (int i = 0,ipos=0; i < inorder.length; i++)
98 SequenceI seq = inorder[i];
100 seqs[ipos] = seq.getSubSequence(startRes, endRes+1);
101 if (seqs[ipos]!=null)
103 seqs[ipos].setDescription(seq.getDescription());
104 seqs[ipos].setDBRef(seq.getDBRef());
105 seqs[ipos].setSequenceFeatures(seq.getSequenceFeatures());
106 if (seq.getDatasetSequence() != null)
108 seqs[ipos].setDatasetSequence(seq.getDatasetSequence());
111 if (seq.getAnnotation() != null)
113 AlignmentAnnotation[] alann = align.getAlignmentAnnotation();
114 // Only copy annotation that is either a score or referenced by the alignment's annotation vector
115 for (int a = 0; a < seq.getAnnotation().length; a++)
117 AlignmentAnnotation tocopy = seq.getAnnotation()[a];
121 for (int pos=0;pos<alann.length; pos++)
123 if (alann[pos]==tocopy)
132 AlignmentAnnotation newannot = new AlignmentAnnotation(seq
133 .getAnnotation()[a]);
134 newannot.restrict(startRes, endRes);
135 newannot.setSequenceRef(seqs[ipos]);
136 newannot.adjustForAlignment();
137 seqs[ipos].addAlignmentAnnotation(newannot);
145 if (iSize!=inorder.length)
147 SequenceI[] nseqs = new SequenceI[iSize];
148 System.arraycopy(seqs, 0, nseqs, 0, iSize);
156 * If sequence ends in gaps, the end residue can
157 * be correctly calculated here
158 * @param seq SequenceI
161 public int findEndRes(SequenceI seq)
166 for (int j = 0; j < endRes + 1 && j < seq.getLength(); j++)
168 ch = seq.getCharAt(j);
169 if (!jalview.util.Comparison.isGap( (ch)))
177 eres += seq.getStart() - 1;
183 public Vector getSequences(Hashtable hiddenReps)
185 if (hiddenReps == null)
191 Vector allSequences = new Vector();
193 for (int i = 0; i < sequences.size(); i++)
195 seq = (SequenceI) sequences.elementAt(i);
196 allSequences.addElement(seq);
197 if (hiddenReps.containsKey(seq))
199 SequenceGroup hsg = (SequenceGroup) hiddenReps.get(seq);
200 for (int h = 0; h < hsg.getSize(); h++)
202 seq2 = hsg.getSequenceAt(h);
204 && !allSequences.contains(seq2))
206 allSequences.addElement(seq2);
216 public SequenceI[] getSequencesAsArray(Hashtable hiddenReps)
218 Vector tmp = getSequences(hiddenReps);
223 SequenceI[] result = new SequenceI[tmp.size()];
224 for (int i = 0; i < result.length; i++)
226 result[i] = (SequenceI) tmp.elementAt(i);
235 * @param col DOCUMENT ME!
237 * @return DOCUMENT ME!
239 public boolean adjustForRemoveLeft(int col)
241 // return value is true if the group still exists
244 startRes = startRes - col;
249 endRes = endRes - col;
251 if (startRes > endRes)
258 // must delete this group!!
268 * @param col DOCUMENT ME!
270 * @return DOCUMENT ME!
272 public boolean adjustForRemoveRight(int col)
291 * @return DOCUMENT ME!
293 public String getName()
298 public String getDescription()
306 * @param name DOCUMENT ME!
308 public void setName(String name)
313 public void setDescription(String desc)
321 * @return DOCUMENT ME!
323 public Conservation getConservation()
331 * @param c DOCUMENT ME!
333 public void setConservation(Conservation c)
339 * Add s to this sequence group
341 * @param s alignment sequence to be added
342 * @param recalc true means Group's conservation should be recalculated
344 public void addSequence(SequenceI s, boolean recalc)
346 if (s != null && !sequences.contains(s))
348 sequences.addElement(s);
353 recalcConservation();
358 * calculate residue conservation for group
360 public void recalcConservation()
369 cs.setConsensus(AAFrequency.calculate(sequences, startRes, endRes + 1));
371 if (cs instanceof ClustalxColourScheme)
373 ( (ClustalxColourScheme) cs).resetClustalX(sequences, getWidth());
376 if (cs.conservationApplied())
378 Conservation c = new Conservation(groupName,
379 ResidueProperties.propHash, 3,
381 startRes, endRes + 1);
383 c.verdict(false, 25);
385 cs.setConservation(c);
387 if (cs instanceof ClustalxColourScheme)
389 ( (ClustalxColourScheme) cs).resetClustalX(sequences,
394 catch (java.lang.OutOfMemoryError err)
396 System.out.println("Out of memory loading groups: " + err);
404 * @param s DOCUMENT ME!
405 * @param recalc DOCUMENT ME!
407 public void addOrRemove(SequenceI s, boolean recalc)
409 if (sequences.contains(s))
411 deleteSequence(s, recalc);
415 addSequence(s, recalc);
422 * @param s DOCUMENT ME!
423 * @param recalc DOCUMENT ME!
425 public void deleteSequence(SequenceI s, boolean recalc)
427 sequences.removeElement(s);
431 recalcConservation();
438 * @return DOCUMENT ME!
440 public int getStartRes()
448 * @return DOCUMENT ME!
450 public int getEndRes()
458 * @param i DOCUMENT ME!
460 public void setStartRes(int i)
468 * @param i DOCUMENT ME!
470 public void setEndRes(int i)
478 * @return DOCUMENT ME!
482 return sequences.size();
488 * @param i DOCUMENT ME!
490 * @return DOCUMENT ME!
492 public SequenceI getSequenceAt(int i)
494 return (SequenceI) sequences.elementAt(i);
500 * @param state DOCUMENT ME!
502 public void setColourText(boolean state)
510 * @return DOCUMENT ME!
512 public boolean getColourText()
520 * @param state DOCUMENT ME!
522 public void setDisplayText(boolean state)
530 * @return DOCUMENT ME!
532 public boolean getDisplayText()
540 * @param state DOCUMENT ME!
542 public void setDisplayBoxes(boolean state)
544 displayBoxes = state;
550 * @return DOCUMENT ME!
552 public boolean getDisplayBoxes()
560 * @return DOCUMENT ME!
562 public int getWidth()
564 // MC This needs to get reset when characters are inserted and deleted
565 if (sequences.size() > 0)
567 width = ( (SequenceI) sequences.elementAt(0)).getLength();
570 for (int i = 1; i < sequences.size(); i++)
572 SequenceI seq = (SequenceI) sequences.elementAt(i);
574 if (seq.getLength() > width)
576 width = seq.getLength();
586 * @param c DOCUMENT ME!
588 public void setOutlineColour(Color c)
596 * @return DOCUMENT ME!
598 public Color getOutlineColour()
600 return outlineColour;
605 * returns the sequences in the group ordered by the ordering given by al
607 * @param al Alignment
608 * @return SequenceI[]
610 public SequenceI[] getSequencesInOrder(AlignmentI al)
612 int sSize = sequences.size();
613 int alHeight = al.getHeight();
615 SequenceI[] seqs = new SequenceI[sSize];
618 for (int i = 0; i < alHeight && index < sSize; i++)
620 if (sequences.contains(al.getSequenceAt(i)))
622 seqs[index++] = al.getSequenceAt(i);