X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapsCommand.java;h=c8dadfa8827903f51e605caa430d64a205a76286;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=9343ec2a0ee62b405f3cb9651aa4ddb7db2f6b96;hpb=ebb678af128304dc13e1b6ec9e0961489bf83d39;p=jalview.git diff --git a/src/jalview/commands/RemoveGapsCommand.java b/src/jalview/commands/RemoveGapsCommand.java index 9343ec2..c8dadfa 100644 --- a/src/jalview/commands/RemoveGapsCommand.java +++ b/src/jalview/commands/RemoveGapsCommand.java @@ -1,111 +1,133 @@ -package jalview.commands; - /* - * Jalview - A Sequence Alignment Editor and Viewer - * Copyright (C) 2006 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle - * - * This program is free software; you can redistribute it and/or - * modify it under the terms of the GNU General Public License - * as published by the Free Software Foundation; either version 2 - * of the License, or (at your option) any later version. - * - * This program is distributed in the hope that it will be useful, - * but WITHOUT ANY WARRANTY; without even the implied warranty of - * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the - * GNU General Public License for more details. - * - * You should have received a copy of the GNU General Public License - * along with this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA - */ - -import jalview.datamodel.*; - -public class RemoveGapsCommand extends EditCommand -{ - public RemoveGapsCommand( String description, - SequenceI[] seqs, char gapChar) - { - this.description = description; - int width = 0; - for(int i=0; iwidth) - width = seqs[i].getLength(); - - findGaps(seqs, 0, width, gapChar); - } - - public RemoveGapsCommand( String description, - SequenceI[] seqs, - int start, int end, char gapChar) - { - this.description = description; - findGaps(seqs, start, end, gapChar); - } - - void findGaps(SequenceI [] seqs, int start, int end, char gapChar) - { - - int startCol = -1, endCol = -1; - int deletedCols = 0; - - edits = new Edit[0]; - - boolean delete = true; - char [] sequence; - for(int s=0; s -1) - { - this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]}, - startCol - deletedCols, - endCol - startCol, - gapChar, - false); - - deletedCols += (endCol - startCol); - startCol = -1; - endCol = -1; - } - } - if (delete && startCol > -1) - { - int width = end - endCol; - - if (endCol == -1) - width = end - start + 1; - - //This is the end of the region. - this.appendEdit(DELETE_GAP, new SequenceI[]{seqs[s]}, - startCol - deletedCols, - width, - gapChar, - false); - } - - } - - performEdit(0); - } - -} +/* + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors + * + * This file is part of Jalview. + * + * Jalview is free software: you can redistribute it and/or + * modify it under the terms of the GNU General Public License + * as published by the Free Software Foundation, either version 3 + * of the License, or (at your option) any later version. + * + * Jalview is distributed in the hope that it will be useful, but + * WITHOUT ANY WARRANTY; without even the implied warranty + * of MERCHANTABILITY or FITNESS FOR A PARTICULAR + * PURPOSE. See the GNU General Public License for more details. + * + * You should have received a copy of the GNU General Public License + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. + */ +package jalview.commands; + +/* + * Jalview - A Sequence Alignment Editor and Viewer Copyright (C) 2007 AM + * Waterhouse, J Procter, G Barton, M Clamp, S Searle + * + * This program is free software; you can redistribute it and/or modify it under + * the terms of the GNU General Public License as published by the Free Software + * Foundation; either version 2 of the License, or (at your option) any later + * version. + * + * This program is distributed in the hope that it will be useful, but WITHOUT + * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS + * FOR A PARTICULAR PURPOSE. See the GNU General Public License for more + * details. + * + * You should have received a copy of the GNU General Public License along with + * this program; if not, write to the Free Software Foundation, Inc., 51 + * Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + */ + +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; + +public class RemoveGapsCommand extends EditCommand +{ + public RemoveGapsCommand(String description, SequenceI[] seqs, + AlignmentI al) + { + this.description = description; + int width = 0; + for (int i = 0; i < seqs.length; i++) + { + if (seqs[i].getLength() > width) + { + width = seqs[i].getLength(); + } + } + + findGaps(seqs, 0, width, al); + } + + public RemoveGapsCommand(String description, SequenceI[] seqs, int start, + int end, AlignmentI al) + { + this.description = description; + findGaps(seqs, start, end, al); + } + + void findGaps(SequenceI[] seqs, int start, int end, AlignmentI al) + { + + int startCol = -1, endCol = -1; + int deletedCols = 0; + + int j, jSize; + + clearEdits(); + + boolean delete = true; + char[] sequence; + + for (int s = 0; s < seqs.length; s++) + { + deletedCols = 0; + startCol = -1; + endCol = -1; + sequence = seqs[s].getSequence(start, end + 1); + + jSize = sequence.length; + for (j = 0; j < jSize; j++) + { + delete = true; + + if (!jalview.util.Comparison.isGap(sequence[j])) + { + if (delete) + { + endCol = j; + } + + delete = false; + } + + if (delete && startCol == -1) + { + startCol = j; + } + + if (!delete && startCol > -1) + { + this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] }, + start + startCol - deletedCols, endCol - startCol, al, + false, null); + + deletedCols += (endCol - startCol); + startCol = -1; + endCol = -1; + } + } + if (delete && startCol > -1) + { + this.appendEdit(Action.DELETE_GAP, new SequenceI[] { seqs[s] }, + start + startCol - deletedCols, jSize - startCol, al, + false, null); + } + + } + + performEdit(0, null); + } + +}