X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FRemoveGapColCommand.java;h=3266874685ec52d5048758b7e11317283a9e3de0;hb=37de9310bec3501cbc6381e0c3dcb282fcaad812;hp=d3aebdb9e2356778e9d122abbcafaa5e2571e9cb;hpb=714af52b3db1dfa2420b0782ef64248b7404adf9;p=jalview.git diff --git a/src/jalview/commands/RemoveGapColCommand.java b/src/jalview/commands/RemoveGapColCommand.java index d3aebdb..3266874 100644 --- a/src/jalview/commands/RemoveGapColCommand.java +++ b/src/jalview/commands/RemoveGapColCommand.java @@ -1,103 +1,120 @@ -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 RemoveGapColCommand extends EditCommand -{ - int columnsDeleted; - public RemoveGapColCommand(String description, - SequenceI[] seqs, - int start, int end, AlignmentI al) - { - this.description = description; - - int j, jSize = seqs.length; - - int startCol = -1, endCol = -1; - columnsDeleted=0; - - edits = new Edit[0]; - - boolean delete = true; - for (int i = start; i <= end; i++) - { - delete = true; - - for (j = 0; j < jSize; j++) - { - if (seqs[j].getLength() > i) - { - if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i))) - { - if (delete) - endCol = i; - - delete = false; - break; - } - } - } - - if (delete && startCol == -1) - { - startCol = i; - } - - if (!delete && startCol > -1) - { - this.appendEdit(DELETE_GAP, seqs, - startCol - columnsDeleted, - endCol - startCol, - al, - false); - - columnsDeleted += (endCol - startCol); - startCol = -1; - endCol = -1; - } - } - - if (delete && startCol > -1) - { - //This is for empty columns at the - //end of the alignment - - this.appendEdit(DELETE_GAP, seqs, - startCol - columnsDeleted, - end - startCol +1, - al, - false); - - columnsDeleted += (end - startCol +1); - } - - - performEdit(0); - } - - public int getSize() - { - //We're interested in the number of columns deleted, - //Not the number of sequence edits. - return columnsDeleted; - } - -} +/* + * 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 RemoveGapColCommand extends EditCommand +{ + int columnsDeleted; + + public RemoveGapColCommand(String description, SequenceI[] seqs, + int start, int end, AlignmentI al) + { + this.description = description; + + int j, jSize = seqs.length; + + int startCol = -1, endCol = -1; + columnsDeleted = 0; + + clearEdits(); + + boolean delete = true; + for (int i = start; i <= end; i++) + { + delete = true; + + for (j = 0; j < jSize; j++) + { + if (seqs[j].getLength() > i) + { + if (!jalview.util.Comparison.isGap(seqs[j].getCharAt(i))) + { + if (delete) + { + endCol = i; + } + + delete = false; + break; + } + } + } + + if (delete && startCol == -1) + { + startCol = i; + } + + if (!delete && startCol > -1) + { + this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted, + endCol - startCol, al, false, null); + + columnsDeleted += (endCol - startCol); + startCol = -1; + endCol = -1; + } + } + + if (delete && startCol > -1) + { + // This is for empty columns at the + // end of the alignment + + this.appendEdit(Action.DELETE_GAP, seqs, startCol - columnsDeleted, + end - startCol + 1, al, false, null); + + columnsDeleted += (end - startCol + 1); + } + + performEdit(0, null); + } + + public int getSize() + { + // We're interested in the number of columns deleted, + // Not the number of sequence edits. + return columnsDeleted; + } + +}