X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=655657e9aec76574971ee98fc867ade01dd57b34;hb=08f7a2be3977da8704dd4751de7245bcc6fc41c3;hp=4110bd1fcd5ecb1c1c5fe82ceb52cdad531679ec;hpb=fa93bb578999b13c0364a712ae368ca8841012a1;p=jalview.git diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java index 4110bd1..655657e 100644 --- a/src/jalview/commands/TrimRegionCommand.java +++ b/src/jalview/commands/TrimRegionCommand.java @@ -1,58 +1,50 @@ /* - * 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 + * 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. - * - * 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. - * + * + * 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 this program; if not, write to the Free Software - * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA + * along with Jalview. If not, see . + * The Jalview Authors are detailed in the 'AUTHORS' file. */ package jalview.commands; -import java.util.*; +import jalview.datamodel.AlignmentI; +import jalview.datamodel.SequenceI; -import jalview.datamodel.*; -import jalview.util.*; - -public class TrimRegionCommand - extends EditCommand +public class TrimRegionCommand extends EditCommand { - public static String TRIM_LEFT = "TrimLeft"; - public static String TRIM_RIGHT = "TrimRight"; - - public ColumnSelection colSel = null; - - int[] start; - - ShiftList shiftList; - - SequenceGroup selectionGroup; - - Vector deletedHiddenColumns; - int columnsDeleted; - public TrimRegionCommand(String description, - String command, - SequenceI[] seqs, - int column, - AlignmentI al, - ColumnSelection colSel, - SequenceGroup selectedRegion) + /** + * Constructs and performs a trim alignment command + * + * @param description + * (to show in Undo/Redo menu) + * @param trimLeft + * if true trim to left of column, else to right + * @param seqs + * the sequences to trim + * @param column + * the alignment column (base 0) from which to trim + * @param al + */ + public TrimRegionCommand(String description, boolean trimLeft, + SequenceI[] seqs, int column, AlignmentI al) { this.description = description; - this.selectionGroup = selectedRegion; - this.colSel = colSel; - if (command.equalsIgnoreCase(TRIM_LEFT)) + if (trimLeft) { if (column == 0) { @@ -61,115 +53,25 @@ public class TrimRegionCommand columnsDeleted = column; - edits = new Edit[] - { - new Edit(CUT, seqs, 0, column, al)}; + setEdit(new Edit(Action.CUT, seqs, 0, column, al)); } - else if (command.equalsIgnoreCase(TRIM_RIGHT)) + else { int width = al.getWidth() - column - 1; - if (width < 2) + if (width < 1) { return; } - columnsDeleted = width - 1; - - edits = new Edit[] - { - new Edit(CUT, seqs, column + 1, width, al)}; - } - - //We need to keep a record of the sequence start - //in order to restore the state after a redo - int i, isize = edits[0].seqs.length; - start = new int[isize]; - for (i = 0; i < isize; i++) - { - start[i] = edits[0].seqs[i].getStart(); - } - - performEdit(0,null); - } - - void cut(Edit command) - { - int column, j, jSize = command.seqs.length; - for (j = 0; j < jSize; j++) - { - if (command.position == 0) - { - //This is a TRIM_LEFT command - column = command.seqs[j].findPosition(command.number); - command.seqs[j].setStart(column); - } - else - { - //This is a TRIM_RIGHT command - column = command.seqs[j].findPosition(command.position) - 1; - command.seqs[j].setEnd(column); - } - } - - super.cut(command, null); - - if (command.position == 0) - { - deletedHiddenColumns = colSel.compensateForEdit(0, command.number); - if (selectionGroup != null) - { - selectionGroup.adjustForRemoveLeft(command.number); - } - } - else - { - deletedHiddenColumns = colSel.compensateForEdit(command.position, - command.number); - if (selectionGroup != null) - { - selectionGroup.adjustForRemoveRight(command.position); - } - } - } - - void paste(Edit command) - { - super.paste(command, null); - int column, j, jSize = command.seqs.length; - for (j = 0; j < jSize; j++) - { - if (command.position == 0) - { - command.seqs[j].setStart(start[j]); - } - else - { - column = command.seqs[j] - .findPosition(command.number + command.position) - 1; - command.seqs[j].setEnd(column); - } - } + columnsDeleted = width; - if (command.position == 0) - { - colSel.compensateForEdit(0, -command.number); - if (selectionGroup != null) - { - selectionGroup.adjustForRemoveLeft( -command.number); - } + setEdit(new Edit(Action.CUT, seqs, column + 1, width, al)); } - if (deletedHiddenColumns != null) - { - int[] region; - for (int i = 0; i < deletedHiddenColumns.size(); i++) - { - region = (int[]) deletedHiddenColumns.elementAt(i); - colSel.hideColumns(region[0], region[1]); - } - } + performEdit(0, null); } + @Override public int getSize() { return columnsDeleted;