X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;ds=sidebyside;f=src%2Fjalview%2Fcommands%2FTrimRegionCommand.java;h=b4d92a03880ee6c5c028755cd9c57bb1a3dfa560;hb=9ad1e437d5d6366f0b06fbfbdb446a720ca57104;hp=4c1dea0f26420edc314b79792864768bcfb356f0;hpb=7bc226b58110fa26d9dbd3f0c78095d06909ffc3;p=jalview.git
diff --git a/src/jalview/commands/TrimRegionCommand.java b/src/jalview/commands/TrimRegionCommand.java
index 4c1dea0..b4d92a0 100644
--- a/src/jalview/commands/TrimRegionCommand.java
+++ b/src/jalview/commands/TrimRegionCommand.java
@@ -1,178 +1,175 @@
-/*
- * 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
- */
-package jalview.commands;
-
-import java.util.*;
-
-import jalview.datamodel.*;
-import jalview.util.*;
-
-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)
- {
- this.description = description;
- this.selectionGroup = selectedRegion;
- this.colSel = colSel;
- if (command.equalsIgnoreCase(TRIM_LEFT))
- {
- if (column == 0)
- {
- return;
- }
-
- columnsDeleted = column;
-
- edits = new Edit[]
- {
- new Edit(CUT, seqs, 0, column, al)};
- }
- else if (command.equalsIgnoreCase(TRIM_RIGHT))
- {
- int width = al.getWidth() - column - 1;
- if (width < 2)
- {
- 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);
- }
-
- 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);
-
- 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);
- 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);
- }
- }
-
- if (command.position == 0)
- {
- colSel.compensateForEdit(0, -command.number);
- if (selectionGroup != null)
- {
- selectionGroup.adjustForRemoveLeft( -command.number);
- }
- }
-
- if (deletedHiddenColumns != null)
- {
- int[] region;
- for (int i = 0; i < deletedHiddenColumns.size(); i++)
- {
- region = (int[]) deletedHiddenColumns.elementAt(i);
- colSel.hideColumns(region[0], region[1]);
- }
- }
- }
-
- public int getSize()
- {
- 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;
+
+import jalview.datamodel.AlignmentI;
+import jalview.datamodel.ColumnSelection;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.util.ShiftList;
+
+import java.util.List;
+
+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;
+
+ List deletedHiddenColumns;
+
+ int columnsDeleted;
+
+ public TrimRegionCommand(String description, String command,
+ SequenceI[] seqs, int column, AlignmentI al,
+ ColumnSelection colSel, SequenceGroup selectedRegion)
+ {
+ this.description = description;
+ this.selectionGroup = selectedRegion;
+ this.colSel = colSel;
+ if (command.equalsIgnoreCase(TRIM_LEFT))
+ {
+ if (column == 0)
+ {
+ return;
+ }
+
+ columnsDeleted = column;
+
+ setEdit(new Edit(Action.CUT, seqs, 0, column, al));
+ }
+ else if (command.equalsIgnoreCase(TRIM_RIGHT))
+ {
+ int width = al.getWidth() - column - 1;
+ if (width < 2)
+ {
+ return;
+ }
+
+ columnsDeleted = width - 1;
+
+ setEdit(new Edit(Action.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 = getEdit(0).seqs.length;
+ start = new int[isize];
+ for (i = 0; i < isize; i++)
+ {
+ start[i] = getEdit(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);
+ }
+ }
+
+ if (command.position == 0)
+ {
+ colSel.compensateForEdit(0, -command.number);
+ if (selectionGroup != null)
+ {
+ selectionGroup.adjustForRemoveLeft(-command.number);
+ }
+ }
+
+ if (deletedHiddenColumns != null)
+ {
+ int[] region;
+ for (int i = 0; i < deletedHiddenColumns.size(); i++)
+ {
+ region = deletedHiddenColumns.get(i);
+ colSel.hideColumns(region[0], region[1]);
+ }
+ }
+ }
+
+ public int getSize()
+ {
+ return columnsDeleted;
+ }
+
+}