-/*\r
- * Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
- *\r
- * This program is free software; you can redistribute it and/or\r
- * modify it under the terms of the GNU General Public License\r
- * as published by the Free Software Foundation; either version 2\r
- * of the License, or (at your option) any later version.\r
- *\r
- * This program is distributed in the hope that it will be useful,\r
- * but WITHOUT ANY WARRANTY; without even the implied warranty of\r
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the\r
- * GNU General Public License for more details.\r
- *\r
- * You should have received a copy of the GNU General Public License\r
- * along with this program; if not, write to the Free Software\r
- * Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA\r
- */\r
-package jalview.gui;\r
-\r
-import jalview.datamodel.*;\r
-\r
-import jalview.jbgui.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.event.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class RedundancyPanel extends GSliderPanel\r
-{\r
- AlignFrame af;\r
- AlignmentPanel ap;\r
- Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
-\r
- /**\r
- * Creates a new RedundancyPanel object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param af DOCUMENT ME!\r
- */\r
- public RedundancyPanel(AlignmentPanel ap, AlignFrame af)\r
- {\r
- this.ap = ap;\r
- this.af = af;\r
- label.setText("Enter the redundancy threshold");\r
-\r
- slider.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- }\r
- });\r
-\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
- slider.setValue(100);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- float threshold = slider.getValue();\r
- Vector del;\r
- historyList.push(new HistoryItem("Remove redundancy",\r
- ap.av.alignment, HistoryItem.HIDE));\r
-\r
- if ((historyList.size() == 1) ||\r
- !af.historyList.contains(historyList.firstElement()))\r
- {\r
- af.addHistoryItem((HistoryItem) historyList.firstElement());\r
- af.updateEditMenuBar();\r
- }\r
-\r
- undoButton.setEnabled(true);\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if ((sg != null) && (sg.getSize() >= 1))\r
- {\r
- del = ap.av.alignment.removeRedundancy(threshold, sg.sequences);\r
-\r
- for (int i = 0; i < del.size(); i++)\r
- {\r
- if (sg.sequences.contains((SequenceI) del.elementAt(i)))\r
- {\r
- sg.deleteSequence((SequenceI) del.elementAt(i), true);\r
- }\r
- }\r
- }\r
- else\r
- {\r
- Vector s = new Vector();\r
- int i = 0;\r
-\r
- while (i < ap.av.alignment.getHeight())\r
- {\r
- s.addElement(ap.av.alignment.getSequenceAt(i));\r
- i++;\r
- }\r
-\r
- del = ap.av.alignment.removeRedundancy(threshold, s);\r
- }\r
-\r
- // This has to be done before the restoreHistoryItem method of alignFrame will\r
- // actually restore these sequences.\r
- if (del.size() > 0)\r
- {\r
- for (int i = 0, j = del.size(); i < j; i++)\r
- {\r
- SequenceI sq = (SequenceI) del.elementAt(i);\r
- sq.deleteChars(0, sq.getLength());\r
- }\r
- }\r
-\r
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
- af.updateEditMenuBar();\r
-\r
-\r
- if (ap.av.getAlignment().getHeight() < 1)\r
- {\r
- try\r
- {\r
- af.setClosed(true);\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void undoButton_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- af.restoreHistoryItem(hi);\r
-\r
- if (historyList.size() == 0)\r
- {\r
- undoButton.setEnabled(false);\r
-\r
- if (af.historyList.contains(hi))\r
- {\r
- af.historyList.remove(hi);\r
- af.updateEditMenuBar();\r
- }\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param e DOCUMENT ME!\r
- */\r
- public void valueField_actionPerformed(ActionEvent e)\r
- {\r
- try\r
- {\r
- int i = Integer.parseInt(valueField.getText());\r
- slider.setValue(i);\r
- }\r
- catch (Exception ex)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- }\r
- }\r
-}\r
+/*
+ * 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 <http://www.gnu.org/licenses/>.
+ * The Jalview Authors are detailed in the 'AUTHORS' file.
+ */
+package jalview.gui;
+
+import java.awt.event.ActionEvent;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Stack;
+import java.util.Vector;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JProgressBar;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+import jalview.analysis.AlignSeq;
+import jalview.commands.CommandI;
+import jalview.commands.EditCommand;
+import jalview.commands.EditCommand.Action;
+import jalview.datamodel.SequenceGroup;
+import jalview.datamodel.SequenceI;
+import jalview.jbgui.GSliderPanel;
+import jalview.util.MessageManager;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class RedundancyPanel extends GSliderPanel implements Runnable
+{
+ AlignFrame af;
+
+ AlignmentPanel ap;
+
+ Stack<CommandI> historyList = new Stack<>();
+
+ // simpler than synching with alignFrame.
+
+ float[] redundancy;
+
+ SequenceI[] originalSequences;
+
+ JInternalFrame frame;
+
+ Vector redundantSeqs;
+
+ /**
+ * Creates a new RedundancyPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param af
+ * DOCUMENT ME!
+ */
+ public RedundancyPanel(final AlignmentPanel ap, AlignFrame af)
+ {
+ this.ap = ap;
+ this.af = af;
+ redundantSeqs = new Vector();
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ valueField.setText(slider.getValue() + "");
+ sliderValueChanged();
+ }
+ });
+
+ applyButton.setText(MessageManager.getString("action.remove"));
+ allGroupsCheck.setVisible(false);
+ slider.setMinimum(0);
+ slider.setMaximum(100);
+ slider.setValue(100);
+
+ Thread worker = new Thread(this);
+ worker.start();
+
+ frame = new JInternalFrame();
+ frame.setFrameIcon(null);
+ frame.setContentPane(this);
+ Desktop.addInternalFrame(frame,
+ MessageManager
+ .getString("label.redundancy_threshold_selection"),
+ true, FRAME_WIDTH, FRAME_HEIGHT, false, true);
+ frame.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosing(InternalFrameEvent evt)
+ {
+ ap.getIdPanel().getIdCanvas().setHighlighted(null);
+ }
+ });
+
+ }
+
+ /**
+ * This is a copy of remove redundancy in jalivew.datamodel.Alignment except
+ * we dont want to remove redundancy, just calculate once so we can use the
+ * slider to dynamically hide redundant sequences
+ *
+ * @param threshold
+ * DOCUMENT ME!
+ * @param sel
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ @Override
+ public void run()
+ {
+ JProgressBar progress = new JProgressBar();
+ progress.setIndeterminate(true);
+ southPanel.add(progress, java.awt.BorderLayout.SOUTH);
+
+ label.setText(MessageManager.getString("label.calculating"));
+
+ slider.setVisible(false);
+ applyButton.setEnabled(false);
+ valueField.setVisible(false);
+
+ validate();
+
+ String[] omitHidden = null;
+
+ SequenceGroup sg = ap.av.getSelectionGroup();
+ int height;
+
+ int start, end;
+
+ if ((sg != null) && (sg.getSize() >= 1))
+ {
+ originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());
+ start = sg.getStartRes();
+ end = sg.getEndRes();
+ }
+ else
+ {
+ originalSequences = ap.av.getAlignment().getSequencesArray();
+ start = 0;
+ end = ap.av.getAlignment().getWidth();
+ }
+
+ height = originalSequences.length;
+ if (ap.av.hasHiddenColumns())
+ {
+ omitHidden = ap.av.getViewAsString(sg != null);
+ }
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
+ omitHidden, start, end, false);
+
+ progress.setIndeterminate(false);
+ progress.setVisible(false);
+ progress = null;
+
+ label.setText(
+ MessageManager.getString("label.enter_redundancy_threshold"));
+ slider.setVisible(true);
+ applyButton.setEnabled(true);
+ valueField.setVisible(true);
+
+ validate();
+ sliderValueChanged();
+ // jalview.bin.Console.outPrintln((System.currentTimeMillis()-start));
+ }
+
+ void sliderValueChanged()
+ {
+ if (redundancy == null)
+ {
+ return;
+ }
+
+ float value = slider.getValue();
+ List<SequenceI> redundantSequences = new ArrayList<>();
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ redundantSequences.add(originalSequences[i]);
+ }
+ }
+ ap.getIdPanel().getIdCanvas().setHighlighted(redundantSequences);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void applyButton_actionPerformed(ActionEvent e)
+ {
+ List<SequenceI> del = new ArrayList<>();
+
+ undoButton.setEnabled(true);
+
+ float value = slider.getValue();
+ SequenceGroup sg = ap.av.getSelectionGroup();
+
+ for (int i = 0; i < redundancy.length; i++)
+ {
+ if (value <= redundancy[i])
+ {
+ del.add(originalSequences[i]);
+ }
+ }
+
+ // This has to be done before the restoreHistoryItem method of alignFrame
+ // will actually restore these sequences.
+ if (del.size() > 0)
+ {
+ SequenceI[] deleted = new SequenceI[del.size()];
+
+ int width = 0;
+ for (int i = 0; i < del.size(); i++)
+ {
+ deleted[i] = del.get(i);
+ if (deleted[i].getLength() > width)
+ {
+ width = deleted[i].getLength();
+ }
+ }
+
+ EditCommand cut = new EditCommand(
+ MessageManager.getString("action.remove_redundancy"),
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());
+
+ for (int i = 0; i < del.size(); i++)
+ {
+ ap.av.getAlignment().deleteSequence(deleted[i]);
+ if (sg != null)
+ {
+ sg.deleteSequence(deleted[i], false);
+ }
+ }
+
+ historyList.push(cut);
+
+ ap.alignFrame.addHistoryItem(cut);
+
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ }
+
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void undoButton_actionPerformed(ActionEvent e)
+ {
+ if (historyList == null || historyList.isEmpty())
+ {
+ undoButton.setEnabled(false);
+ return;
+ }
+
+ CommandI command = historyList.pop();
+ if (ap.av.getHistoryList().contains(command))
+ {
+ command.undoCommand(af.getViewAlignments());
+ ap.av.getHistoryList().remove(command);
+ ap.av.firePropertyChange("alignment", null,
+ ap.av.getAlignment().getSequences());
+ af.updateEditMenuBar();
+ }
+
+ ap.paintAlignment(true, true);
+
+ if (historyList.size() == 0)
+ {
+ undoButton.setEnabled(false);
+ }
+ }
+
+}