-/*
- * 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.appletgui;
-
-import jalview.analysis.AlignSeq;
-import jalview.bin.JalviewLite;
-import jalview.commands.CommandI;
-import jalview.commands.EditCommand;
-import jalview.commands.EditCommand.Action;
-import jalview.datamodel.AlignmentI;
-import jalview.datamodel.SequenceGroup;
-import jalview.datamodel.SequenceI;
-import jalview.util.MessageManager;
-
-import javax.swing.JFrame;
-import java.awt.event.ActionEvent;
-import java.awt.event.AdjustmentEvent;
-import java.awt.event.AdjustmentListener;
-import java.awt.event.WindowEvent;
-import java.awt.event.WindowListener;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.Stack;
-import java.util.Vector;
-
-public class RedundancyPanel extends SliderPanel implements Runnable,
- WindowListener
-{
- Stack historyList = new Stack(); // simpler than synching with alignFrame.
-
- float[] redundancy;
-
- SequenceI[] originalSequences;
-
- JFrame frame;
-
- Vector redundantSeqs;
-
- public RedundancyPanel(AlignmentPanel ap)
- {
- super(ap, 0, false, null);
-
- redundantSeqs = new Vector();
- this.ap = ap;
- undoButton.setVisible(true);
- applyButton.setVisible(true);
- allGroupsCheck.setVisible(false);
-
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
- valueField.setText("100");
-
- slider.setVisibleAmount(1);
- slider.setMinimum(0);
- slider.setMaximum(100 + slider.getVisibleAmount());
- slider.setValue(100);
-
- slider.addAdjustmentListener(new AdjustmentListener()
- {
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- valueField.setText(slider.getValue() + "");
- sliderValueChanged();
- }
- });
-
- frame = new JFrame();
- frame.add(this);
- JalviewLite.addFrame(frame, MessageManager
- .getString("label.redundancy_threshold_selection"), 400, 100);
-
- frame.addWindowListener(this);
-
- Thread worker = new Thread(this);
- worker.start();
- }
-
- /**
- * 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!
- */
- public void run()
- {
- 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;
-
- redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,
- omitHidden, start, end, false);
- label.setText(MessageManager
- .getString("label.enter_redundancy_threshold"));
- slider.setVisible(true);
- applyButton.setEnabled(true);
- valueField.setVisible(true);
-
- validate();
- sliderValueChanged();
- // System.out.println("blob done "+ (System.currentTimeMillis()-start));
- }
-
- void sliderValueChanged()
- {
- if (redundancy == null)
- {
- return;
- }
-
- float value = slider.getValue();
-
- List<SequenceI> redundantSequences = new ArrayList<SequenceI>();
- for (int i = 0; i < redundancy.length; i++)
- {
- if (value <= redundancy[i])
- {
- redundantSequences.add(originalSequences[i]);
- }
- }
-
- ap.idPanel.idCanvas.setHighlighted(redundantSequences);
- PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);
-
- }
-
- public void applyButton_actionPerformed()
- {
- Vector del = new Vector();
-
- 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.addElement(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] = (SequenceI) del.elementAt(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());
- AlignmentI alignment = ap.av.getAlignment();
- for (int i = 0; i < del.size(); i++)
- {
- alignment.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());
- }
-
- }
-
- public void undoButton_actionPerformed()
- {
- CommandI command = (CommandI) historyList.pop();
- command.undoCommand(null);
-
- if (ap.av.getHistoryList().contains(command))
- {
- ap.av.getHistoryList().remove(command);
- ap.alignFrame.updateEditMenuBar();
- ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());
- }
-
- ap.paintAlignment(true);
-
- if (historyList.size() == 0)
- {
- undoButton.setEnabled(false);
- }
- }
-
- public void valueField_actionPerformed(ActionEvent e)
- {
- try
- {
- int i = Integer.parseInt(valueField.getText());
- slider.setValue(i);
- } catch (Exception ex)
- {
- valueField.setText(slider.getValue() + "");
- }
- }
-
- public void windowOpened(WindowEvent evt)
- {
- }
-
- public void windowClosing(WindowEvent evt)
- {
- ap.idPanel.idCanvas.setHighlighted(null);
- }
-
- public void windowClosed(WindowEvent evt)
- {
- }
-
- public void windowActivated(WindowEvent evt)
- {
- }
-
- public void windowDeactivated(WindowEvent evt)
- {
- }
-
- public void windowIconified(WindowEvent evt)
- {
- }
-
- public void windowDeiconified(WindowEvent evt)
- {
- }
-}
+/*\r
+ * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)\r
+ * Copyright (C) $$Year-Rel$$ The Jalview Authors\r
+ * \r
+ * This file is part of Jalview.\r
+ * \r
+ * Jalview 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 3\r
+ * of the License, or (at your option) any later version.\r
+ * \r
+ * Jalview is distributed in the hope that it will be useful, but \r
+ * WITHOUT ANY WARRANTY; without even the implied warranty \r
+ * of MERCHANTABILITY or FITNESS FOR A PARTICULAR \r
+ * PURPOSE. See the GNU General Public License for more details.\r
+ * \r
+ * You should have received a copy of the GNU General Public License\r
+ * along with Jalview. If not, see <http://www.gnu.org/licenses/>.\r
+ * The Jalview Authors are detailed in the 'AUTHORS' file.\r
+ */\r
+package jalview.appletgui;\r
+\r
+import jalview.analysis.AlignSeq;\r
+import jalview.bin.JalviewLite;\r
+import jalview.commands.CommandI;\r
+import jalview.commands.EditCommand;\r
+import jalview.commands.EditCommand.Action;\r
+import jalview.datamodel.AlignmentI;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.datamodel.SequenceI;\r
+import jalview.util.MessageManager;\r
+\r
+import javax.swing.JFrame;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.AdjustmentEvent;\r
+import java.awt.event.AdjustmentListener;\r
+import java.awt.event.WindowEvent;\r
+import java.awt.event.WindowListener;\r
+import java.util.ArrayList;\r
+import java.util.List;\r
+import java.util.Stack;\r
+import java.util.Vector;\r
+\r
+public class RedundancyPanel extends SliderPanel implements Runnable,\r
+ WindowListener\r
+{\r
+ Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
+\r
+ float[] redundancy;\r
+\r
+ SequenceI[] originalSequences;\r
+\r
+ JFrame frame;\r
+\r
+ Vector redundantSeqs;\r
+\r
+ public RedundancyPanel(AlignmentPanel ap)\r
+ {\r
+ super(ap, 0, false, null);\r
+\r
+ redundantSeqs = new Vector();\r
+ this.ap = ap;\r
+ undoButton.setVisible(true);\r
+ applyButton.setVisible(true);\r
+ allGroupsCheck.setVisible(false);\r
+\r
+ label.setText(MessageManager\r
+ .getString("label.enter_redundancy_threshold"));\r
+ valueField.setText("100");\r
+\r
+ slider.setVisibleAmount(1);\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(100 + slider.getVisibleAmount());\r
+ slider.setValue(100);\r
+\r
+ slider.addAdjustmentListener(new AdjustmentListener()\r
+ {\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ sliderValueChanged();\r
+ }\r
+ });\r
+\r
+ frame = new JFrame();\r
+ frame.add(this);\r
+ JalviewLite.addFrame(frame, MessageManager\r
+ .getString("label.redundancy_threshold_selection"), 400, 100);\r
+\r
+ frame.addWindowListener(this);\r
+\r
+ Thread worker = new Thread(this);\r
+ worker.start();\r
+ }\r
+\r
+ /**\r
+ * This is a copy of remove redundancy in jalivew.datamodel.Alignment except\r
+ * we dont want to remove redundancy, just calculate once so we can use the\r
+ * slider to dynamically hide redundant sequences\r
+ * \r
+ * @param threshold\r
+ * DOCUMENT ME!\r
+ * @param sel\r
+ * DOCUMENT ME!\r
+ * \r
+ * @return DOCUMENT ME!\r
+ */\r
+ public void run()\r
+ {\r
+ label.setText(MessageManager.getString("label.calculating"));\r
+\r
+ slider.setVisible(false);\r
+ applyButton.setEnabled(false);\r
+ valueField.setVisible(false);\r
+\r
+ validate();\r
+\r
+ String[] omitHidden = null;\r
+\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+ int height;\r
+\r
+ int start, end;\r
+\r
+ if ((sg != null) && (sg.getSize() >= 1))\r
+ {\r
+ originalSequences = sg.getSequencesInOrder(ap.av.getAlignment());\r
+ start = sg.getStartRes();\r
+ end = sg.getEndRes();\r
+ }\r
+ else\r
+ {\r
+ originalSequences = ap.av.getAlignment().getSequencesArray();\r
+ start = 0;\r
+ end = ap.av.getAlignment().getWidth();\r
+ }\r
+\r
+ height = originalSequences.length;\r
+\r
+ redundancy = AlignSeq.computeRedundancyMatrix(originalSequences,\r
+ omitHidden, start, end, false);\r
+ label.setText(MessageManager\r
+ .getString("label.enter_redundancy_threshold"));\r
+ slider.setVisible(true);\r
+ applyButton.setEnabled(true);\r
+ valueField.setVisible(true);\r
+\r
+ validate();\r
+ sliderValueChanged();\r
+ // System.out.println("blob done "+ (System.currentTimeMillis()-start));\r
+ }\r
+\r
+ void sliderValueChanged()\r
+ {\r
+ if (redundancy == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ float value = slider.getValue();\r
+\r
+ List<SequenceI> redundantSequences = new ArrayList<SequenceI>();\r
+ for (int i = 0; i < redundancy.length; i++)\r
+ {\r
+ if (value <= redundancy[i])\r
+ {\r
+ redundantSequences.add(originalSequences[i]);\r
+ }\r
+ }\r
+\r
+ ap.idPanel.idCanvas.setHighlighted(redundantSequences);\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);\r
+\r
+ }\r
+\r
+ public void applyButton_actionPerformed()\r
+ {\r
+ Vector del = new Vector();\r
+\r
+ undoButton.setEnabled(true);\r
+\r
+ float value = slider.getValue();\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\r
+\r
+ for (int i = 0; i < redundancy.length; i++)\r
+ {\r
+ if (value <= redundancy[i])\r
+ {\r
+ del.addElement(originalSequences[i]);\r
+ }\r
+ }\r
+\r
+ // This has to be done before the restoreHistoryItem method of alignFrame\r
+ // will\r
+ // actually restore these sequences.\r
+ if (del.size() > 0)\r
+ {\r
+ SequenceI[] deleted = new SequenceI[del.size()];\r
+\r
+ int width = 0;\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ deleted[i] = (SequenceI) del.elementAt(i);\r
+ if (deleted[i].getLength() > width)\r
+ {\r
+ width = deleted[i].getLength();\r
+ }\r
+ }\r
+\r
+ EditCommand cut = new EditCommand(MessageManager.getString("action.remove_redundancy"),\r
+ Action.CUT, deleted, 0, width, ap.av.getAlignment());\r
+ AlignmentI alignment = ap.av.getAlignment();\r
+ for (int i = 0; i < del.size(); i++)\r
+ {\r
+ alignment.deleteSequence(deleted[i]);\r
+ if (sg != null)\r
+ {\r
+ sg.deleteSequence(deleted[i], false);\r
+ }\r
+ }\r
+\r
+ historyList.push(cut);\r
+\r
+ ap.alignFrame.addHistoryItem(cut);\r
+\r
+ PaintRefresher.Refresh(this, ap.av.getSequenceSetId(), true, true);\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
+ }\r
+\r
+ }\r
+\r
+ public void undoButton_actionPerformed()\r
+ {\r
+ CommandI command = (CommandI) historyList.pop();\r
+ command.undoCommand(null);\r
+\r
+ if (ap.av.getHistoryList().contains(command))\r
+ {\r
+ ap.av.getHistoryList().remove(command);\r
+ ap.alignFrame.updateEditMenuBar();\r
+ ap.av.firePropertyChange("alignment", null, ap.av.getAlignment().getSequences());\r
+ }\r
+\r
+ ap.paintAlignment(true);\r
+\r
+ if (historyList.size() == 0)\r
+ {\r
+ undoButton.setEnabled(false);\r
+ }\r
+ }\r
+\r
+ public void valueField_actionPerformed(ActionEvent e)\r
+ {\r
+ try\r
+ {\r
+ int i = Integer.parseInt(valueField.getText());\r
+ slider.setValue(i);\r
+ } catch (Exception ex)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ }\r
+ }\r
+\r
+ public void windowOpened(WindowEvent evt)\r
+ {\r
+ }\r
+\r
+ public void windowClosing(WindowEvent evt)\r
+ {\r
+ ap.idPanel.idCanvas.setHighlighted(null);\r
+ }\r
+\r
+ public void windowClosed(WindowEvent evt)\r
+ {\r
+ }\r
+\r
+ public void windowActivated(WindowEvent evt)\r
+ {\r
+ }\r
+\r
+ public void windowDeactivated(WindowEvent evt)\r
+ {\r
+ }\r
+\r
+ public void windowIconified(WindowEvent evt)\r
+ {\r
+ }\r
+\r
+ public void windowDeiconified(WindowEvent evt)\r
+ {\r
+ }\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff