*/\r
package jalview.gui;\r
\r
-import java.util.*;\r
+import jalview.datamodel.*;\r
+\r
+import jalview.jbgui.*;\r
\r
import java.awt.event.*;\r
-import javax.swing.event.*;\r
\r
-import jalview.datamodel.*;\r
-import jalview.jbgui.*;\r
+import java.util.*;\r
\r
-public class RedundancyPanel\r
- extends GSliderPanel\r
-{\r
- AlignFrame af;\r
- AlignmentPanel ap;\r
- Stack historyList = new Stack(); // simpler than synching with alignFrame.\r
+import javax.swing.event.*;\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
- public void applyButton_actionPerformed(ActionEvent e)\r
- {\r
- float threshold = slider.getValue();\r
- Vector del;\r
- HistoryItem it;\r
- historyList.push(it = new HistoryItem("Remove redundancy",\r
- ap.av.alignment, HistoryItem.HIDE));\r
-\r
- if ( (historyList.size() == 1) ||\r
- !af.historyList.contains(historyList.firstElement()))\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
- af.addHistoryItem( (HistoryItem) historyList.firstElement());\r
- af.updateEditMenuBar();\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
- undoButton.setEnabled(true);\r
-\r
- SequenceGroup sg = ap.av.getSelectionGroup();\r
-\r
- if ( (sg != null) && (sg.getSize() >= 1))\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void applyButton_actionPerformed(ActionEvent e)\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
+ float threshold = slider.getValue();\r
+ Vector del;\r
+ HistoryItem it;\r
+ historyList.push(it = new HistoryItem("Remove redundancy",\r
+ ap.av.alignment, HistoryItem.HIDE));\r
+\r
+ if ((historyList.size() == 1) ||\r
+ !af.historyList.contains(historyList.firstElement()))\r
{\r
- sg.deleteSequence( (SequenceI) del.elementAt(i), true);\r
+ af.addHistoryItem((HistoryItem) historyList.firstElement());\r
+ af.updateEditMenuBar();\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
+ undoButton.setEnabled(true);\r
\r
- del = ap.av.alignment.removeRedundancy(threshold, s);\r
- }\r
+ SequenceGroup sg = ap.av.getSelectionGroup();\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
+ 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
- ap.av.firePropertyChange("alignment", null,\r
- ap.av.getAlignment().getSequences());\r
- ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
+ while (i < ap.av.alignment.getHeight())\r
+ {\r
+ s.addElement(ap.av.alignment.getSequenceAt(i));\r
+ i++;\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
+ del = ap.av.alignment.removeRedundancy(threshold, s);\r
+ }\r
\r
- ap.av.updateConservation();\r
- ap.av.updateConsensus();\r
- af.updateEditMenuBar();\r
- ap.repaint();\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
- public void undoButton_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- af.restoreHistoryItem(hi);\r
+ ap.av.firePropertyChange("alignment", null,\r
+ ap.av.getAlignment().getSequences());\r
+ ap.av.resetSeqLimits(ap.seqPanel.seqCanvas.getHeight());\r
\r
- if (historyList.size() == 0)\r
- {\r
- undoButton.setEnabled(false);\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
- if (af.historyList.contains(hi))\r
- {\r
- af.historyList.remove(hi);\r
+ ap.av.updateConservation();\r
+ ap.av.updateConsensus();\r
af.updateEditMenuBar();\r
- }\r
+ ap.repaint();\r
}\r
- }\r
\r
- public void valueField_actionPerformed(ActionEvent e)\r
- {\r
- try\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void undoButton_actionPerformed(ActionEvent e)\r
{\r
- int i = Integer.parseInt(valueField.getText());\r
- slider.setValue(i);\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
- catch (Exception ex)\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ public void valueField_actionPerformed(ActionEvent e)\r
{\r
- valueField.setText(slider.getValue() + "");\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
}\r
git://source.jalview.org / jalview.git / blobdiff