-/*\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 jalview.schemes.*;\r
-\r
-import java.awt.event.*;\r
-\r
-import java.util.*;\r
-\r
-import javax.swing.*;\r
-import javax.swing.event.*;\r
-\r
-\r
-/**\r
- * DOCUMENT ME!\r
- *\r
- * @author $author$\r
- * @version $Revision$\r
- */\r
-public class SliderPanel extends GSliderPanel\r
-{\r
- static JInternalFrame conservationSlider;\r
- static JInternalFrame PIDSlider;\r
- AlignmentPanel ap;\r
- boolean forConservation = true;\r
- ColourSchemeI cs;\r
-\r
- /**\r
- * Creates a new SliderPanel object.\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param value DOCUMENT ME!\r
- * @param forConserve DOCUMENT ME!\r
- * @param cs DOCUMENT ME!\r
- */\r
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
- ColourSchemeI cs)\r
- {\r
- this.ap = ap;\r
- this.cs = cs;\r
- forConservation = forConserve;\r
- undoButton.setVisible(false);\r
- applyButton.setVisible(false);\r
-\r
- if (forConservation)\r
- {\r
- label.setText("Enter value to increase conservation visibility");\r
- slider.setMinimum(0);\r
- slider.setMaximum(50);\r
- }\r
- else\r
- {\r
- label.setText("Enter % identity above which to colour residues");\r
- slider.setMinimum(0);\r
- slider.setMaximum(100);\r
- }\r
-\r
- slider.addChangeListener(new ChangeListener()\r
- {\r
- public void stateChanged(ChangeEvent evt)\r
- {\r
- valueField.setText(slider.getValue() + "");\r
- valueChanged(slider.getValue());\r
- }\r
- });\r
-\r
- slider.setValue(value);\r
- valueField.setText(value + "");\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param cs DOCUMENT ME!\r
- * @param source DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static int setConservationSlider(AlignmentPanel ap,\r
- ColourSchemeI cs, String source)\r
- {\r
- SliderPanel sp = null;\r
- ConservationColourScheme ccs = (ConservationColourScheme) cs;\r
-\r
- if (conservationSlider == null)\r
- {\r
- sp = new SliderPanel(ap, ccs.inc, true, cs);\r
- conservationSlider = new JInternalFrame();\r
- conservationSlider.setContentPane(sp);\r
- conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
- else\r
- {\r
- sp = (SliderPanel) conservationSlider.getContentPane();\r
- sp.cs = cs;\r
- }\r
-\r
- conservationSlider.setTitle("Conservation Colour Increment (" +\r
- source + ")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- {\r
- sp.setAllGroupsCheckEnabled(true);\r
- }\r
- else\r
- {\r
- sp.setAllGroupsCheckEnabled(false);\r
- }\r
-\r
- return sp.getValue();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public static void showConservationSlider()\r
- {\r
- try\r
- {\r
- PIDSlider.setClosed(true);\r
- PIDSlider = null;\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- if (!conservationSlider.isVisible())\r
- {\r
- Desktop.addInternalFrame(conservationSlider,\r
- conservationSlider.getTitle(), 420, 90, false);\r
- conservationSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent e)\r
- {\r
- conservationSlider = null;\r
- }\r
- });\r
- conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param ap DOCUMENT ME!\r
- * @param cs DOCUMENT ME!\r
- * @param source DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
- String source)\r
- {\r
- SliderPanel pid = null;\r
-\r
- int threshold = 50;\r
-\r
- if (cs instanceof ResidueColourScheme)\r
- {\r
- threshold = (((ResidueColourScheme) cs).getThreshold());\r
- }\r
- else if (cs instanceof ScoreColourScheme)\r
- {\r
- threshold = (((ScoreColourScheme) cs).getThreshold());\r
- }\r
-\r
- if (PIDSlider == null)\r
- {\r
- pid = new SliderPanel(ap, threshold, false, cs);\r
- PIDSlider = new JInternalFrame();\r
- PIDSlider.setContentPane(pid);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
- else\r
- {\r
- pid = (SliderPanel) PIDSlider.getContentPane();\r
- pid.cs = cs;\r
- }\r
-\r
- PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- {\r
- pid.setAllGroupsCheckEnabled(true);\r
- }\r
- else\r
- {\r
- pid.setAllGroupsCheckEnabled(false);\r
- }\r
-\r
- return pid.getValue();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- */\r
- public static void showPIDSlider()\r
- {\r
- try\r
- {\r
- conservationSlider.setClosed(true);\r
- conservationSlider = null;\r
- }\r
- catch (Exception ex)\r
- {\r
- }\r
-\r
- if (!PIDSlider.isVisible())\r
- {\r
- Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,\r
- false);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- PIDSlider.addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(\r
- javax.swing.event.InternalFrameEvent e)\r
- {\r
- PIDSlider = null;\r
- }\r
- });\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param i DOCUMENT ME!\r
- */\r
- public void valueChanged(int i)\r
- {\r
- if (cs == null)\r
- {\r
- return;\r
- }\r
-\r
- ColourSchemeI toChange = null;\r
- Vector allGroups = null;\r
- int groupIndex = 0;\r
-\r
- if (allGroupsCheck.isSelected())\r
- {\r
- allGroups = ap.av.alignment.getGroups();\r
- groupIndex = allGroups.size() - 1;\r
- }\r
- else\r
- {\r
- toChange = cs;\r
- }\r
-\r
- while (groupIndex > -1)\r
- {\r
- if (allGroups != null)\r
- {\r
- toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;\r
-\r
- if (toChange == null)\r
- {\r
- groupIndex--;\r
-\r
- continue;\r
- }\r
- }\r
-\r
- if (forConservation)\r
- {\r
- if (toChange instanceof ConservationColourScheme)\r
- {\r
- ((ConservationColourScheme) toChange).inc = i;\r
- }\r
- }\r
- else\r
- {\r
- ((ResidueColourScheme) toChange).setThreshold(i);\r
- }\r
-\r
- groupIndex--;\r
- }\r
-\r
- ap.seqPanel.seqCanvas.repaint();\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param b DOCUMENT ME!\r
- */\r
- public void setAllGroupsCheckEnabled(boolean b)\r
- {\r
- allGroupsCheck.setEnabled(b);\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
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @param value DOCUMENT ME!\r
- */\r
- public void setValue(int value)\r
- {\r
- slider.setValue(value);\r
- }\r
-\r
- /**\r
- * DOCUMENT ME!\r
- *\r
- * @return DOCUMENT ME!\r
- */\r
- public int getValue()\r
- {\r
- return Integer.parseInt(valueField.getText());\r
- }\r
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.7)
+ * Copyright (C) 2011 J Procter, AM Waterhouse, J Engelhardt, LM Lui, G Barton, M Clamp, S Searle
+ *
+ * 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/>.
+ */
+package jalview.gui;
+
+import java.util.*;
+
+import java.awt.event.*;
+import javax.swing.*;
+import javax.swing.event.*;
+
+import jalview.datamodel.*;
+import jalview.jbgui.*;
+import jalview.schemes.*;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel extends GSliderPanel
+{
+ static JInternalFrame conservationSlider;
+
+ static JInternalFrame PIDSlider;
+
+ AlignmentPanel ap;
+
+ boolean forConservation = true;
+
+ ColourSchemeI cs;
+
+ /**
+ * Creates a new SliderPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ * @param forConserve
+ * DOCUMENT ME!
+ * @param cs
+ * DOCUMENT ME!
+ */
+ public SliderPanel(final AlignmentPanel ap, int value,
+ boolean forConserve, ColourSchemeI cs)
+ {
+ this.ap = ap;
+ this.cs = cs;
+ forConservation = forConserve;
+ undoButton.setVisible(false);
+ applyButton.setVisible(false);
+
+ if (forConservation)
+ {
+ label.setText("Enter value to increase conservation visibility");
+ slider.setMinimum(0);
+ slider.setMaximum(100);
+ }
+ else
+ {
+ label.setText("Enter % identity above which to colour residues");
+ slider.setMinimum(0);
+ slider.setMaximum(100);
+ }
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ public void stateChanged(ChangeEvent evt)
+ {
+ valueField.setText(slider.getValue() + "");
+ valueChanged(slider.getValue());
+ }
+ });
+
+ slider.addMouseListener(new MouseAdapter()
+ {
+ public void mouseReleased(MouseEvent evt)
+ {
+ ap.paintAlignment(true);
+ }
+ });
+
+ slider.setValue(value);
+ valueField.setText(value + "");
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param cs
+ * DOCUMENT ME!
+ * @param source
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setConservationSlider(AlignmentPanel ap,
+ ColourSchemeI cs, String source)
+ {
+ SliderPanel sp = null;
+
+ if (conservationSlider == null)
+ {
+ sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);
+ conservationSlider = new JInternalFrame();
+ conservationSlider.setContentPane(sp);
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ else
+ {
+ sp = (SliderPanel) conservationSlider.getContentPane();
+ sp.cs = cs;
+ }
+
+ conservationSlider.setTitle("Conservation Colour Increment (" + source
+ + ")");
+
+ if (ap.av.alignment.getGroups() != null)
+ {
+ sp.setAllGroupsCheckEnabled(true);
+ }
+ else
+ {
+ sp.setAllGroupsCheckEnabled(false);
+ }
+
+ return sp.getValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static void showConservationSlider()
+ {
+ try
+ {
+ PIDSlider.setClosed(true);
+ PIDSlider = null;
+ } catch (Exception ex)
+ {
+ }
+
+ if (!conservationSlider.isVisible())
+ {
+ Desktop.addInternalFrame(conservationSlider,
+ conservationSlider.getTitle(), 420, 90, false);
+ conservationSlider
+ .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent e)
+ {
+ conservationSlider = null;
+ }
+ });
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param cs
+ * DOCUMENT ME!
+ * @param source
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
+ String source)
+ {
+ SliderPanel pid = null;
+
+ int threshold = cs.getThreshold();
+
+ if (PIDSlider == null)
+ {
+ pid = new SliderPanel(ap, threshold, false, cs);
+ PIDSlider = new JInternalFrame();
+ PIDSlider.setContentPane(pid);
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ else
+ {
+ pid = (SliderPanel) PIDSlider.getContentPane();
+ pid.cs = cs;
+ }
+
+ PIDSlider.setTitle("Percentage Identity Threshold (" + source + ")");
+
+ if (ap.av.alignment.getGroups() != null)
+ {
+ pid.setAllGroupsCheckEnabled(true);
+ }
+ else
+ {
+ pid.setAllGroupsCheckEnabled(false);
+ }
+
+ return pid.getValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static void showPIDSlider()
+ {
+ try
+ {
+ conservationSlider.setClosed(true);
+ conservationSlider = null;
+ } catch (Exception ex)
+ {
+ }
+
+ if (!PIDSlider.isVisible())
+ {
+ Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90,
+ false);
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ PIDSlider
+ .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter()
+ {
+ public void internalFrameClosed(
+ javax.swing.event.InternalFrameEvent e)
+ {
+ PIDSlider = null;
+ }
+ });
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param i
+ * DOCUMENT ME!
+ */
+ public void valueChanged(int i)
+ {
+ if (cs == null)
+ {
+ return;
+ }
+
+ ColourSchemeI toChange = null;
+ Vector allGroups = null;
+ int groupIndex = 0;
+
+ if (allGroupsCheck.isSelected())
+ {
+ allGroups = ap.av.alignment.getGroups();
+ groupIndex = allGroups.size() - 1;
+ }
+ else
+ {
+ toChange = cs;
+ }
+
+ while (groupIndex > -1)
+ {
+ if (allGroups != null)
+ {
+ toChange = ((SequenceGroup) allGroups.get(groupIndex)).cs;
+
+ if (toChange == null)
+ {
+ groupIndex--;
+
+ continue;
+ }
+ }
+
+ if (forConservation)
+ {
+ if (toChange.conservationApplied())
+ {
+ toChange.setConservationInc(i);
+ }
+ }
+ else
+ {
+ toChange.setThreshold(i, ap.av.getIgnoreGapsConsensus());
+ }
+
+ groupIndex--;
+ }
+
+ ap.seqPanel.seqCanvas.repaint();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setAllGroupsCheckEnabled(boolean b)
+ {
+ allGroupsCheck.setEnabled(b);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ public void valueField_actionPerformed(ActionEvent e)
+ {
+ try
+ {
+ int i = Integer.parseInt(valueField.getText());
+ slider.setValue(i);
+ } catch (NumberFormatException ex)
+ {
+ valueField.setText(slider.getValue() + "");
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param value
+ * DOCUMENT ME!
+ */
+ public void setValue(int value)
+ {
+ slider.setValue(value);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return DOCUMENT ME!
+ */
+ public int getValue()
+ {
+ return Integer.parseInt(valueField.getText());
+ }
+
+ public void slider_mouseReleased(MouseEvent e)
+ {
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+
+}
git://source.jalview.org / jalview.git / blobdiff