-/*
- * 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.bin.JalviewLite;
-import jalview.datamodel.SequenceGroup;
-import jalview.schemes.ColourSchemeI;
-import jalview.util.MessageManager;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.FlowLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.AdjustmentEvent;
-import java.awt.event.AdjustmentListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-import java.util.Iterator;
-
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-import javax.swing.JScrollBar;
-import javax.swing.JTextField;
-
-public class SliderPanel extends JPanel implements ActionListener,
- AdjustmentListener, MouseListener
-{
- AlignmentPanel ap;
-
- boolean forConservation = true;
-
- ColourSchemeI cs;
-
- static JFrame conservationSlider;
-
- static JFrame PIDSlider;
-
- 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 JFrame();
- conservationSlider.add(sp);
- }
- else
- {
- sp = (SliderPanel) conservationSlider.getComponent(0);
- sp.cs = cs;
- }
-
- conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));
- if (ap.av.getAlignment().getGroups() != null)
- {
- sp.setAllGroupsCheckEnabled(true);
- }
- else
- {
- sp.setAllGroupsCheckEnabled(false);
- }
-
- return sp.getValue();
- }
-
- public static void showConservationSlider()
- {
- try
- {
- PIDSlider.setVisible(false);
- PIDSlider = null;
- } catch (Exception ex)
- {
- }
-
- if (!conservationSlider.isVisible())
- {
- JalviewLite.addFrame(conservationSlider,
- conservationSlider.getTitle(), 420, 100);
- conservationSlider.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- conservationSlider = null;
- }
- });
-
- }
-
- }
-
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,
- String source)
- {
- SliderPanel pid = null;
- if (PIDSlider == null)
- {
- pid = new SliderPanel(ap, 50, false, cs);
- PIDSlider = new JFrame();
- PIDSlider.add(pid);
- }
- else
- {
- pid = (SliderPanel) PIDSlider.getComponent(0);
- pid.cs = cs;
- }
- PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));
-
- if (ap.av.getAlignment().getGroups() != null)
- {
- pid.setAllGroupsCheckEnabled(true);
- }
- else
- {
- pid.setAllGroupsCheckEnabled(false);
- }
-
- return pid.getValue();
-
- }
-
- public static void showPIDSlider()
- {
- try
- {
- conservationSlider.setVisible(false);
- conservationSlider = null;
- } catch (Exception ex)
- {
- }
-
- if (!PIDSlider.isVisible())
- {
- JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),
- 420, 100);
- PIDSlider.addWindowListener(new WindowAdapter()
- {
- public void windowClosing(WindowEvent e)
- {
- PIDSlider = null;
- }
- });
- }
-
- }
-
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,
- ColourSchemeI cs)
- {
- try
- {
- jbInit();
- } catch (Exception e)
- {
- e.printStackTrace();
- }
- this.ap = ap;
- this.cs = cs;
- forConservation = forConserve;
- undoButton.setVisible(false);
- applyButton.setVisible(false);
- if (forConservation)
- {
- label.setText(MessageManager
- .getString("label.modify_conservation_visibility"));
- slider.setMinimum(0);
- slider.setMaximum(50 + slider.getVisibleAmount());
- slider.setUnitIncrement(1);
- }
- else
- {
- label.setText(MessageManager
- .getString("label.colour_residues_above_occurence"));
- slider.setMinimum(0);
- slider.setMaximum(100 + slider.getVisibleAmount());
- slider.setBlockIncrement(1);
- }
-
- slider.addAdjustmentListener(this);
- slider.addMouseListener(this);
-
- slider.setValue(value);
- valueField.setText(value + "");
- }
-
- public void valueChanged(int i)
- {
- if (cs == null)
- {
- return;
- }
-
- ColourSchemeI toChange = cs;
- Iterator<SequenceGroup> allGroups = null;
-
- if (allGroupsCheck.isSelected())
- {
- allGroups = ap.av.getAlignment().getGroups().listIterator();
- }
-
- while (toChange != null)
- {
- if (forConservation)
- {
- toChange.setConservationInc(i);
- }
- else
- {
- toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());
- }
- if (allGroups != null && allGroups.hasNext())
- {
- while ((toChange = allGroups.next().cs) == null
- && allGroups.hasNext())
- {
- ;
- }
- }
- else
- {
- toChange = null;
- }
- }
-
- ap.seqPanel.seqCanvas.repaint();
-
- }
-
- public void setAllGroupsCheckEnabled(boolean b)
- {
- allGroupsCheck.setEnabled(b);
- }
-
- public void actionPerformed(ActionEvent evt)
- {
- if (evt.getSource() == applyButton)
- {
- applyButton_actionPerformed();
- }
- else if (evt.getSource() == undoButton)
- {
- undoButton_actionPerformed();
- }
- else if (evt.getSource() == valueField)
- {
- valueField_actionPerformed();
- }
- }
-
- public void adjustmentValueChanged(AdjustmentEvent evt)
- {
- valueField.setText(slider.getValue() + "");
- valueChanged(slider.getValue());
- }
-
- public void valueField_actionPerformed()
- {
- try
- {
- int i = Integer.parseInt(valueField.getText());
- slider.setValue(i);
- } catch (Exception ex)
- {
- valueField.setText(slider.getValue() + "");
- }
- }
-
- public void setValue(int value)
- {
- slider.setValue(value);
- }
-
- public int getValue()
- {
- return Integer.parseInt(valueField.getText());
- }
-
- // this is used for conservation colours, PID colours and redundancy threshold
- protected JScrollBar slider = new JScrollBar();
-
- protected JTextField valueField = new JTextField();
-
- protected JLabel label = new JLabel();
-
- JPanel jPanel1 = new JPanel();
-
- JPanel jPanel2 = new JPanel();
-
- protected JButton applyButton = new JButton();
-
- protected JButton undoButton = new JButton();
-
- FlowLayout flowLayout1 = new FlowLayout();
-
- protected JCheckBox allGroupsCheck = new JCheckBox();
-
- BorderLayout borderLayout1 = new BorderLayout();
-
- BorderLayout borderLayout2 = new BorderLayout();
-
- FlowLayout flowLayout2 = new FlowLayout();
-
- private void jbInit() throws Exception
- {
- this.setLayout(borderLayout2);
-
- // slider.setMajorTickSpacing(10);
- // slider.setMinorTickSpacing(1);
- // slider.setPaintTicks(true);
- slider.setBackground(Color.white);
- slider.setFont(new java.awt.Font("Verdana", 0, 11));
- slider.setOrientation(0);
- valueField.setFont(new java.awt.Font("Verdana", 0, 11));
- valueField.setText(" ");
- valueField.addActionListener(this);
- valueField.setColumns(3);
- label.setFont(new java.awt.Font("Verdana", 0, 11));
- label.setText(MessageManager.getString("label.set_this_label_text"));
- jPanel1.setLayout(borderLayout1);
- jPanel2.setLayout(flowLayout1);
- applyButton.setFont(new java.awt.Font("Verdana", 0, 11));
- applyButton.setLabel(MessageManager.getString("action.apply"));
- applyButton.addActionListener(this);
- undoButton.setEnabled(false);
- undoButton.setFont(new java.awt.Font("Verdana", 0, 11));
- undoButton.setLabel(MessageManager.getString("action.undo"));
- undoButton.addActionListener(this);
- allGroupsCheck.setEnabled(false);
- allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));
- allGroupsCheck.setLabel(MessageManager
- .getString("action.apply_threshold_all_groups"));
- allGroupsCheck.setName(MessageManager
- .getString("action.apply_all_groups"));
- this.setBackground(Color.white);
- this.setForeground(Color.black);
- jPanel2.add(label, null);
- jPanel2.add(applyButton, null);
- jPanel2.add(undoButton, null);
- jPanel2.add(allGroupsCheck);
- jPanel1.add(valueField, java.awt.BorderLayout.EAST);
- jPanel1.add(slider, java.awt.BorderLayout.CENTER);
- this.add(jPanel1, java.awt.BorderLayout.SOUTH);
- this.add(jPanel2, java.awt.BorderLayout.CENTER);
- }
-
- protected void applyButton_actionPerformed()
- {
- }
-
- protected void undoButton_actionPerformed()
- {
- }
-
- public void mousePressed(MouseEvent evt)
- {
- }
-
- public void mouseReleased(MouseEvent evt)
- {
- ap.paintAlignment(true);
- }
-
- public void mouseClicked(MouseEvent evt)
- {
- }
-
- public void mouseEntered(MouseEvent evt)
- {
- }
-
- public void mouseExited(MouseEvent 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.bin.JalviewLite;\r
+import jalview.datamodel.SequenceGroup;\r
+import jalview.schemes.ColourSchemeI;\r
+import jalview.util.MessageManager;\r
+\r
+import java.awt.BorderLayout;\r
+import java.awt.Color;\r
+import java.awt.FlowLayout;\r
+import java.awt.event.ActionEvent;\r
+import java.awt.event.ActionListener;\r
+import java.awt.event.AdjustmentEvent;\r
+import java.awt.event.AdjustmentListener;\r
+import java.awt.event.MouseEvent;\r
+import java.awt.event.MouseListener;\r
+import java.awt.event.WindowAdapter;\r
+import java.awt.event.WindowEvent;\r
+import java.util.Iterator;\r
+\r
+import javax.swing.JButton;\r
+import javax.swing.JCheckBox;\r
+import javax.swing.JFrame;\r
+import javax.swing.JLabel;\r
+import javax.swing.JPanel;\r
+import javax.swing.JScrollBar;\r
+import javax.swing.JTextField;\r
+\r
+public class SliderPanel extends JPanel implements ActionListener,\r
+ AdjustmentListener, MouseListener\r
+{\r
+ AlignmentPanel ap;\r
+\r
+ boolean forConservation = true;\r
+\r
+ ColourSchemeI cs;\r
+\r
+ static JFrame conservationSlider;\r
+\r
+ static JFrame PIDSlider;\r
+\r
+ public static int setConservationSlider(AlignmentPanel ap,\r
+ ColourSchemeI cs, String source)\r
+ {\r
+ SliderPanel sp = null;\r
+\r
+ if (conservationSlider == null)\r
+ {\r
+ sp = new SliderPanel(ap, cs.getConservationInc(), true, cs);\r
+ conservationSlider = new JFrame();\r
+ conservationSlider.add(sp);\r
+ }\r
+ else\r
+ {\r
+ sp = (SliderPanel) conservationSlider.getComponent(0);\r
+ sp.cs = cs;\r
+ }\r
+\r
+ conservationSlider.setTitle(MessageManager.formatMessage("label.conservation_colour_increment", new String[]{source}));\r
+ if (ap.av.getAlignment().getGroups() != null)\r
+ {\r
+ sp.setAllGroupsCheckEnabled(true);\r
+ }\r
+ else\r
+ {\r
+ sp.setAllGroupsCheckEnabled(false);\r
+ }\r
+\r
+ return sp.getValue();\r
+ }\r
+\r
+ public static void showConservationSlider()\r
+ {\r
+ try\r
+ {\r
+ PIDSlider.setVisible(false);\r
+ PIDSlider = null;\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (!conservationSlider.isVisible())\r
+ {\r
+ JalviewLite.addFrame(conservationSlider,\r
+ conservationSlider.getTitle(), 420, 100);\r
+ conservationSlider.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ conservationSlider = null;\r
+ }\r
+ });\r
+\r
+ }\r
+\r
+ }\r
+\r
+ public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs,\r
+ String source)\r
+ {\r
+ SliderPanel pid = null;\r
+ if (PIDSlider == null)\r
+ {\r
+ pid = new SliderPanel(ap, 50, false, cs);\r
+ PIDSlider = new JFrame();\r
+ PIDSlider.add(pid);\r
+ }\r
+ else\r
+ {\r
+ pid = (SliderPanel) PIDSlider.getComponent(0);\r
+ pid.cs = cs;\r
+ }\r
+ PIDSlider.setTitle(MessageManager.formatMessage("label.percentage_identity_thereshold", new String[]{source}));\r
+\r
+ if (ap.av.getAlignment().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
+ public static void showPIDSlider()\r
+ {\r
+ try\r
+ {\r
+ conservationSlider.setVisible(false);\r
+ conservationSlider = null;\r
+ } catch (Exception ex)\r
+ {\r
+ }\r
+\r
+ if (!PIDSlider.isVisible())\r
+ {\r
+ JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(),\r
+ 420, 100);\r
+ PIDSlider.addWindowListener(new WindowAdapter()\r
+ {\r
+ public void windowClosing(WindowEvent e)\r
+ {\r
+ PIDSlider = null;\r
+ }\r
+ });\r
+ }\r
+\r
+ }\r
+\r
+ public SliderPanel(AlignmentPanel ap, int value, boolean forConserve,\r
+ ColourSchemeI cs)\r
+ {\r
+ try\r
+ {\r
+ jbInit();\r
+ } catch (Exception e)\r
+ {\r
+ e.printStackTrace();\r
+ }\r
+ this.ap = ap;\r
+ this.cs = cs;\r
+ forConservation = forConserve;\r
+ undoButton.setVisible(false);\r
+ applyButton.setVisible(false);\r
+ if (forConservation)\r
+ {\r
+ label.setText(MessageManager\r
+ .getString("label.modify_conservation_visibility"));\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(50 + slider.getVisibleAmount());\r
+ slider.setUnitIncrement(1);\r
+ }\r
+ else\r
+ {\r
+ label.setText(MessageManager\r
+ .getString("label.colour_residues_above_occurence"));\r
+ slider.setMinimum(0);\r
+ slider.setMaximum(100 + slider.getVisibleAmount());\r
+ slider.setBlockIncrement(1);\r
+ }\r
+\r
+ slider.addAdjustmentListener(this);\r
+ slider.addMouseListener(this);\r
+\r
+ slider.setValue(value);\r
+ valueField.setText(value + "");\r
+ }\r
+\r
+ public void valueChanged(int i)\r
+ {\r
+ if (cs == null)\r
+ {\r
+ return;\r
+ }\r
+\r
+ ColourSchemeI toChange = cs;\r
+ Iterator<SequenceGroup> allGroups = null;\r
+\r
+ if (allGroupsCheck.isSelected())\r
+ {\r
+ allGroups = ap.av.getAlignment().getGroups().listIterator();\r
+ }\r
+\r
+ while (toChange != null)\r
+ {\r
+ if (forConservation)\r
+ {\r
+ toChange.setConservationInc(i);\r
+ }\r
+ else\r
+ {\r
+ toChange.setThreshold(i, ap.av.isIgnoreGapsConsensus());\r
+ }\r
+ if (allGroups != null && allGroups.hasNext())\r
+ {\r
+ while ((toChange = allGroups.next().cs) == null\r
+ && allGroups.hasNext())\r
+ {\r
+ ;\r
+ }\r
+ }\r
+ else\r
+ {\r
+ toChange = null;\r
+ }\r
+ }\r
+\r
+ ap.seqPanel.seqCanvas.repaint();\r
+\r
+ }\r
+\r
+ public void setAllGroupsCheckEnabled(boolean b)\r
+ {\r
+ allGroupsCheck.setEnabled(b);\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ if (evt.getSource() == applyButton)\r
+ {\r
+ applyButton_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == undoButton)\r
+ {\r
+ undoButton_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == valueField)\r
+ {\r
+ valueField_actionPerformed();\r
+ }\r
+ }\r
+\r
+ public void adjustmentValueChanged(AdjustmentEvent evt)\r
+ {\r
+ valueField.setText(slider.getValue() + "");\r
+ valueChanged(slider.getValue());\r
+ }\r
+\r
+ public void valueField_actionPerformed()\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 setValue(int value)\r
+ {\r
+ slider.setValue(value);\r
+ }\r
+\r
+ public int getValue()\r
+ {\r
+ return Integer.parseInt(valueField.getText());\r
+ }\r
+\r
+ // this is used for conservation colours, PID colours and redundancy threshold\r
+ protected JScrollBar slider = new JScrollBar();\r
+\r
+ protected JTextField valueField = new JTextField();\r
+\r
+ protected JLabel label = new JLabel();\r
+\r
+ JPanel jPanel1 = new JPanel();\r
+\r
+ JPanel jPanel2 = new JPanel();\r
+\r
+ protected JButton applyButton = new JButton();\r
+\r
+ protected JButton undoButton = new JButton();\r
+ \r
+ FlowLayout flowLayout1 = new FlowLayout();\r
+\r
+ protected JCheckBox allGroupsCheck = new JCheckBox();\r
+\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+\r
+ BorderLayout borderLayout2 = new BorderLayout();\r
+\r
+ FlowLayout flowLayout2 = new FlowLayout();\r
+\r
+ private void jbInit() throws Exception\r
+ {\r
+ this.setLayout(borderLayout2);\r
+\r
+ // slider.setMajorTickSpacing(10);\r
+ // slider.setMinorTickSpacing(1);\r
+ // slider.setPaintTicks(true);\r
+ slider.setBackground(Color.white);\r
+ slider.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ slider.setOrientation(0);\r
+ valueField.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ valueField.setText(" ");\r
+ valueField.addActionListener(this);\r
+ valueField.setColumns(3);\r
+ label.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ label.setText(MessageManager.getString("label.set_this_label_text"));\r
+ jPanel1.setLayout(borderLayout1);\r
+ jPanel2.setLayout(flowLayout1);\r
+ applyButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ applyButton.setLabel(MessageManager.getString("action.apply"));\r
+ applyButton.addActionListener(this);\r
+ undoButton.setEnabled(false);\r
+ undoButton.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ undoButton.setLabel(MessageManager.getString("action.undo"));\r
+ undoButton.addActionListener(this);\r
+ allGroupsCheck.setEnabled(false);\r
+ allGroupsCheck.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ allGroupsCheck.setLabel(MessageManager\r
+ .getString("action.apply_threshold_all_groups"));\r
+ allGroupsCheck.setName(MessageManager\r
+ .getString("action.apply_all_groups"));\r
+ this.setBackground(Color.white);\r
+ this.setForeground(Color.black);\r
+ jPanel2.add(label, null);\r
+ jPanel2.add(applyButton, null);\r
+ jPanel2.add(undoButton, null);\r
+ jPanel2.add(allGroupsCheck);\r
+ jPanel1.add(valueField, java.awt.BorderLayout.EAST);\r
+ jPanel1.add(slider, java.awt.BorderLayout.CENTER);\r
+ this.add(jPanel1, java.awt.BorderLayout.SOUTH);\r
+ this.add(jPanel2, java.awt.BorderLayout.CENTER);\r
+ }\r
+\r
+ protected void applyButton_actionPerformed()\r
+ {\r
+ }\r
+\r
+ protected void undoButton_actionPerformed()\r
+ {\r
+ }\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {\r
+ ap.paintAlignment(true);\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {\r
+ }\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {\r
+ }\r
+}\r
git://source.jalview.org / jalviewjs.git / blobdiff