-/*\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
-\r
-package jalview.appletgui;\r
-\r
-import java.util.*;\r
-\r
-import java.awt.*;\r
-import java.awt.event.*;\r
-\r
-import jalview.datamodel.*;\r
-import jalview.jbappletgui.*;\r
-import jalview.schemes.*;\r
-\r
-public class SliderPanel\r
- extends GSliderPanel\r
-{\r
- AlignmentPanel ap;\r
- boolean forConservation = true;\r
- ColourSchemeI cs;\r
-\r
- static Frame conservationSlider;\r
- static Frame PIDSlider;\r
-\r
- public static int setConservationSlider(AlignmentPanel ap, ColourSchemeI cs,\r
- 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 Frame();\r
- conservationSlider.add(sp);\r
- }\r
- else\r
- {\r
- sp = (SliderPanel) conservationSlider.getComponent(0);\r
- sp.cs = cs;\r
- }\r
-\r
- conservationSlider.setTitle("Conservation Colour Increment (" + 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
- public static void showConservationSlider()\r
- {\r
- try\r
- {\r
- PIDSlider.setVisible(false);\r
- PIDSlider = null;\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- if (!conservationSlider.isVisible())\r
- {\r
- jalview.bin.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 Frame();\r
- PIDSlider.add(pid);\r
- }\r
- else\r
- {\r
- pid = (SliderPanel) PIDSlider.getComponent(0);\r
- pid.cs = cs;\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
- public static void showPIDSlider()\r
- {\r
- try\r
- {\r
- conservationSlider.setVisible(false);\r
- conservationSlider = null;\r
- }\r
- catch (Exception ex)\r
- {}\r
-\r
- if (!PIDSlider.isVisible())\r
- {\r
- jalview.bin.JalviewLite.addFrame(PIDSlider, PIDSlider.getTitle(), 420,\r
- 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
- 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("Modify conservation visibility");\r
- slider.setMinimum(0);\r
- slider.setMaximum(50 + slider.getVisibleAmount());\r
- slider.setUnitIncrement(1);\r
- }\r
- else\r
- {\r
- label.setText("Colour residues above % occurence");\r
- slider.setMinimum(0);\r
- slider.setMaximum(100 + slider.getVisibleAmount());\r
- slider.setBlockIncrement(1);\r
- }\r
-\r
- slider.addAdjustmentListener(new AdjustmentListener()\r
- {\r
- public void adjustmentValueChanged(AdjustmentEvent 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
- 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.getState())\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.elementAt(groupIndex)).cs;\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, ap.av.getIgnoreGapsConsensus());\r
- }\r
-\r
- groupIndex--;\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 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
- 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
-}\r
+/*
+ * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9)
+ * Copyright (C) 2015 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.datamodel.SequenceGroup;
+import jalview.schemes.ColourSchemeI;
+import jalview.util.MessageManager;
+
+import java.awt.BorderLayout;
+import java.awt.Button;
+import java.awt.Checkbox;
+import java.awt.Color;
+import java.awt.FlowLayout;
+import java.awt.Frame;
+import java.awt.Label;
+import java.awt.Panel;
+import java.awt.Scrollbar;
+import java.awt.TextField;
+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;
+
+public class SliderPanel extends Panel implements ActionListener,
+ AdjustmentListener, MouseListener
+{
+ AlignmentPanel ap;
+
+ boolean forConservation = true;
+
+ ColourSchemeI cs;
+
+ static Frame conservationSlider;
+
+ static Frame 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 Frame();
+ 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())
+ {
+ jalview.bin.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 Frame();
+ 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())
+ {
+ jalview.bin.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.getState())
+ {
+ 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 Scrollbar slider = new Scrollbar();
+
+ protected TextField valueField = new TextField();
+
+ protected Label label = new Label();
+
+ Panel jPanel1 = new Panel();
+
+ Panel jPanel2 = new Panel();
+
+ protected Button applyButton = new Button();
+
+ protected Button undoButton = new Button();
+
+ FlowLayout flowLayout1 = new FlowLayout();
+
+ protected Checkbox allGroupsCheck = new Checkbox();
+
+ 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)
+ {
+ }
+}
git://source.jalview.org / jalview.git / blobdiff