-package jalview.gui;\r
-\r
-import jalview.jbgui.*;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import java.awt.event.*;\r
-import javax.swing.event.*;\r
-import javax.swing.*;\r
-import java.util.*;\r
-\r
-public class SliderPanel extends GSliderPanel\r
-{\r
- AlignmentPanel ap;\r
- boolean forConservation = true;\r
- ColourSchemeI cs;\r
-\r
- static JInternalFrame conservationSlider;\r
- static JInternalFrame PIDSlider;\r
-\r
- public static int setConservationSlider(AlignmentPanel ap, 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 ("+source+")");\r
- if(ap.av.alignment.getGroups()!=null)\r
- sp.setAllGroupsCheckEnabled( true );\r
- else\r
- sp.setAllGroupsCheckEnabled( false);\r
-\r
- return sp.getValue();\r
- }\r
-\r
- public static void showConservationSlider()\r
- {\r
- try{\r
- PIDSlider.setClosed(true);\r
- PIDSlider = null;\r
- }catch(Exception ex){}\r
-\r
-\r
- if(!conservationSlider.isVisible())\r
- {\r
- Desktop.addInternalFrame(conservationSlider, conservationSlider.getTitle(), 420, 90, false);\r
- conservationSlider.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
- {\r
- conservationSlider = null;\r
- }\r
- });\r
- conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
-\r
- }\r
-\r
- public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, String source)\r
- {\r
- SliderPanel pid = null;\r
-\r
- int threshold = 50;\r
- if (cs instanceof ResidueColourScheme)\r
- threshold = ( ( (ResidueColourScheme) cs).getThreshold());\r
- else if (cs instanceof ScoreColourScheme)\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
- PIDSlider.setTitle("Percentage Identity Threshold ("+source+")");\r
-\r
- if (ap.av.alignment.getGroups() != null)\r
- pid.setAllGroupsCheckEnabled(true);\r
- else\r
- pid.setAllGroupsCheckEnabled(false);\r
-\r
- return pid.getValue();\r
-\r
- }\r
-\r
- public static void showPIDSlider()\r
- {\r
- try{\r
- conservationSlider.setClosed(true);\r
- conservationSlider = null;\r
- }catch(Exception ex){}\r
-\r
- if(!PIDSlider.isVisible())\r
- {\r
- Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90, false);\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- PIDSlider.addInternalFrameListener(new javax.swing.event.\r
- InternalFrameAdapter()\r
- {\r
- public void internalFrameClosed(javax.swing.event.InternalFrameEvent e)\r
- {\r
- PIDSlider = null;\r
- }\r
- });\r
- PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);\r
- }\r
-\r
- }\r
-\r
-\r
- public SliderPanel(AlignmentPanel ap, int value, boolean forConserve, 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("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
-\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
- public void valueChanged(int i)\r
- {\r
- if(cs == null)\r
- return;\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
- toChange = cs;\r
-\r
-\r
- while( groupIndex > -1 )\r
- {\r
- if(allGroups!=null)\r
- toChange = ((SequenceGroup)allGroups.get(groupIndex)).cs;\r
-\r
- if (forConservation)\r
- {\r
- if (toChange instanceof ConservationColourScheme)\r
- ( (ConservationColourScheme) toChange).inc = i;\r
- }\r
- else\r
- {\r
- ( (ResidueColourScheme) toChange).setThreshold(i);\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
-\r
- public void valueField_actionPerformed(ActionEvent e)\r
- {\r
- try{\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
- public int getValue()\r
- {\r
- return Integer.parseInt(valueField.getText());\r
- }\r
-\r
-\r
-}\r
+/*
+ * 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.gui;
+
+import jalview.analysis.Conservation;
+import jalview.datamodel.SequenceGroup;
+import jalview.jbgui.GSliderPanel;
+import jalview.renderer.ResidueShaderI;
+import jalview.util.MessageManager;
+
+import java.awt.event.ActionEvent;
+import java.awt.event.MouseAdapter;
+import java.awt.event.MouseEvent;
+import java.beans.PropertyVetoException;
+import java.util.List;
+
+import javax.swing.JInternalFrame;
+import javax.swing.JLayeredPane;
+import javax.swing.event.ChangeEvent;
+import javax.swing.event.ChangeListener;
+import javax.swing.event.InternalFrameAdapter;
+import javax.swing.event.InternalFrameEvent;
+
+/**
+ * DOCUMENT ME!
+ *
+ * @author $author$
+ * @version $Revision$
+ */
+public class SliderPanel extends GSliderPanel
+{
+ private static final String BACKGROUND = "Background";
+
+ static JInternalFrame conservationSlider;
+
+ static JInternalFrame PIDSlider;
+
+ AlignmentPanel ap;
+
+ boolean forConservation = true;
+
+ ResidueShaderI cs;
+
+ /**
+ * Returns the currently displayed slider panel (or null if none).
+ *
+ * @return
+ */
+ public static SliderPanel getSliderPanel()
+ {
+ if (conservationSlider != null && conservationSlider.isVisible())
+ {
+ return (SliderPanel) conservationSlider.getContentPane();
+ }
+ if (PIDSlider != null && PIDSlider.isVisible())
+ {
+ return (SliderPanel) PIDSlider.getContentPane();
+ }
+ return null;
+ }
+
+ /**
+ * Creates a new SliderPanel object.
+ *
+ * @param ap
+ * DOCUMENT ME!
+ * @param value
+ * DOCUMENT ME!
+ * @param forConserve
+ * DOCUMENT ME!
+ * @param scheme
+ * DOCUMENT ME!
+ */
+ public SliderPanel(final AlignmentPanel ap, int value,
+ boolean forConserve, ResidueShaderI scheme)
+ {
+ this.ap = ap;
+ this.cs = scheme;
+ forConservation = forConserve;
+ undoButton.setVisible(false);
+ applyButton.setVisible(false);
+
+ if (forConservation)
+ {
+ label.setText(MessageManager.getString(
+ "label.enter_value_increase_conservation_visibility"));
+ slider.setMinimum(0);
+ slider.setMaximum(100);
+ }
+ else
+ {
+ label.setText(MessageManager.getString(
+ "label.enter_percentage_identity_above_which_colour_residues"));
+ slider.setMinimum(0);
+ slider.setMaximum(100);
+ }
+
+ slider.addChangeListener(new ChangeListener()
+ {
+ @Override
+ public void stateChanged(ChangeEvent evt)
+ {
+ valueField.setText(String.valueOf(slider.getValue()));
+ valueChanged(slider.getValue());
+ }
+ });
+
+ slider.addMouseListener(new MouseAdapter()
+ {
+ @Override
+ public void mouseReleased(MouseEvent evt)
+ {
+ ap.paintAlignment(true, true);
+ }
+ });
+
+ slider.setValue(value);
+ valueField.setText(String.valueOf(value));
+ }
+
+ /**
+ * Method to 'set focus' of the Conservation slider panel
+ *
+ * @param ap
+ * the panel to repaint on change of slider
+ * @param rs
+ * the colour scheme to update on change of slider
+ * @param source
+ * a text description for the panel's title
+ *
+ * @return
+ */
+ public static int setConservationSlider(AlignmentPanel ap,
+ ResidueShaderI rs, String source)
+ {
+ SliderPanel sliderPanel = null;
+
+ if (conservationSlider == null)
+ {
+ sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs);
+ conservationSlider = new JInternalFrame();
+ conservationSlider.setContentPane(sliderPanel);
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ else
+ {
+ sliderPanel = (SliderPanel) conservationSlider.getContentPane();
+ sliderPanel.valueField
+ .setText(String.valueOf(rs.getConservationInc()));
+ sliderPanel.cs = rs;
+ sliderPanel.ap = ap;
+ sliderPanel.slider.setValue(rs.getConservationInc());
+ }
+
+ conservationSlider.setTitle(MessageManager.formatMessage(
+ "label.conservation_colour_increment", new String[]
+ { source == null ? BACKGROUND : source }));
+
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ if (groups != null && !groups.isEmpty())
+ {
+ sliderPanel.setAllGroupsCheckEnabled(true);
+ sliderPanel.allGroupsCheck
+ .setSelected(ap.av.getColourAppliesToAllGroups());
+ }
+ else
+ {
+ sliderPanel.setAllGroupsCheckEnabled(false);
+ }
+
+ return sliderPanel.getValue();
+ }
+
+ /**
+ * Hides the PID slider panel if it is shown
+ */
+ public static void hidePIDSlider()
+ {
+ if (PIDSlider != null)
+ {
+ try
+ {
+ PIDSlider.setClosed(true);
+ PIDSlider = null;
+ } catch (PropertyVetoException ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * Hides the conservation slider panel if it is shown
+ */
+ public static void hideConservationSlider()
+ {
+ if (conservationSlider != null)
+ {
+ try
+ {
+ conservationSlider.setClosed(true);
+ conservationSlider = null;
+ } catch (PropertyVetoException ex)
+ {
+ }
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ */
+ public static void showConservationSlider()
+ {
+ hidePIDSlider();
+
+ if (!conservationSlider.isVisible())
+ {
+ Desktop.addInternalFrame(conservationSlider,
+ conservationSlider.getTitle(), true, FRAME_WIDTH,
+ FRAME_HEIGHT, false, true);
+ conservationSlider.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ conservationSlider = null;
+ }
+ });
+ conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ }
+
+ /**
+ * Method to 'set focus' of the PID slider panel
+ *
+ * @param ap
+ * the panel to repaint on change of slider
+ * @param rs
+ * the colour scheme to update on change of slider
+ * @param source
+ * a text description for the panel's title
+ *
+ * @return
+ */
+ public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs,
+ String source)
+ {
+ int threshold = rs.getThreshold();
+
+ SliderPanel sliderPanel = null;
+
+ if (PIDSlider == null)
+ {
+ sliderPanel = new SliderPanel(ap, threshold, false, rs);
+ PIDSlider = new JInternalFrame();
+ PIDSlider.setContentPane(sliderPanel);
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ else
+ {
+ sliderPanel = (SliderPanel) PIDSlider.getContentPane();
+ sliderPanel.cs = rs;
+ sliderPanel.ap = ap;
+ sliderPanel.valueField.setText(String.valueOf(rs.getThreshold()));
+ sliderPanel.slider.setValue(rs.getThreshold());
+ }
+
+ PIDSlider.setTitle(MessageManager.formatMessage(
+ "label.percentage_identity_threshold", new String[]
+ { source == null ? BACKGROUND : source }));
+
+ if (ap.av.getAlignment().getGroups() != null)
+ {
+ sliderPanel.setAllGroupsCheckEnabled(true);
+ }
+ else
+ {
+ sliderPanel.setAllGroupsCheckEnabled(false);
+ }
+
+ return sliderPanel.getValue();
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @return
+ */
+ public static JInternalFrame showPIDSlider()
+ {
+ hideConservationSlider();
+
+ if (!PIDSlider.isVisible())
+ {
+ Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), true,
+ FRAME_WIDTH, FRAME_HEIGHT, false, true);
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ PIDSlider.addInternalFrameListener(new InternalFrameAdapter()
+ {
+ @Override
+ public void internalFrameClosed(InternalFrameEvent e)
+ {
+ PIDSlider = null;
+ }
+ });
+ PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER);
+ }
+ return PIDSlider;
+ }
+
+ /**
+ * Updates the colour scheme with the current (identity threshold or
+ * conservation) percentage value. Also updates all groups if 'apply to all
+ * groups' is selected.
+ *
+ * @param percent
+ */
+ public void valueChanged(int percent)
+ {
+ if (!forConservation)
+ {
+ ap.av.setThreshold(percent);
+ }
+ updateColourScheme(percent, cs, null);
+
+ if (allGroupsCheck.isSelected())
+ {
+ List<SequenceGroup> groups = ap.av.getAlignment().getGroups();
+ for (SequenceGroup sg : groups)
+ {
+ updateColourScheme(percent, sg.getGroupColourScheme(), sg);
+ }
+ }
+
+ ap.getSeqPanel().seqCanvas.repaint();
+ }
+
+ /**
+ * Updates the colour scheme (if not null) with the current (identity
+ * threshold or conservation) percentage value
+ *
+ * @param percent
+ * @param scheme
+ * @param sg
+ */
+ protected void updateColourScheme(int percent, ResidueShaderI scheme,
+ SequenceGroup sg)
+ {
+ if (scheme == null)
+ {
+ return;
+ }
+ if (forConservation)
+ {
+ if (!scheme.conservationApplied() && sg != null)
+ {
+ /*
+ * first time the colour scheme has had Conservation shading applied
+ * - compute conservation
+ */
+ Conservation c = new Conservation("Group", sg.getSequences(null),
+ sg.getStartRes(), sg.getEndRes());
+ c.calculate();
+ c.verdict(false, ap.av.getConsPercGaps());
+ sg.cs.setConservation(c);
+
+ }
+ scheme.setConservationApplied(true);
+ scheme.setConservationInc(percent);
+ }
+ else
+ {
+ scheme.setThreshold(percent, ap.av.isIgnoreGapsConsensus());
+ }
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param b
+ * DOCUMENT ME!
+ */
+ public void setAllGroupsCheckEnabled(boolean b)
+ {
+ allGroupsCheck.setEnabled(b);
+ }
+
+ /**
+ * DOCUMENT ME!
+ *
+ * @param e
+ * DOCUMENT ME!
+ */
+ @Override
+ public void valueField_actionPerformed()
+ {
+ 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());
+ }
+
+ @Override
+ public void slider_mouseReleased(MouseEvent e)
+ {
+ if (ap.overviewPanel != null)
+ {
+ ap.overviewPanel.updateOverviewImage();
+ }
+ }
+
+ public static int getConservationValue()
+ {
+ return getValue(conservationSlider);
+ }
+
+ static int getValue(JInternalFrame slider)
+ {
+ return slider == null ? 0
+ : ((SliderPanel) slider.getContentPane()).getValue();
+ }
+
+ public static int getPIDValue()
+ {
+ return getValue(PIDSlider);
+ }
+
+ /**
+ * Answers true if the SliderPanel is for Conservation, false if it is for PID
+ * threshold
+ *
+ * @return
+ */
+ public boolean isForConservation()
+ {
+ return forConservation;
+ }
+
+ /**
+ * Answers the title for the slider panel; this may include 'Background' if
+ * for the alignment, or the group id if for a group
+ *
+ * @return
+ */
+ public String getTitle()
+ {
+ String title = null;
+ if (isForConservation())
+ {
+ if (conservationSlider != null)
+ {
+ title = conservationSlider.getTitle();
+ }
+ }
+ else if (PIDSlider != null)
+ {
+ title = PIDSlider.getTitle();
+ }
+ return title;
+ }
+}
git://source.jalview.org / jalview.git / blobdiff