X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=37ab21974dbe015c9305c4b5e118ccc644f9baa7;hb=69b246bd6330f05271ca15a440c8442b03b7db6c;hp=02a8ed7e6cd031b6e975ce97b456daafd15b5469;hpb=17e77c3f2949a0729322b4a8d907f3f34b6a9914;p=jalview.git diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 02a8ed7..37ab219 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9) - * Copyright (C) 2015 The Jalview Authors + * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$) + * Copyright (C) $$Year-Rel$$ The Jalview Authors * * This file is part of Jalview. * @@ -20,20 +20,24 @@ */ package jalview.gui; +import jalview.analysis.Conservation; import jalview.datamodel.SequenceGroup; import jalview.jbgui.GSliderPanel; -import jalview.schemes.ColourSchemeI; +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.util.Iterator; +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! @@ -43,6 +47,8 @@ import javax.swing.event.ChangeListener; */ public class SliderPanel extends GSliderPanel { + private static final String BACKGROUND = "Background"; + static JInternalFrame conservationSlider; static JInternalFrame PIDSlider; @@ -51,7 +57,25 @@ public class SliderPanel extends GSliderPanel boolean forConservation = true; - ColourSchemeI cs; + 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. @@ -62,256 +86,309 @@ public class SliderPanel extends GSliderPanel * DOCUMENT ME! * @param forConserve * DOCUMENT ME! - * @param cs + * @param scheme * DOCUMENT ME! */ public SliderPanel(final AlignmentPanel ap, int value, - boolean forConserve, ColourSchemeI cs) + boolean forConserve, ResidueShaderI scheme) { this.ap = ap; - this.cs = cs; + this.cs = scheme; forConservation = forConserve; undoButton.setVisible(false); applyButton.setVisible(false); if (forConservation) { - label.setText(MessageManager - .getString("label.enter_value_increase_conservation_visibility")); + 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")); + 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(slider.getValue() + ""); + valueField.setText(String.valueOf(slider.getValue())); valueChanged(slider.getValue()); } }); slider.addMouseListener(new MouseAdapter() { + @Override public void mouseReleased(MouseEvent evt) { - ap.paintAlignment(true); + ap.paintAlignment(true, true); } }); slider.setValue(value); - valueField.setText(value + ""); + valueField.setText(String.valueOf(value)); } /** - * DOCUMENT ME! + * Method to 'set focus' of the Conservation slider panel * * @param ap - * DOCUMENT ME! - * @param cs - * DOCUMENT ME! + * the panel to repaint on change of slider + * @param rs + * the colour scheme to update on change of slider * @param source - * DOCUMENT ME! + * a text description for the panel's title * - * @return DOCUMENT ME! + * @return */ public static int setConservationSlider(AlignmentPanel ap, - ColourSchemeI cs, String source) + ResidueShaderI rs, String source) { - SliderPanel sp = null; + SliderPanel sliderPanel = null; if (conservationSlider == null) { - sp = new SliderPanel(ap, cs.getConservationInc(), true, cs); + sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs); conservationSlider = new JInternalFrame(); - conservationSlider.setContentPane(sp); + conservationSlider.setContentPane(sliderPanel); conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); } else { - sp = (SliderPanel) conservationSlider.getContentPane(); - sp.cs = cs; + 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 })); + conservationSlider.setTitle(MessageManager.formatMessage( + "label.conservation_colour_increment", new String[] + { source == null ? BACKGROUND : source })); - if (ap.av.getAlignment().getGroups() != null) + List groups = ap.av.getAlignment().getGroups(); + if (groups != null && !groups.isEmpty()) { - sp.setAllGroupsCheckEnabled(true); + sliderPanel.setAllGroupsCheckEnabled(true); + sliderPanel.allGroupsCheck + .setSelected(ap.av.getColourAppliesToAllGroups()); } else { - sp.setAllGroupsCheckEnabled(false); + sliderPanel.setAllGroupsCheckEnabled(false); } - return sp.getValue(); + return sliderPanel.getValue(); } /** - * DOCUMENT ME! + * Hides the PID slider panel if it is shown */ - public static void showConservationSlider() + public static void hidePIDSlider() { - try + if (PIDSlider != null) { - PIDSlider.setClosed(true); - PIDSlider = null; - } catch (Exception ex) + 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(), 420, 90, false); - conservationSlider - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent e) - { - conservationSlider = null; - } - }); + 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); } } /** - * DOCUMENT ME! + * Method to 'set focus' of the PID slider panel * * @param ap - * DOCUMENT ME! - * @param cs - * DOCUMENT ME! + * the panel to repaint on change of slider + * @param rs + * the colour scheme to update on change of slider * @param source - * DOCUMENT ME! + * a text description for the panel's title * - * @return DOCUMENT ME! + * @return */ - public static int setPIDSliderSource(AlignmentPanel ap, ColourSchemeI cs, + public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs, String source) { - SliderPanel pid = null; + int threshold = rs.getThreshold(); - int threshold = cs.getThreshold(); + SliderPanel sliderPanel = null; if (PIDSlider == null) { - pid = new SliderPanel(ap, threshold, false, cs); + sliderPanel = new SliderPanel(ap, threshold, false, rs); PIDSlider = new JInternalFrame(); - PIDSlider.setContentPane(pid); + PIDSlider.setContentPane(sliderPanel); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); } else { - pid = (SliderPanel) PIDSlider.getContentPane(); - pid.cs = cs; + 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_thereshold", - new String[] { source })); + PIDSlider.setTitle(MessageManager.formatMessage( + "label.percentage_identity_threshold", new String[] + { source == null ? BACKGROUND : source })); if (ap.av.getAlignment().getGroups() != null) { - pid.setAllGroupsCheckEnabled(true); + sliderPanel.setAllGroupsCheckEnabled(true); } else { - pid.setAllGroupsCheckEnabled(false); + sliderPanel.setAllGroupsCheckEnabled(false); } - return pid.getValue(); + return sliderPanel.getValue(); } /** * DOCUMENT ME! + * + * @return */ - public static void showPIDSlider() + public static JInternalFrame showPIDSlider() { - try - { - conservationSlider.setClosed(true); - conservationSlider = null; - } catch (Exception ex) - { - } + hideConservationSlider(); if (!PIDSlider.isVisible()) { - Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), 420, 90, - false); + Desktop.addInternalFrame(PIDSlider, PIDSlider.getTitle(), true, + FRAME_WIDTH, FRAME_HEIGHT, false, true); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); - PIDSlider - .addInternalFrameListener(new javax.swing.event.InternalFrameAdapter() - { - public void internalFrameClosed( - javax.swing.event.InternalFrameEvent e) - { - PIDSlider = null; - } - }); + PIDSlider.addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + PIDSlider = null; + } + }); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); } + return PIDSlider; } /** - * DOCUMENT ME! + * 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 i - * DOCUMENT ME! + * @param percent */ - public void valueChanged(int i) + public void valueChanged(int percent) { - if (cs == null) + if (!forConservation) { - return; + ap.av.setThreshold(percent); } - - ColourSchemeI toChange = cs; - Iterator allGroups = null; + updateColourScheme(percent, cs, null); if (allGroupsCheck.isSelected()) { - allGroups = ap.av.getAlignment().getGroups().listIterator(); + List groups = ap.av.getAlignment().getGroups(); + for (SequenceGroup sg : groups) + { + updateColourScheme(percent, sg.getGroupColourScheme(), sg); + } } - while (toChange != null) + 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) { - 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 + return; + } + if (forConservation) + { + if (!scheme.conservationApplied() && sg != null) { - toChange = 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()); } - - ap.getSeqPanel().seqCanvas.repaint(); } /** @@ -331,7 +408,8 @@ public class SliderPanel extends GSliderPanel * @param e * DOCUMENT ME! */ - public void valueField_actionPerformed(ActionEvent e) + @Override + public void valueField_actionPerformed() { try { @@ -364,6 +442,7 @@ public class SliderPanel extends GSliderPanel return Integer.parseInt(valueField.getText()); } + @Override public void slider_mouseReleased(MouseEvent e) { if (ap.overviewPanel != null) @@ -372,4 +451,53 @@ public class SliderPanel extends GSliderPanel } } + 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; + } }