X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=93a245759ac2d6527fe1b124972f280e843e9a36;hb=66e8b94c2ea875d4671ceec07a5c60954f4b12e3;hp=40f86b8250eaee4ec751ab43b950ef0927bca556;hpb=3538805166769a407d01240d196c723d9a458bed;p=jalview.git diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 40f86b8..93a2457 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -20,14 +20,16 @@ */ package jalview.gui; +import jalview.analysis.Conservation; import jalview.datamodel.SequenceGroup; import jalview.jbgui.GSliderPanel; -import jalview.schemes.CollectionColourSchemeI; +import jalview.renderer.ResidueShaderI; import jalview.util.MessageManager; 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; @@ -44,6 +46,8 @@ import javax.swing.event.InternalFrameEvent; */ public class SliderPanel extends GSliderPanel { + private static final String BACKGROUND = "Background"; + static JInternalFrame conservationSlider; static JInternalFrame PIDSlider; @@ -52,18 +56,24 @@ public class SliderPanel extends GSliderPanel boolean forConservation = true; - CollectionColourSchemeI cs; - - private static SliderPanel sliderPanel; + ResidueShaderI cs; /** - * Returns the currently active slider panel (or null if none). + * Returns the currently displayed slider panel (or null if none). * * @return */ public static SliderPanel getSliderPanel() { - return sliderPanel; + if (conservationSlider != null && conservationSlider.isVisible()) + { + return (SliderPanel) conservationSlider.getContentPane(); + } + if (PIDSlider != null && PIDSlider.isVisible()) + { + return (SliderPanel) PIDSlider.getContentPane(); + } + return null; } /** @@ -79,7 +89,7 @@ public class SliderPanel extends GSliderPanel * DOCUMENT ME! */ public SliderPanel(final AlignmentPanel ap, int value, - boolean forConserve, CollectionColourSchemeI scheme) + boolean forConserve, ResidueShaderI scheme) { this.ap = ap; this.cs = scheme; @@ -89,15 +99,15 @@ public class SliderPanel extends GSliderPanel 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); } @@ -117,7 +127,7 @@ public class SliderPanel extends GSliderPanel @Override public void mouseReleased(MouseEvent evt) { - ap.paintAlignment(true); + ap.paintAlignment(true, true); } }); @@ -126,25 +136,25 @@ public class SliderPanel extends GSliderPanel } /** - * DOCUMENT ME! + * Method to 'set focus' of the Conservation slider panel * * @param ap - * DOCUMENT ME! - * @param ccs - * 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, - CollectionColourSchemeI ccs, String source) + ResidueShaderI rs, String source) { - sliderPanel = null; + SliderPanel sliderPanel = null; if (conservationSlider == null) { - sliderPanel = new SliderPanel(ap, ccs.getConservationInc(), true, ccs); + sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs); conservationSlider = new JInternalFrame(); conservationSlider.setContentPane(sliderPanel); conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); @@ -152,16 +162,19 @@ public class SliderPanel extends GSliderPanel else { sliderPanel = (SliderPanel) conservationSlider.getContentPane(); - sliderPanel.valueField.setText(String.valueOf(ccs.getConservationInc())); - sliderPanel.cs = ccs; + 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()) { sliderPanel.setAllGroupsCheckEnabled(true); } @@ -218,39 +231,40 @@ public class SliderPanel extends GSliderPanel { Desktop.addInternalFrame(conservationSlider, conservationSlider.getTitle(), 420, 90, false); - conservationSlider - .addInternalFrameListener(new InternalFrameAdapter() - { - @Override - public void internalFrameClosed(InternalFrameEvent e) - { - conservationSlider = null; - } - }); + 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 ccs - * 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, - CollectionColourSchemeI ccs, String source) + public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs, + String source) { - int threshold = ccs.getThreshold(); + int threshold = rs.getThreshold(); + + SliderPanel sliderPanel = null; if (PIDSlider == null) { - sliderPanel = new SliderPanel(ap, threshold, false, ccs); + sliderPanel = new SliderPanel(ap, threshold, false, rs); PIDSlider = new JInternalFrame(); PIDSlider.setContentPane(sliderPanel); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); @@ -258,14 +272,15 @@ public class SliderPanel extends GSliderPanel else { sliderPanel = (SliderPanel) PIDSlider.getContentPane(); - sliderPanel.cs = ccs; - sliderPanel.valueField.setText(String.valueOf(ccs.getThreshold())); + 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 })); + PIDSlider.setTitle(MessageManager.formatMessage( + "label.percentage_identity_threshold", new String[] + { source == null ? BACKGROUND : source })); if (ap.av.getAlignment().getGroups() != null) { @@ -319,13 +334,14 @@ public class SliderPanel extends GSliderPanel { ap.av.setThreshold(percent); } - updateColourScheme(percent, cs); + updateColourScheme(percent, cs, null); if (allGroupsCheck.isSelected()) { - for (SequenceGroup sg : ap.av.getAlignment().getGroups()) + List groups = ap.av.getAlignment().getGroups(); + for (SequenceGroup sg : groups) { - updateColourScheme(percent, sg.getGroupColourScheme()); + updateColourScheme(percent, sg.getGroupColourScheme(), sg); } } @@ -338,8 +354,10 @@ public class SliderPanel extends GSliderPanel * * @param percent * @param scheme + * @param sg */ - protected void updateColourScheme(int percent, CollectionColourSchemeI scheme) + protected void updateColourScheme(int percent, ResidueShaderI scheme, + SequenceGroup sg) { if (scheme == null) { @@ -347,6 +365,20 @@ public class SliderPanel extends GSliderPanel } 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 @@ -364,6 +396,7 @@ public class SliderPanel extends GSliderPanel public void setAllGroupsCheckEnabled(boolean b) { allGroupsCheck.setEnabled(b); + allGroupsCheck.setSelected(ap.av.getColourAppliesToAllGroups()); } /** @@ -422,8 +455,8 @@ public class SliderPanel extends GSliderPanel static int getValue(JInternalFrame slider) { - return slider == null ? 0 : ((SliderPanel) slider.getContentPane()) - .getValue(); + return slider == null ? 0 + : ((SliderPanel) slider.getContentPane()).getValue(); } public static int getPIDValue()