X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FSliderPanel.java;h=31ad0836f03accf1c9ceac9c7334cbfad043835d;hb=e6b6f08502b7a31b22ae18e31c4ada1dba58be54;hp=0c4e03e89f57b538279384c4f4eb2fb462f2d466;hpb=424f6f03e8fb5e40cceca09fc8ffd72b41e3a9e4;p=jalview.git diff --git a/src/jalview/gui/SliderPanel.java b/src/jalview/gui/SliderPanel.java index 0c4e03e..31ad083 100755 --- a/src/jalview/gui/SliderPanel.java +++ b/src/jalview/gui/SliderPanel.java @@ -20,6 +20,7 @@ */ package jalview.gui; +import jalview.analysis.Conservation; import jalview.datamodel.SequenceGroup; import jalview.jbgui.GSliderPanel; import jalview.renderer.ResidueShaderI; @@ -28,6 +29,7 @@ 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; @@ -42,14 +44,11 @@ import javax.swing.event.InternalFrameEvent; * @author $author$ * @version $Revision$ */ +@SuppressWarnings("serial") public class SliderPanel extends GSliderPanel { private static final String BACKGROUND = "Background"; - static JInternalFrame conservationSlider; - - static JInternalFrame PIDSlider; - AlignmentPanel ap; boolean forConservation = true; @@ -63,6 +62,12 @@ public class SliderPanel extends GSliderPanel */ public static SliderPanel getSliderPanel() { + + JInternalFrame conservationSlider = Desktop + .getInstance().conservationSlider; + + JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider; + if (conservationSlider != null && conservationSlider.isVisible()) { return (SliderPanel) conservationSlider.getContentPane(); @@ -97,15 +102,15 @@ 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); } @@ -115,7 +120,7 @@ public class SliderPanel extends GSliderPanel @Override public void stateChanged(ChangeEvent evt) { - valueField.setText(slider.getValue() + ""); + valueField.setText(String.valueOf(slider.getValue())); valueChanged(slider.getValue()); } }); @@ -125,12 +130,12 @@ public class SliderPanel extends GSliderPanel @Override public void mouseReleased(MouseEvent evt) { - ap.paintAlignment(true); + ap.paintAlignment(true, true); } }); slider.setValue(value); - valueField.setText(value + ""); + valueField.setText(String.valueOf(value)); } /** @@ -150,27 +155,33 @@ public class SliderPanel extends GSliderPanel { SliderPanel sliderPanel = null; + JInternalFrame conservationSlider = Desktop + .getInstance().conservationSlider; + if (conservationSlider == null) { sliderPanel = new SliderPanel(ap, rs.getConservationInc(), true, rs); - conservationSlider = new JInternalFrame(); + conservationSlider = Desktop + .getInstance().conservationSlider = new JInternalFrame(); conservationSlider.setContentPane(sliderPanel); conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); } else { sliderPanel = (SliderPanel) conservationSlider.getContentPane(); - sliderPanel.valueField.setText(String.valueOf(rs.getConservationInc())); + 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 })); + "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); } @@ -187,12 +198,14 @@ public class SliderPanel extends GSliderPanel */ public static void hidePIDSlider() { + JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider; + if (PIDSlider != null) { try { PIDSlider.setClosed(true); - PIDSlider = null; + Desktop.getInstance().PIDSlider = null; } catch (PropertyVetoException ex) { } @@ -204,12 +217,15 @@ public class SliderPanel extends GSliderPanel */ public static void hideConservationSlider() { + JInternalFrame conservationSlider = Desktop + .getInstance().conservationSlider; + if (conservationSlider != null) { try { conservationSlider.setClosed(true); - conservationSlider = null; + Desktop.getInstance().conservationSlider = null; } catch (PropertyVetoException ex) { } @@ -223,19 +239,22 @@ public class SliderPanel extends GSliderPanel { hidePIDSlider(); + JInternalFrame conservationSlider = Desktop + .getInstance().conservationSlider; + if (!conservationSlider.isVisible()) { Desktop.addInternalFrame(conservationSlider, - conservationSlider.getTitle(), 420, 90, false); - conservationSlider - .addInternalFrameListener(new InternalFrameAdapter() - { - @Override - public void internalFrameClosed(InternalFrameEvent e) - { - conservationSlider = null; - } - }); + conservationSlider.getTitle(), true, FRAME_WIDTH, + FRAME_HEIGHT, false, true); + conservationSlider.addInternalFrameListener(new InternalFrameAdapter() + { + @Override + public void internalFrameClosed(InternalFrameEvent e) + { + Desktop.getInstance().conservationSlider = null; + } + }); conservationSlider.setLayer(JLayeredPane.PALETTE_LAYER); } } @@ -252,17 +271,19 @@ public class SliderPanel extends GSliderPanel * * @return */ - public static int setPIDSliderSource(AlignmentPanel ap, - ResidueShaderI rs, String source) + public static int setPIDSliderSource(AlignmentPanel ap, ResidueShaderI rs, + String source) { int threshold = rs.getThreshold(); SliderPanel sliderPanel = null; + JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider; + if (PIDSlider == null) { sliderPanel = new SliderPanel(ap, threshold, false, rs); - PIDSlider = new JInternalFrame(); + PIDSlider = Desktop.getInstance().PIDSlider = new JInternalFrame(); PIDSlider.setContentPane(sliderPanel); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); } @@ -276,8 +297,8 @@ public class SliderPanel extends GSliderPanel } PIDSlider.setTitle(MessageManager.formatMessage( - "label.percentage_identity_threshold", - new String[] { source == null ? BACKGROUND : source })); + "label.percentage_identity_threshold", new String[] + { source == null ? BACKGROUND : source })); if (ap.av.getAlignment().getGroups() != null) { @@ -300,17 +321,19 @@ public class SliderPanel extends GSliderPanel { hideConservationSlider(); + JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider; + 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 InternalFrameAdapter() { @Override public void internalFrameClosed(InternalFrameEvent e) { - PIDSlider = null; + Desktop.getInstance().PIDSlider = null; } }); PIDSlider.setLayer(JLayeredPane.PALETTE_LAYER); @@ -331,13 +354,14 @@ 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); } } @@ -350,8 +374,10 @@ public class SliderPanel extends GSliderPanel * * @param percent * @param scheme + * @param sg */ - protected void updateColourScheme(int percent, ResidueShaderI scheme) + protected void updateColourScheme(int percent, ResidueShaderI scheme, + SequenceGroup sg) { if (scheme == null) { @@ -359,6 +385,20 @@ 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 @@ -429,18 +469,18 @@ public class SliderPanel extends GSliderPanel public static int getConservationValue() { - return getValue(conservationSlider); + return getValue(Desktop.getInstance().conservationSlider); } 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() { - return getValue(PIDSlider); + return getValue(Desktop.getInstance().PIDSlider); } /** @@ -463,6 +503,10 @@ public class SliderPanel extends GSliderPanel public String getTitle() { String title = null; + JInternalFrame conservationSlider = Desktop + .getInstance().conservationSlider; + JInternalFrame PIDSlider = Desktop.getInstance().PIDSlider; + if (isForConservation()) { if (conservationSlider != null)