X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=5e15364d48c229f1f90bb65b762328007c14c758;hb=32c56f877253fa8917d4f4640ed65d6e63376dac;hp=5bad4d67f6200e3df73e9d5d087a74b683349bf8;hpb=db93a1adcbe0a4eaaf06e0a70ade0d6c5c1961c3;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 5bad4d6..5e15364 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -1,6 +1,6 @@ /* - * Jalview - A Sequence Alignment Editor and Viewer (Version 2.9.0b2) - * 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. * @@ -58,13 +58,15 @@ import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; import java.util.Arrays; import java.util.Enumeration; +import java.util.HashSet; import java.util.List; import java.util.Map; +import java.util.Set; import java.util.Vector; -public class FeatureSettings extends Panel implements ItemListener, - MouseListener, MouseMotionListener, ActionListener, - AdjustmentListener, FeatureSettingsControllerI +public class FeatureSettings extends Panel + implements ItemListener, MouseListener, MouseMotionListener, + ActionListener, AdjustmentListener, FeatureSettingsControllerI { FeatureRenderer fr; @@ -106,6 +108,7 @@ public class FeatureSettings extends Panel implements ItemListener, { fr.findAllFeatures(true); // was default - now true to make all visible } + groupPanel = new Panel(); discoverAllFeatureData(); @@ -133,17 +136,22 @@ public class FeatureSettings extends Panel implements ItemListener, add(lowerPanel, BorderLayout.SOUTH); - if (groupPanel != null) - { - groupPanel.setLayout(new GridLayout( - (fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote - this was - // scaled on number of - // visible groups. seems - // broken - groupPanel.validate(); + groupPanel.setLayout( + new GridLayout((fr.getFeatureGroupsSize()) / 4 + 1, 4)); // JBPNote + // - this + // was + // scaled + // on + // number + // of + // visible + // groups. + // seems + // broken + groupPanel.validate(); + + add(groupPanel, BorderLayout.NORTH); - add(groupPanel, BorderLayout.NORTH); - } frame = new Frame(); frame.add(this); final FeatureSettings me = this; @@ -174,14 +182,12 @@ public class FeatureSettings extends Panel implements ItemListener, public void paint(Graphics g) { g.setColor(Color.black); - g.drawString(MessageManager - .getString("label.no_features_added_to_this_alignment"), 10, 20); - g.drawString(MessageManager - .getString("label.features_can_be_added_from_searches_1"), 10, - 40); - g.drawString(MessageManager - .getString("label.features_can_be_added_from_searches_2"), 10, - 60); + g.drawString(MessageManager.getString( + "label.no_features_added_to_this_alignment"), 10, 20); + g.drawString(MessageManager.getString( + "label.features_can_be_added_from_searches_1"), 10, 40); + g.drawString(MessageManager.getString( + "label.features_can_be_added_from_searches_2"), 10, 60); } protected void popupSort(final MyCheckbox check, @@ -189,8 +195,9 @@ public class FeatureSettings extends Panel implements ItemListener, { final String type = check.type; final FeatureColourI typeCol = fr.getFeatureStyle(type); - PopupMenu men = new PopupMenu(MessageManager.formatMessage( - "label.settings_for_type", new String[] { type })); + PopupMenu men = new PopupMenu(MessageManager + .formatMessage("label.settings_for_type", new String[] + { type })); java.awt.MenuItem scr = new MenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); @@ -201,8 +208,9 @@ public class FeatureSettings extends Panel implements ItemListener, @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays - .asList(new String[] { type })); + me.ap.alignFrame.avc + .sortAlignmentByFeatureScore(Arrays.asList(new String[] + { type })); } }); @@ -214,8 +222,9 @@ public class FeatureSettings extends Panel implements ItemListener, @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays - .asList(new String[] { type })); + me.ap.alignFrame.avc + .sortAlignmentByFeatureDensity(Arrays.asList(new String[] + { type })); } }); @@ -279,8 +288,8 @@ public class FeatureSettings extends Panel implements ItemListener, }); men.add(selectContaining); - MenuItem selectNotContaining = new MenuItem( - MessageManager.getString("label.select_columns_not_containing")); + MenuItem selectNotContaining = new MenuItem(MessageManager + .getString("label.select_columns_not_containing")); selectNotContaining.addActionListener(new ActionListener() { @Override @@ -326,44 +335,43 @@ public class FeatureSettings extends Panel implements ItemListener, if (fr.getAllFeatureColours() != null && fr.getAllFeatureColours().size() > 0) { - rebuildGroups(); + // rebuildGroups(); } resetTable(false); } /** - * rebuilds the group panel + * Answers the visibility of the given group, and adds a checkbox for it if + * there is not one already */ - public void rebuildGroups() + public boolean checkGroupState(String group) { - boolean rdrw = false; - if (groupPanel == null) - { - groupPanel = new Panel(); - } - else - { - rdrw = true; - groupPanel.removeAll(); - } - // TODO: JAL-964 - smoothly incorporate new group entries if panel already - // displayed and new groups present - for (String group : fr.getFeatureGroups()) - { - boolean vis = fr.checkGroupVisibility(group, false); - Checkbox check = new MyCheckbox(group, vis, false); - check.addMouseListener(this); - check.setFont(new Font("Serif", Font.BOLD, 12)); - check.addItemListener(groupItemListener); - // note - visibility seems to correlate with displayed. ???wtf ?? - check.setVisible(vis); - groupPanel.add(check); - } - if (rdrw) + boolean visible = fr.checkGroupVisibility(group, true); + + /* + * is there already a checkbox for this group? + */ + for (int g = 0; g < groupPanel.getComponentCount(); g++) { - groupPanel.validate(); + if (((Checkbox) groupPanel.getComponent(g)).getLabel().equals(group)) + { + ((Checkbox) groupPanel.getComponent(g)).setState(visible); + return visible; + } } + + /* + * add a new checkbox + */ + Checkbox check = new MyCheckbox(group, visible, false); + check.addMouseListener(this); + check.setFont(new Font("Serif", Font.BOLD, 12)); + check.addItemListener(groupItemListener); + groupPanel.add(check); + + groupPanel.validate(); + return visible; } // This routine adds and removes checkboxes depending on @@ -373,7 +381,9 @@ public class FeatureSettings extends Panel implements ItemListener, SequenceFeature[] tmpfeatures; String group = null, type; Vector visibleChecks = new Vector(); + Set foundGroups = new HashSet(); AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { if (alignment.getSequenceAt(i).getSequenceFeatures() == null) @@ -386,8 +396,9 @@ public class FeatureSettings extends Panel implements ItemListener, while (index < tmpfeatures.length) { group = tmpfeatures[index].featureGroup; + foundGroups.add(group); - if (group == null || fr.checkGroupVisibility(group, true)) + if (group == null || checkGroupState(group)) { type = tmpfeatures[index].getType(); if (!visibleChecks.contains(type)) @@ -399,6 +410,11 @@ public class FeatureSettings extends Panel implements ItemListener, } } + /* + * remove any checkboxes for groups not present + */ + pruneGroups(foundGroups); + Component[] comps; int cSize = featurePanel.getComponentCount(); MyCheckbox check; @@ -445,8 +461,8 @@ public class FeatureSettings extends Panel implements ItemListener, addCheck(groupsChanged, en.nextElement().toString()); } - featurePanel.setLayout(new GridLayout(featurePanel.getComponentCount(), - 1, 10, 5)); + featurePanel.setLayout( + new GridLayout(featurePanel.getComponentCount(), 1, 10, 5)); featurePanel.validate(); if (scrollPane != null) @@ -458,6 +474,25 @@ public class FeatureSettings extends Panel implements ItemListener, } /** + * Remove from the groups panel any checkboxes for groups that are not in the + * foundGroups set. This enables removing a group from the display when the + * last feature in that group is deleted. + * + * @param foundGroups + */ + protected void pruneGroups(Set foundGroups) + { + for (int g = 0; g < groupPanel.getComponentCount(); g++) + { + Checkbox checkbox = (Checkbox) groupPanel.getComponent(g); + if (!foundGroups.contains(checkbox.getLabel())) + { + groupPanel.remove(checkbox); + } + } + } + + /** * update the checklist of feature types with the given type * * @param groupsChanged @@ -517,7 +552,7 @@ public class FeatureSettings extends Panel implements ItemListener, Checkbox check = (Checkbox) featurePanel.getComponent(i); check.setState(!check.getState()); } - selectionChanged(); + selectionChanged(true); } private ItemListener groupItemListener = new ItemListener() @@ -540,10 +575,10 @@ public class FeatureSettings extends Panel implements ItemListener, @Override public void itemStateChanged(ItemEvent evt) { - selectionChanged(); + selectionChanged(true); } - void selectionChanged() + void selectionChanged(boolean updateOverview) { Component[] comps = featurePanel.getComponents(); int cSize = comps.length; @@ -564,7 +599,7 @@ public class FeatureSettings extends Panel implements ItemListener, fr.setFeaturePriority(data); - ap.paintAlignment(true); + ap.paintAlignment(updateOverview); } MyCheckbox selectedCheck; @@ -606,8 +641,8 @@ public class FeatureSettings extends Panel implements ItemListener, } else { - comp = featurePanel.getComponentAt(evt.getX(), evt.getY() - + evt.getComponent().getLocation().y); + comp = featurePanel.getComponentAt(evt.getX(), + evt.getY() + evt.getComponent().getLocation().y); } if (comp != null && comp instanceof Checkbox) @@ -696,8 +731,7 @@ public class FeatureSettings extends Panel implements ItemListener, public void adjustmentValueChanged(AdjustmentEvent evt) { fr.setTransparency((100 - transparency.getValue()) / 100f); - ap.seqPanel.seqCanvas.repaint(); - + ap.paintAlignment(true); } class MyCheckbox extends Checkbox