X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=a60aacdf873648d45dd023b9e60c3230c76a1a5a;hb=948bd3bcbacc509da0cefaae3eedd97300a6ccce;hp=2c454a40105db7b5808c2e5dcd2f95c854157ecb;hpb=37de9310bec3501cbc6381e0c3dcb282fcaad812;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 2c454a4..a60aacd 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -23,8 +23,9 @@ package jalview.appletgui; import jalview.api.FeatureColourI; import jalview.api.FeatureSettingsControllerI; import jalview.datamodel.AlignmentI; -import jalview.datamodel.SequenceFeature; +import jalview.datamodel.SequenceI; import jalview.util.MessageManager; +import jalview.viewmodel.seqfeatures.FeatureRendererModel.FeatureSettingsBean; import java.awt.BorderLayout; import java.awt.Button; @@ -56,14 +57,15 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; import java.awt.event.WindowAdapter; import java.awt.event.WindowEvent; +import java.util.ArrayList; import java.util.Arrays; -import java.util.Enumeration; +import java.util.HashSet; import java.util.List; import java.util.Map; -import java.util.Vector; +import java.util.Set; -public class FeatureSettings extends Panel implements ItemListener, - MouseListener, MouseMotionListener, ActionListener, +public class FeatureSettings extends Panel + implements ItemListener, MouseListener, MouseMotionListener, 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(); @@ -118,8 +121,17 @@ public class FeatureSettings extends Panel implements ItemListener, add(scrollPane, BorderLayout.CENTER); } - Button invert = new Button("Invert Selection"); - invert.addActionListener(this); + Button invert = new Button( + MessageManager.getString("label.invert_selection")); + invert.addActionListener(new ActionListener() + { + + @Override + public void actionPerformed(ActionEvent e) + { + invertSelection(); + } + }); Panel lowerPanel = new Panel(new GridLayout(2, 1, 5, 10)); lowerPanel.add(invert); @@ -133,17 +145,22 @@ 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 +191,12 @@ 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 +204,9 @@ 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 +217,9 @@ 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 +231,9 @@ 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 +297,8 @@ 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 @@ -326,79 +344,88 @@ 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 // Group selection states void resetTable(boolean groupsChanged) { - SequenceFeature[] tmpfeatures; - String group = null, type; - Vector visibleChecks = new Vector(); + List displayableTypes = new ArrayList<>(); + Set foundGroups = new HashSet<>(); + AlignmentI alignment = av.getAlignment(); + for (int i = 0; i < alignment.getHeight(); i++) { - if (alignment.getSequenceAt(i).getSequenceFeatures() == null) - { - continue; - } + SequenceI seq = alignment.getSequenceAt(i); - tmpfeatures = alignment.getSequenceAt(i).getSequenceFeatures(); - int index = 0; - while (index < tmpfeatures.length) + /* + * get the sequence's groups for positional features + * and keep track of which groups are visible + */ + Set groups = seq.getFeatures().getFeatureGroups(true); + Set visibleGroups = new HashSet<>(); + for (String group : groups) { - group = tmpfeatures[index].featureGroup; - - if (group == null || fr.checkGroupVisibility(group, true)) + // if (group == null || fr.checkGroupVisibility(group, true)) + if (group == null || checkGroupState(group)) { - type = tmpfeatures[index].getType(); - if (!visibleChecks.contains(type)) - { - visibleChecks.addElement(type); - } + visibleGroups.add(group); } - index++; } + foundGroups.addAll(groups); + + /* + * get distinct feature types for visible groups + * record distinct visible types + */ + Set types = seq.getFeatures().getFeatureTypesForGroups(true, + visibleGroups.toArray(new String[visibleGroups.size()])); + displayableTypes.addAll(types); } + /* + * remove any checkboxes for groups not present + */ + pruneGroups(foundGroups); + Component[] comps; int cSize = featurePanel.getComponentCount(); MyCheckbox check; @@ -408,7 +435,7 @@ public class FeatureSettings extends Panel implements ItemListener, { comps = featurePanel.getComponents(); check = (MyCheckbox) comps[i]; - if (!visibleChecks.contains(check.type)) + if (!displayableTypes.contains(check.type)) { featurePanel.remove(i); cSize--; @@ -425,28 +452,28 @@ public class FeatureSettings extends Panel implements ItemListener, { String item = rol.get(ro); - if (!visibleChecks.contains(item)) + if (!displayableTypes.contains(item)) { continue; } - visibleChecks.removeElement(item); + displayableTypes.remove(item); addCheck(false, item); } } - // now add checkboxes which should be visible, - // if they have not already been added - Enumeration en = visibleChecks.elements(); - - while (en.hasMoreElements()) + /* + * now add checkboxes which should be visible, + * if they have not already been added + */ + for (String type : displayableTypes) { - addCheck(groupsChanged, en.nextElement().toString()); + addCheck(groupsChanged, type); } - 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 +485,25 @@ 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 @@ -509,15 +555,14 @@ public class FeatureSettings extends Panel implements ItemListener, } } - @Override - public void actionPerformed(ActionEvent evt) + protected void invertSelection() { for (int i = 0; i < featurePanel.getComponentCount(); i++) { Checkbox check = (Checkbox) featurePanel.getComponent(i); check.setState(!check.getState()); } - selectionChanged(); + selectionChanged(true); } private ItemListener groupItemListener = new ItemListener() @@ -540,31 +585,28 @@ 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; - - Object[][] tmp = new Object[cSize][3]; - int tmpSize = 0; - for (int i = 0; i < cSize; i++) + FeatureSettingsBean[] rowData = new FeatureSettingsBean[cSize]; + int i = 0; + for (Component comp : comps) { - MyCheckbox check = (MyCheckbox) comps[i]; - tmp[tmpSize][0] = check.type; - tmp[tmpSize][1] = fr.getFeatureStyle(check.type); - tmp[tmpSize][2] = new Boolean(check.getState()); - tmpSize++; + MyCheckbox check = (MyCheckbox) comp; + // feature filter set to null as not (yet) offered in applet + FeatureColourI colour = fr.getFeatureStyle(check.type); + rowData[i] = new FeatureSettingsBean(check.type, colour, null, + check.getState()); + i++; } - Object[][] data = new Object[tmpSize][3]; - System.arraycopy(tmp, 0, data, 0, tmpSize); - - fr.setFeaturePriority(data); + fr.setFeaturePriority(rowData); - ap.paintAlignment(true); + ap.paintAlignment(updateOverview, updateOverview); } MyCheckbox selectedCheck; @@ -606,8 +648,8 @@ 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) @@ -644,7 +686,7 @@ public class FeatureSettings extends Panel implements ItemListener, { featurePanel.removeAll(); resetTable(false); - ap.paintAlignment(true); + ap.paintAlignment(true, true); } @Override @@ -696,8 +738,7 @@ 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, true); } class MyCheckbox extends Checkbox