X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=7db1fbe4b7cdac2a3cb9dd3bb642209d5ec76dd3;hb=1a34e43f7fb8e6d4f559026c6f0a207893124c6d;hp=bfac241814915028e6959f8c386ba453a2ea975f;hpb=bf0d052fef43e9809b7170dbfd372b3ea116391b;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index bfac241..7db1fbe 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; @@ -56,16 +57,23 @@ 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, - AdjustmentListener, FeatureSettingsControllerI +public class FeatureSettings extends Panel + implements ItemListener, MouseListener, MouseMotionListener, + ActionListener, AdjustmentListener, FeatureSettingsControllerI { + private static final int TYPE_COLUMN = 0; + + private static final int COLOUR_COLUMN = 1; + + private static final int SHOW_COLUMN = 2; + FeatureRenderer fr; AlignmentPanel ap; @@ -106,6 +114,7 @@ public class FeatureSettings extends Panel implements ItemListener, { fr.findAllFeatures(true); // was default - now true to make all visible } + groupPanel = new Panel(); discoverAllFeatureData(); @@ -133,17 +142,22 @@ 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; @@ -174,24 +188,22 @@ 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, - final Map minmax, - int x, int y) + final Map minmax, int x, int y) { 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); @@ -202,8 +214,9 @@ 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 })); } }); @@ -215,8 +228,9 @@ 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 })); } }); @@ -280,8 +294,8 @@ 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 @@ -327,79 +341,88 @@ 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; @@ -409,7 +432,7 @@ 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--; @@ -426,28 +449,28 @@ 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) @@ -459,6 +482,25 @@ 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 @@ -518,7 +560,7 @@ 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() @@ -541,33 +583,54 @@ 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]; + /* + * temporary! leave column[2] empty - used for Filter in + * gui.FeatureSettings + */ + int columnCount = 4; + Object[][] tmp = new Object[cSize][columnCount]; int tmpSize = 0; for (int i = 0; i < cSize; i++) { MyCheckbox check = (MyCheckbox) comps[i]; - tmp[tmpSize][0] = check.type; - tmp[tmpSize][1] = fr.getFeatureStyle(check.type); - tmp[tmpSize][2] = new Boolean(check.getState()); + tmp[tmpSize][TYPE_COLUMN /* 0 */] = check.type; + tmp[tmpSize][COLOUR_COLUMN /* 1 */] = fr.getFeatureStyle(check.type); + tmp[tmpSize][SHOW_COLUMN /* 3 */] = new Boolean(check.getState()); tmpSize++; } - Object[][] data = new Object[tmpSize][3]; + Object[][] data = new Object[tmpSize][columnCount]; System.arraycopy(tmp, 0, data, 0, tmpSize); - fr.setFeaturePriority(data); + fr.setFeaturePriority(getTableAsBeans(data)); - ap.paintAlignment(true); + ap.paintAlignment(updateOverview, updateOverview); } + /** + * Converts table data into an array of data beans + */ + private FeatureSettingsBean[] getTableAsBeans(Object[][] data) + { + FeatureSettingsBean[] rowData = new FeatureSettingsBean[data.length]; + for (int i = 0; i < data.length; i++) + { + String type = (String) data[i][TYPE_COLUMN]; + FeatureColourI colour = (FeatureColourI) data[i][COLOUR_COLUMN]; + Boolean isShown = (Boolean) data[i][SHOW_COLUMN]; + // feature filter set to null as not (yet) offered in applet + rowData[i] = new FeatureSettingsBean(type, colour, null, isShown); + } + return rowData; + } MyCheckbox selectedCheck; boolean dragging = false; @@ -607,8 +670,8 @@ 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) @@ -645,7 +708,7 @@ public class FeatureSettings extends Panel implements ItemListener, { featurePanel.removeAll(); resetTable(false); - ap.paintAlignment(true); + ap.paintAlignment(true, true); } @Override @@ -697,8 +760,7 @@ 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 @@ -763,28 +825,31 @@ public class FeatureSettings extends Panel implements ItemListener, public void paint(Graphics g) { Dimension d = getSize(); - if (col.isColourByLabel()) + if (col != null) { - g.setColor(Color.white); - g.fillRect(d.width / 2, 0, d.width / 2, d.height); - /* - * g.setColor(Color.black); Font f=g.getFont().deriveFont(9); - * g.setFont(f); - * - * // g.setFont(g.getFont().deriveFont( // - * AffineTransform.getScaleInstance( // - * width/g.getFontMetrics().stringWidth("Label"), // - * height/g.getFontMetrics().getHeight()))); g.drawString("Label", - * width/2, 0); - */ + if (col.isColourByLabel()) + { + g.setColor(Color.white); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + /* + * g.setColor(Color.black); Font f=g.getFont().deriveFont(9); + * g.setFont(f); + * + * // g.setFont(g.getFont().deriveFont( // + * AffineTransform.getScaleInstance( // + * width/g.getFontMetrics().stringWidth("Label"), // + * height/g.getFontMetrics().getHeight()))); g.drawString("Label", + * width/2, 0); + */ - } - else if (col.isGraduatedColour()) - { - Color maxCol = col.getMaxColour(); - g.setColor(maxCol); - g.fillRect(d.width / 2, 0, d.width / 2, d.height); + } + else if (col.isGraduatedColour()) + { + Color maxCol = col.getMaxColour(); + g.setColor(maxCol); + g.fillRect(d.width / 2, 0, d.width / 2, d.height); + } } if (hasLink) @@ -801,11 +866,10 @@ public class FeatureSettings extends Panel implements ItemListener, * @param type * @param columnsContaining */ - void hideFeatureColumns(final String type, - boolean columnsContaining) + void hideFeatureColumns(final String type, boolean columnsContaining) { - if (ap.alignFrame.avc.markColumnsContainingFeatures( - columnsContaining, false, false, type)) + if (ap.alignFrame.avc.markColumnsContainingFeatures(columnsContaining, + false, false, type)) { if (ap.alignFrame.avc.markColumnsContainingFeatures( !columnsContaining, false, false, type))