X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fappletgui%2FFeatureSettings.java;h=7d00afdcde9cd6f73f62952ab26206749b1e5720;hb=7bb9eaabdb22172fedefd9d47cdd9543063e9999;hp=203605b209ecd76345f2924b729d4502243b8f7a;hpb=0b1c761dfaa8242f122cf868e8897a06ec6eb727;p=jalview.git diff --git a/src/jalview/appletgui/FeatureSettings.java b/src/jalview/appletgui/FeatureSettings.java index 203605b..7d00afd 100755 --- a/src/jalview/appletgui/FeatureSettings.java +++ b/src/jalview/appletgui/FeatureSettings.java @@ -56,9 +56,12 @@ import java.awt.event.MouseListener; import java.awt.event.MouseMotionListener; 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, @@ -93,14 +96,7 @@ public class FeatureSettings extends Panel implements ItemListener, transparency = new Scrollbar(Scrollbar.HORIZONTAL, 100 - (int) (fr.getTransparency() * 100), 1, 1, 100); - if (fr.isTransparencyAvailable()) - { - transparency.addAdjustmentListener(this); - } - else - { - transparency.setEnabled(false); - } + transparency.addAdjustmentListener(this); java.net.URL url = getClass().getResource("/images/link.gif"); if (url != null) @@ -112,6 +108,7 @@ public class FeatureSettings extends Panel implements ItemListener, { fr.findAllFeatures(true); // was default - now true to make all visible } + groupPanel = new Panel(); discoverAllFeatureData(); @@ -132,33 +129,22 @@ public class FeatureSettings extends Panel implements ItemListener, Panel tPanel = new Panel(new BorderLayout()); - if (fr.isTransparencyAvailable()) - { - tPanel.add(transparency, BorderLayout.CENTER); - tPanel.add(new Label("Transparency"), BorderLayout.EAST); - } - else - { - tPanel.add( - new Label("Transparency not available in this web browser"), - BorderLayout.CENTER); - } + tPanel.add(transparency, BorderLayout.CENTER); + tPanel.add(new Label("Transparency"), BorderLayout.EAST); lowerPanel.add(tPanel, BorderLayout.SOUTH); 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; @@ -200,14 +186,13 @@ public class FeatureSettings extends Panel implements ItemListener, } 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 })); - MenuItem scr = new MenuItem( + java.awt.MenuItem scr = new MenuItem( MessageManager.getString("label.sort_by_score")); men.add(scr); final FeatureSettings me = this; @@ -217,8 +202,8 @@ public class FeatureSettings extends Panel implements ItemListener, @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc - .sortAlignmentByFeatureScore(new String[] { type }); + me.ap.alignFrame.avc.sortAlignmentByFeatureScore(Arrays + .asList(new String[] { type })); } }); @@ -230,12 +215,13 @@ public class FeatureSettings extends Panel implements ItemListener, @Override public void actionPerformed(ActionEvent e) { - me.ap.alignFrame.avc - .sortAlignmentByFeatureDensity(new String[] { type }); + me.ap.alignFrame.avc.sortAlignmentByFeatureDensity(Arrays + .asList(new String[] { type })); } }); men.add(dens); + if (minmax != null) { final float[][] typeMinMax = minmax.get(type); @@ -280,6 +266,57 @@ public class FeatureSettings extends Panel implements ItemListener, }); } } + + MenuItem selectContaining = new MenuItem( + MessageManager.getString("label.select_columns_containing")); + selectContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + me.ap.alignFrame.avc.markColumnsContainingFeatures(false, false, + false, type); + } + }); + men.add(selectContaining); + + MenuItem selectNotContaining = new MenuItem( + MessageManager.getString("label.select_columns_not_containing")); + selectNotContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + me.ap.alignFrame.avc.markColumnsContainingFeatures(true, false, + false, type); + } + }); + men.add(selectNotContaining); + + MenuItem hideContaining = new MenuItem( + MessageManager.getString("label.hide_columns_containing")); + hideContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideFeatureColumns(type, true); + } + }); + men.add(hideContaining); + + MenuItem hideNotContaining = new MenuItem( + MessageManager.getString("label.hide_columns_not_containing")); + hideNotContaining.addActionListener(new ActionListener() + { + @Override + public void actionPerformed(ActionEvent e) + { + hideFeatureColumns(type, false); + } + }); + men.add(hideNotContaining); + this.featurePanel.add(men); men.show(this.featurePanel, x, y); } @@ -290,46 +327,43 @@ 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, - (fr.featureLinks != null && fr.featureLinks - .containsKey(group))); - 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 @@ -339,7 +373,9 @@ 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) @@ -352,8 +388,9 @@ 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)) @@ -365,6 +402,11 @@ public class FeatureSettings extends Panel implements ItemListener, } } + /* + * remove any checkboxes for groups not present + */ + pruneGroups(foundGroups); + Component[] comps; int cSize = featurePanel.getComponentCount(); MyCheckbox check; @@ -424,6 +466,25 @@ 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 @@ -456,10 +517,7 @@ public class FeatureSettings extends Panel implements ItemListener, selected = true; } - check = new MyCheckbox( - type, - selected, - (fr.featureLinks != null && fr.featureLinks.containsKey(type)), + check = new MyCheckbox(type, selected, false, fr.getFeatureStyle(type)); check.addMouseListener(this); @@ -486,7 +544,7 @@ 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() @@ -509,10 +567,10 @@ 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; @@ -533,7 +591,7 @@ public class FeatureSettings extends Panel implements ItemListener, fr.setFeaturePriority(data); - ap.paintAlignment(true); + ap.paintAlignment(updateOverview); } MyCheckbox selectedCheck; @@ -541,23 +599,6 @@ public class FeatureSettings extends Panel implements ItemListener, boolean dragging = false; @Override - public void mousePressed(MouseEvent evt) - { - - selectedCheck = (MyCheckbox) evt.getSource(); - - if (fr.featureLinks != null - && fr.featureLinks.containsKey(selectedCheck.type)) - { - if (evt.getX() > selectedCheck.stringWidth + 20) - { - evt.consume(); - } - } - - } - - @Override public void mouseDragged(MouseEvent evt) { if (((Component) evt.getSource()).getParent() != featurePanel) @@ -651,16 +692,6 @@ public class FeatureSettings extends Panel implements ItemListener, { this.popupSort(check, fr.getMinMax(), evt.getX(), evt.getY()); } - if (fr.featureLinks != null && fr.featureLinks.containsKey(check.type)) - { - if (evt.getX() > check.stringWidth + 20) - { - evt.consume(); - String link = fr.featureLinks.get(check.type).toString(); - ap.alignFrame.showURL(link.substring(link.indexOf("|") + 1), - link.substring(0, link.indexOf("|"))); - } - } if (check.getParent() != featurePanel) { @@ -692,8 +723,7 @@ 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 @@ -758,28 +788,31 @@ 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) @@ -790,4 +823,30 @@ public class FeatureSettings extends Panel implements ItemListener, } } + /** + * Hide columns containing (or not containing) a given feature type + * + * @param type + * @param 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)) + { + ap.alignFrame.viewport.hideSelectedColumns(); + } + } + } + + @Override + public void mousePressed(MouseEvent e) + { + // TODO Auto-generated method stub + + } + }